active genes walid mahrez , minerva susana trejo arellano · 24 in eukaryotic cells, ... 74 and has...

1

H3K36ac is an evolutionary conserved plant histone modification that marks 1

active genes 2

Walid Mahrez12 Minerva Susana Trejo Arellano1 Jordi Moreno-Romero1 Miyuki 3

Nakamura1 Huan Shu2 Paolo Nanni3 Claudia Koumlhler1 Wilhelm Gruissem2 and Lars 4

Hennig1 5

6

1Swedish University of Agricultural Sciences Department of Plant Biology and 7

Linnean Center for Plant Biology PO-Box 7080 SE-75007 Uppsala Sweden 8

2Department of Biology and Zurich-Basel Plant Science Center ETH Zurich CH-8092 9

Zurich Switzerland 10

3Functional Genomics Center Zurich University of ZurichETH Zurich CH-8057 11

Zurich Switzerland 12

13

Author for correspondence 14

Lars Hennig 15

Department of Plant Biology Uppsala BioCenter Swedish University of Agricultural 16

Sciences and Linnean Center for Plant Biology 17

SE-75007 Uppsala Sweden 18

LarsHennigsluse 19

20

Running title H3K36ac is an active histone mark in plants 21

22

Plant Physiology Preview Published on January 13 2016 as DOI101104pp1501744

Copyright 2016 by the American Society of Plant Biologists

wwwplantphysiolorgon July 4 2018 - Published by Downloaded from Copyright copy 2016 American Society of Plant Biologists All rights reserved

2

Abstract 23

In eukaryotic cells histones are subject to a large number of post-translational 24

modifications whose sequential or combinatorial action affects chromatin structure and 25

genome function We have identified acetylation at lysine 36 in histone H3 (H3K36ac) 26

as a new chromatin modification in plants The H3K36ac modification is evolutionary 27

conserved in seed plants including the gymnosperm Norway spruce and the 28

angiosperms rice tobacco and Arabidopsis thaliana In Arabidopsis H3K36ac is highly 29

enriched in euchromatin but not in heterochromatin Genome-wide ChIP-seq 30

experiments revealed that H3K36ac peaks at the 5rsquo end of genes mainly on the two 31

nucleosomes immediately distal to the transcription start site independently of gene 32

length H3K36ac overlaps with H3K4me3 and the H2AZ histone variant The histone 33

acetyl transferase GCN5 and the histone deacetylase HDA19 are required for H3K36ac 34

homeostasis H3K36ac and H3K36me3 show negative crosstalk which is mediated by 35

GCN5 and the histone methyl transferase SDG8 Although H3K36ac is associated with 36

gene activity we did not find a linear relationship between H3K36ac and transcript 37

levels suggesting that H3K36ac is a binary indicator of transcription 38

39

40

One sentence summary 41

Profiling of histone H3 modifications by MSMS identified H3K36ac which is 42

introduced at the first 500 bp of active Arabidopsis genes by GCN5 and is conserved in 43

gymnosperms and angiosperms 44

45

Introduction 46


3

47

Nuclear DNA of eukaryotes is packed in chromatin the basic unit of which is the 48

nucleosome consisting of 147 bp of DNA wrapped around a protein octamer formed by 49

two copies each of four histones (H2A H2B H3 H4) Chromatin structure and 50

composition are dynamically regulated both temporally and spatially within the nucleus 51

Covalent modifications of histones play an important role in the regulation of gene 52

expression by changing chromatin structure (Strahl et al 2000 Jenuwein et al 2001) 53

Many histone modifications have been identified including acetylation methylation 54

phosphorylation and ubiquitinylation (Cannon 1955 Zhang et al 2007) It has been 55

proposed that histone modifications act in a combinatorial manner to establish specific 56

chromatin states that regulate gene expression (Strahl et al 2000 Jenuwein et al 57

2001) It has been argued however that chromatin-dependent gene activity is only a 58

consequence of the cumulative effect of histone modifications rather than the 59

interpretation of an alphabet (Henikoff 2005) Using high-throughput methods with 60

improved sensitivity specificity and resolution such as mass spectrometry and 61

chromatin immunoprecipitation (ChIP) coupled to sequencing (ChIP-seq) the genomic 62

localization combinatorial patterns and enrichment of histone modifications can be 63

resolved at the level of individual nucleosomes (Liu et al 2005 Kharchenko et al 64

2011) 65

Histone acetylation is a dynamic and reversible modification in which an acetyl 66

group is transferred from acetyl-CoA to histone lysine residues Lysine acetylation 67

neutralizes positive charges of the histone tails thus decreasing their affinity for 68

negatively charged DNA (Hong et al 1993) Acetylated lysines can be recognized by 69

histone code readers such as Bromo domain proteins (Sanchez et al 2014) which then 70


4

may promote the recruitment of additional chromatin remodeler or modifier complexes 71

to relax chromatin and facilitate the binding or activation of RNA polymerases 72

(Bannister et al 2011) Histone lysine acetylation is often associated with transcription 73

and has important roles in numerous developmental and biological processes including 74

the regulation of cell cycle flowering time response to environmental conditions and 75

hormone signals (Chen et al 2007 Luo et al 2012) 76

Several amino-terminal lysine residues of histone H3 (K9 K14 K18 K23 and 77

K27) and H4 (K5 K8 K12 K16 and K20) are known to be acetylated in Arabidopsis 78

thaliana (Berr et al 2011) Histone acetylation is dynamically regulated with a usual 79

half-life of 2-3 minutes in human cell lines that rarely exceeds 30-40 minutes (for 80

review see (Iwamoto et al 2015) This rapid turn-over strongly suggests that instead of 81

influencing long-term epigenetic memory acetylation participates in short-term 82

alterations of chromatin states (Barth et al 2010) Homeostasis of histone acetylation is 83

maintained by histone acetyl transferases (HATs) which catalyze the histone 84

acetylation and histone deacetylases (HDACs) which remove the acetyl group (Pandey 85

et al 2002) 86

Histone lysine methylation is another well-studied epigenetic modification with 87

both activating and repressing roles in gene expression Histone lysine residues can be 88

mono- di- or tri-methylated Each distinct methylation state confers different functional 89

outcomes depending on the methylated histone residue the degree of methylation and 90

the chromatin context (Liu et al 2010) Methylated lysines constitute landmarks for 91

binding of chromo MBT Tudor W40 domain or PHD fingers containing proteins 92

which subsequently recruit additional protein complexes resulting in the compaction or 93

relaxation of chromatin structure (Greer et al 2012) 94


5

Compared to yeast and animals much less is known about the repertoire of 95

histone modification sites in plants Pioneering work in Arabidopsis includes genome-96

wide chromatin indexing by ChIP (Roudier et al 2011 Sequeira-Mendes et al 2014) 97

and characterization of histone modifications by mass spectrometry (Johnson et al 98

2004 Bergmuumlller et al 2007 Zhang et al 2007) In order to expand this knowledge 99

we implemented high-performance liquid chromatography (HPLC) histone separation 100

in combination with mass spectrometry to identify uncharacterized modifications on the 101

amino-terminal tail of histone H3 in Arabidopsis and its close relative Brassica 102

oleracea (cauliflower) We found H3K36 acetylation (H3K36ac) as a novel histone 103

modification in plants GCN5 a HAT and HDA19 an HDAC contribute to H3K36ac 104

homeostasis H3K36ac is enriched in euchromatic regions and excluded from 105

heterochromatin In addition H3K36ac is generally found at the 5rsquo end of 106

transcriptionally active genes where it overlaps with H3K4me3 and the H2AZ histone 107

variant As H3K36 can also be mono- di- or tri-methylated we tested if the 108

mechanisms of tri-methylation or acetylation of H3K36 are interdependent H3K36ac 109

was increased in a mutant with reduced H3K36me3 and H3K36me3 was increased in 110

gcn5 mutants with reduced H3K36ac Thus acetylation and methylation at H3K36 are 111

in a competitive equilibrium that defines two alternative states 112

113

Results 114

The histone H3 modification profile is conserved in Brassicaceae 115

A histone extract from cauliflower (Brassica oleracea) heads was subjected to reverse-116

phase HPLC and fractions corresponding to H3 based on immunoblot detection were 117

collected and analyzed by liquid chromatography-tandem mass spectrometry (LC-118


6

MSMS) using an LTQ-Orbitrap XL instrument For the analysis of long peptides both 119

CID (Collision-Induced Dissociation) and ETD (Electron Transfer Dissociation) 120

fragmentation were performed (Supplemental Fig S1) The high accuracy achieved in 121

the MS measurements allowed to distinguish between tri-methylated and acetylated 122

peptides (Δm = 00364 Da) Data were submitted to the Mascot search engine for 123

identification of proteins and post-translational modifications with a focus on 124

acetylation and methylation This produced a map of H3 acetylation and methylation in 125

cauliflower inflorescences (Supplemental Tab S1) Most of the identified H3 126

modifications and their combinations are consistent with those in Arabidopsis (Johnson 127

et al 2004 Zhang et al 2007) suggesting a high conservation of the histone 128

modifications 129

130

H3K36ac is a new modification in Arabidopsis 131

We identified H3K36ac as a novel H3 modification in plants (Supplemental Tab S1) 132

H3K36ac was found in two independent experiments using different enzymes 133

(Chymotrypsin and ArgC) The confidence for the localization of the modification site 134

was higher than 90 The MSMS spectrum of the ArgC-digested histone H3 shown in 135

Figure 1A details the c and z fragmentation ions for the parent peptide with an observed 136

mass of mz 15048468 The accurate mass of the recorded parent ion was consistent 137

with peptide acetylation (ΔM = 420106 Da) and not tri-methylation 138

(ΔM = 420470 Da) Importantly we detected H3K36 mono- di- and tri-methylation 139

on other H3 peptides confirming that this amino acid can be either methylated or 140

acetylated (Fig 1A Supplemental Fig S2 S3) 141


7

To validate and extend the mass spectrometry results a histone extract from 142

Arabidopsis inflorescences was separated by polyacrylamide gel electrophoresis and 143

probed with an anti-H3K36ac antibody The antibody was previously tested for 144

specificity in dot blots and proteinimmuno blots using modified and unmodified 145

peptides and validated for ChIP-seq (Morris et al 2007 Egelhofer et al 2011) The 146

antibody showed no cross-reactivity with eleven different tested acetylated histone 147

peptides (H2AK5ac H3K14ac H3K18ac H3K27ac H3K4ac H3K9ac H4K12ac 148

H4K16ac H4K581216ac H4K5ac H4K8ac) and many unmodified or methylated 149

histone peptides The positive signals for Arabidopsis histone extracts (Fig 2A) 150

confirmed the mass spectrometric identification of the H3K36ac modification in plants 151

Together proteomic and molecular methods support the identification of H3K36ac as a 152

novel histone modification in Brassicacea 153

154

H3K36ac is present in euchromatin 155

To establish the distribution of H3K36ac in the nucleus paraformaldehyde-fixed 156

Arabidopsis root-tip nuclei were immuno-stained using the anti-H3K36ac antibody 157

H3K36ac fluorescence signals were absent from nucleoli and DAPI-dense 158

chromocenters which are mostly comprised of centromeric and pericentromeric repeats 159

In contrast H3K36ac staining was observed in euchromatic regions (Fig 2B-E) 160

indicating that most H3K36ac is associated with less condensed gene-rich regions and 161

possibly active genes To test this prediction formaldehyde-crosslinked ChIP (X-ChIP) 162

was performed using anti-H3K36ac and anti-H3 antibodies Indeed H3K36ac levels 163

were high at the transcribed euchromatic ACTIN7 gene but low at the silent 164

heterochromatic Ta2 transposon (Fig 2F) The increased H3 signal at Ta2 is consistent 165


8

with earlier reports and might be related to the more compact chromatin structure in 166

heterochromatin (Rehrauer et al 2010 Shu et al 2012) Together these results suggest 167

that H3K36ac is present on active genes in euchromatin but not on heterochromatic loci 168

169

H3K36ac is associated with the first two nucleosomes of transcriptionally active 170

genes 171

We performed a native ChIP-seq (N-ChIP-seq) experiment to determine the genome-172

wide localization of H3K36ac at mono-nucleosome resolution (Supplemental Tab S2) 173

To control for nucleosome density H3K36ac reads were normalized to the anti-H3 read 174

counts After mapping to the five Arabidopsis chromosomes the highest enrichment 175

was found along chromosome arms In contrast pericentromeric heterochromatic 176

regions were considerably less enriched (Supplemental Fig S4) Furthermore the 177

H3K36ac coverage profile was similar to the gene density distribution consistent with 178

an enrichment of H3K36ac at or near genes These results support the H3K36ac 179

immunolocalisation data To explore the distribution of H3K36ac along gene bodies in 180

more detail averaged coverage profiles were plotted around transcriptional start sites 181

(TSS) and transcriptional termination sites (TTS) for all annotated gene models (Fig 182

3A) The results show a strong enrichment of H3K36ac between 35 bp and 516 bp 183

downstream of the TSS (positions with 50 of maximal peak height) In contrast 184

H3K36ac was not enriched in promoter regions in gene bodies beyond the first 500 bp 185

distal to the TSS or around transcriptional termination sites (TTS) 186

Next we tested whether the width of the H3K36ac peak depended on gene 187

length by plotting averaged H3K36ac profiles separately for bins of increasing gene 188

length (Fig 3B) This analysis revealed that position shape and width of the H3K36ac 189


9

enrichment peak are independent of gene length and that H3K36ac covered only about 190

480 bp downstream of the TSS This invariant pattern of the H3K36ac modification 191

allowed the calculation of a gene-specific H3K36ac score as the mean H3K36ac signal 192

within a TSS-distal 35 bp to 516 bp window The H3K36ac score has a bimodal 193

distribution (Fig 3C) that allowed to separate 16431 genes with low H3K36ac (score 194

lt=27) from 10920 genes with high H3K36ac (score gt27) To avoid confounding effects 195

of alternative transcripts only genes with a single annotated transcript were included in 196

this analysis Since H3K36ac is found at genes and the differential enrichment of this 197

modification allows the clear distinction of two gene classes we asked if its presence is 198

a binary signal for transcription Globally genes with higher H3K36ac scores had also 199

higher mRNA levels (Fig 3D) Only active but not inactive genes had the pronounced 200

H3K36ac peak near the TSS (Fig 3E) However the relationship between H3K36ac 201

and transcript levels is not linear but strongly sigmoidal (red trend line in Supplemental 202

Fig S5) indicating that H3K36ac levels are only weakly proportional to transcription 203

rate and instead are a qualitative indicator of transcriptional activity This interpretation 204

is consistent with the bimodal distribution of H3K36ac scores (Fig 3C) 205

Since H3K36ac is associated with gene activity we analyzed its relationship to 206

other chromatin marks associated with transcription namely H3K4me3 H3K36me2 207

H3K36me3 and the histone variant H2AZ Similar to H3K36ac position shape and 208

width of the H3K4me3 and H2AZ enrichment peaks are independent of gene length 209

(Supplemental Fig S6) In contrast H3K36me3 and H3K36me2 profiles depend 210

strongly on gene length Next averaged H3K4me3 H3K36me2 H3K36me3 and 211

H2AZ profiles were plotted separately for five bins of increasing H3K36ac scores All 212

tested chromatin marks showed a positive correlation with H3K36ac but the correlation 213


10

with H3K4me3 and H3K36me3 was most pronounced (Supplemental Fig S7) 214

H3K4me3 H3K36me3 and H2AZ are restricted to the 5rsquo-end of genes while 215

H3K36me2 increases towards the 3rsquo-end To better compare peak positions averaged 216

profiles for the analyzed marks were plotted together (Fig 4) This analysis revealed 217

that H3K36ac and H2AZ are localized closest to the TSS and likely associated with 218

transcription initiation and the transition to transcription elongation (H3K36ac peaks at 219

199 bp and H2AZ at 252 bp distal to the TSS) Downstream of the H2AZ peak 220

H3K4me3 and H3K36me3 (peaks at 368 bp and 629 bp respectively) become more 221

dominating until H3K36me2 which is associated with elongating RNA Polymerase II 222

(Pol II) (Oh et al 2008) increases towards the 3rsquo-end of genes 223

Profiling of H3K36ac specifically along active genes showed the highest 224

enrichment around the TSS irrespective of feature length (Fig 5A B) consistent with 225

the distribution obtained when all genes were used (Fig 3A) Enrichment of 226

H3K36me3 on the other hand also reaches a peak right after the TSS but then extends 227

further towards the 3rsquo-end (Fig 5C D) Interestingly we observed that the enrichment 228

of H3K36me3 along the whole gene body increased with gene length (Fig 5D) This is 229

consistent with the model that H3K36me3 is associated with Pol II processivity (Oh et 230

al 2008) 231

Together H3K36ac is most enriched on +1 and +2 nucleosomes of the TSS of 232

transcriptionally active genes and correlates with H3K4me3 H3K36me2 H3K36me3 233

and the histone variant H2AZ 234

235

H3K36ac depends on GCN5 in Arabidopsis 236


11

Histone acetylation is established by HATs Arabidopsis has 12 different HAT genes 237

that are grouped into four classes (Pandey et al 2002) of which GCN5 (GENERAL 238

CONTROL NON DEREPRESSIBLE PROTEIN 5) is highly expressed in most 239

sporophytic tissues (Zimmermann et al 2004) In yeast GCN5 acetylates H3K14 (Roth 240

et al 2001) Because GCN5 is conserved in plants and because the H3 sequences 241

around K14 and K36 are similar (STGGK14AP versus STGGVK36KP) we tested if 242

Arabidopsis GCN5 acetylates H3K36 using the gcn5-1 mutant for X-ChIP assays The 243

TSS regions of two genes with high H3K36ac levels were analyzed using qPCR Their 244

H3K36ac levels were reduced more than five-fold in gcn5-1 (Fig 6A) indicating that 245

GCN5 is required for full H3K36 acetylation in vivo but that other HATs can also 246

acetylate H3K36 explaining the residual H3K36ac in gcn5-1 247

To test whether GCN5 can directly acetylate H3K36 in vitro HAT assays were 248

performed using amino-terminal H3 fragments and purified recombinant GST and GST-249

GCN5 Acetylated histone fragments were probed with anti-H3K36ac antibody A 250

strong signal was obtained when using GCN5 enzyme while no signal was obtained 251

with control GST or H3 alone (Fig 6B) The in vivo and in vitro assays therefore 252

establish Arabidopsis GCN5 as an H3K36 acetyl transferase and strongly suggest that it 253

is the main enzyme depositing H3K36ac in vivo 254

255

Competing modifications targeting H3K36 256

H3K36 can also be mono- di- or tri- methylated at its ɛ-amino group The Arabidopsis 257

histone lysine methyltransferase SET DOMAIN GROUP 8 (SDG 8) deposits di- and tri-258

methylation on H3K36 (Zhao et al 2005 Xu et al 2008) Considering that GNC5 and 259

SDG8 both modify H3K36 we tested the mechanistic dependency of acetylation and 260


12

methylation at H3K36 We performed X-ChIP-seq using the anti-H3K36ac antibody in 261

sdg8-2 and an anti-H3K36me3 antibody in gcn5-1 because in our experience X-ChIP is 262

more robust than N-ChIP when comparing genotypes Crosstalk between GCN5 and 263

SDG8 could result in reciprocal effects on H3K36ac and H3K36me3 enrichments 264

respectively To avoid confounding effects from inactive genes we restricted our 265

analysis to active protein-coding genes (see Methods) Globally H3K36ac levels in 266

genes increased in sdg8-2 in particular close to the TSS (Fig 7A) In addition 267

H3K36ac increased close to the TTS of genes in which its levels are normally low 268

Similarly enrichment of H3K36me3 increased in gcn5-1 and was highest in the center 269

of genes (Fig 7B) This increase in enrichment of acetylation and methylation in sdg8-2 270

and gcn5-1 respectively indicates that both modifications affect each other Because 271

the differences were found in distinct regions along gene bodies this crosstalk probably 272

does not reflect a direct competition for the H3K36 but an indirect functional repressive 273

interaction between the acetylation and methylation enzymes 274

275

HDA19 but not HDA6 affects H3K36ac levels 276

Eighteen different HDACs have been identified in Arabidopsis and grouped into three 277

different classes (Pandey et al 2002) To identify HDACs responsible for H3K36 278

deacetylation we tested the possible involvement of HDA6 and HDA19 which are two 279

major Arabidopsis HDACs HDA6 removes acetyl groups from H3K9ac H3K14ac 280

H3K18ac H3K23ac H3K27ac H4K5ac H4K8ac and H4K12ac (reviewed in 281

(Hollender et al 2008)) To test if HDA6 deacetylates H3K36ac we performed X-ChIP 282

assays with wild-type hda6-1 and 35SHDA6-FLAG plants using two genes with high 283

H3K36ac levels in wild type No significant differences of H3K36ac levels were found 284


13

in HDA6 loss-of-function or overexpressing plants (Supplemental Fig S8) suggesting 285

that HDA6 does not deacetylate H3K36 in vivo at least at these two loci In contrast a 286

considerable increase of H3K36ac levels was found for the same genes in an HDA19 287

RNAi line (Fig 8) indicating that HDA19 is one of the Arabidopsis HDACs that 288

deacetylase H3K36ac 289

290

H3K36ac is a conserved histone modification in plants 291

Histones are among the most highly conserved eukaryotic proteins and K36 is found in 292

H3 of mouse yeast and plants such as Arabidopsis tobacco wheat rice and Norway 293

spruce (Fig 9A) To test if H3K36ac exists only in Brassicaceae or also in other plant 294

species histones were extracted from tobacco rice wheat and spruce as representatives 295

of monocotyledonous and dicotyledonous angiosperms as well as gymnosperms The 296

presence of H3K36ac was analyzed using protein immunoblotting with anti-H3K36ac 297

antibody A distinct H3K36ac band was visible in all histone preparations (Fig 9B) 298

indicating that H3K36ac is a highly conserved modification in seed plants and likely has 299

a conserved biological function 300

To test whether the H3K36ac enrichment on active genes is conserved in other 301

plant species X-ChIP was performed using Norway spruce cell culture Two loci with 302

low expression (MA_16054g0010 and the EnSpm transposon-like locus MA_10270349) 303

and two loci with high expression (MA_491379g0010 and MA_94077g0010) were 304

selected for ChIP analysis (Supplemental Fig S9) using two primer sets for each gene ndash 305

one set probing a region upstream of the transcriptional unit and the other set probing a 306

region downstream of the TSS in the gene body near the start codon Similar to the 307

results in Arabidopsis strong H3K36ac ChIP signals were present at the active genes 308


14

MA_491379g0010 and MA_94077g0010 but no or only weak signals were present at 309

the silent or lowly expressed genes (Fig 9C) In addition H3K36ac was much higher 310

enriched distal of the TSS than in the promoter region Together these results suggest 311

that H3K36ac is present in the 5-region of active genes in the angiosperm Arabidopsis 312

and the gymnosperm Norway spruce revealing a wide conservation of this modification 313

among seed plants 314

315

Discussion 316

Applying the sensitive and specific CIDETD LC-MSMS method (Syka et al 2004) to 317

histone extracts from cauliflower inflorescences we have identified a novel H3 318

acetylation on K36 in plants CIDETD LC-MSMS allows sequencing of long highly 319

charged peptides (gt20 aa) and even of intact proteins and has been successfully used 320

already to determine histone PTMs (Taverna et al 2007 Xiong et al 2010 Jufvas et 321

al 2011) Our analysis confirmed most of the known Arabidopsis lysine acetylation 322

and methylation modifications We did not detect phosphorylated H3 peptides which 323

require phospho-peptide enrichment during histone extraction (Zhang et al 2007) 324

However our approach identified previously unreported plant histone modifications 325

including H3K36ac that we analyzed in more detail A complete list of the identified H3 326

post-translational modification is reported in Supplemental Table S1 327

H3K36ac was previously found in yeast Tetrahymena and mammals (Morris et 328

al 2007) Using a high-specificity antibody we confirmed the MSMS identification of 329

H3K36ac in plants In addition to cauliflower H3K36ac was also found in several other 330

seed plants The presence of H3K36ac in yeast ciliates animals and plants suggests an 331

evolutionary conserved function 332


15

In Arabidopsis H3K36ac is associated with euchromatin and excluded from 333

heterochromatic chromocenters It is enriched within the first 500 bp and particularly at 334

+1 and +2 nucleosomes distal to the TSS of transcriptionally active genes irrespective 335

of their lengths This presence of H3K36ac distal to the TSS of Arabidopsis genes is in 336

contrast to yeast in which H3K36ac is highest at promoters but mostly absent from 337

transcribed regions (Morris et al 2007) The restriction of H3K36ac to the 5rsquo-end of 338

genes and the positive correlation with gene expression suggests that it is associated 339

with the early phase of transcription but not with elongation Although H3K36ac marks 340

active genes its levels are not significantly correlated with transcription rates H3K36ac 341

rather marks transcribed genes in a qualitative manner with full acetylation reached 342

even at moderate transcription rates 343

The peak of H3K36ac enrichment in Arabidopsis coincided well with the H2AZ 344

peak at the 5rsquo-end of gene bodies It is not clear whether the different width of the 345

H2AZ and H3K36ac peaks is genuine or the result of the different ChIP methods in our 346

study and the report for H2AZ (Zilberman et al 2008) The coincidence of H2AZ and 347

H3K36ac suggests that nucleosomes in which H3K36 is acetylated often contain the 348

histone variant H2AZ It remains to be established however whether incorporation or 349

presence of H2AZ favors acetylation of H3K36 andor H3K36ac favors H2AZ 350

incorporation Similar to H3K36ac and H2AZ H3K4me3 and H3K36me3 peak at 5rsquo-351

ends of transcriptionally active genes In the case of H3K4me3 the peak width is 352

independent of gene length but the peak summit is shifted to the TTS The H3K36me3 353

peak is shifted even further towards the 3rsquo-end than the H3K4me3 peak The extension 354

of the H3K36me3 peak strongly depends on gene length H3K36me2 increases 355

downstream of the H3K36me3 peak and reaches its maximum only at the 3rsquo-end The 356


16

gradient of H3K36ac H2AZ H3K4me3 H3K36me2 and H3K36me3 along transcribed 357

genes provides a spatial map of histone modifications along transcription units 358

Histone acetylation is regulated by antagonistic HAT and HDAC activities The 359

Arabidopsis HAT GCN5 acetylates H3K36 in vitro and is necessary to achieve full 360

H3K36ac levels in vivo These results are consistent with the reported activity of GCN5 361

in yeast (Morris et al 2007) supporting a conserved mechanism for H3K36 acetylation 362

in eukaryotes although as described above the H3K36ac patterns differ between yeast 363

and plants (Morris et al 2007) 364

The Arabidopsis genome encodes 18 HDAC proteins that are grouped into three 365

main subfamilies (RPD3 HD2 and SIR2 family) (Pandey et al 2002) We found that 366

H3K36ac was increased in HDA19 RNAi lines suggesting that HDA19 is required for 367

H3K36ac homeostasis on target genes in vivo It remains to be established whether 368

other HDACs also modulate H3K36ac levels 369

Despite the evolutionary conservation of H3K36 modifications animals and 370

yeast seem to use them in functionally different mechanisms than plants In animals and 371

yeast H3K36me3 is associated with transcriptional elongation peaking towards the 3rsquo-372

end and H3K36ac in yeast is restricted to promoters In plants H3K36me3 peaks in the 373

5rsquo-half of the gene and H3K36ac is restricted to an approximately 480 bp distal to the 374

TSS In Arabidopsis H3K36ac and H3K36me3 are found in overlapping regions 375

downstream of the TSS Our genome-wide analysis revealed a negative crosstalk 376

between the HAT GCN5 and the HKMT SDG8 This resulted in increased H3K36ac 377

levels when H3K36me3 is reduced and vice versa the distinct spatial patterns of 378

H3K36ac and H3K36me3 were however not affected Further work will be required to 379

understand the mechanistic basis for this crosstalk It is tempting to speculate that 380


17

acetylation and methylation at H3K36 form a molecular switch in which one of the two 381

dominates However since nucleosomes have two H3 molecules concomitant 382

acetylation and methylation at H3K36 in the same nucleosome are possible It remains 383

to be shown whether such nucleosomes with asymmetrical K36 modifications do indeed 384

exist 385

386

Experimental procedures 387

Plant material 388

The following Arabidopsis thaliana lines were previously described HDA19-RNAi1 389

(Zhou et al 2005) gcn5-1 (Vlachonasios et al 2003) 35SFlag-HDA6 (Earley et al 390

2006) hda6-1 (Aufsatz et al 2002) and sdg8-2 (Xu et al 2008) The HDA19-RNAi1 391

was shown to have no off-target effects on the close HDA19 homolog HDA6 (Zhou et 392

al 2005 Mehdi et al 2015) Seeds were sown on 05times basal salts Murashige and 393

Skoog (MS) medium (Duchefa Haarlem The Netherlands) stratified at 4degC for one 394

day and then transferred to growth chambers for germination at 20degC under long-day 395

(LD 16 h light) photoperiods for ten days The seedlings were transferred to pots 396

containing soil and cultivated in growth chambers under LD conditions Tobacco 397

(Nicotiana tabacum) wheat (Triticum aestivum) and rice (Oryza sativa) were grown in 398

a greenhouse at 22degC in LD Cauliflower (Brassica oleracea) was obtained from a local 399

supermarket Norway spruce (Picea abies) needles were collected from an 400

approximately 15-years-old wild-grown tree in a forest close to Uppsala (Sweden) 401

located at 5981ordm N 1766ordm E For ChIP and RT-qPCR in Norway spruce embryogenic 402

calli (line 111811) derived from a zygotic embryo were used (von Arnold et al 403

2008) 404


18

405

Histone extraction and purification from plants 406

To extract histones from inflorescences of cauliflower and Arabidopsis or from fully 407

developed leaves of tobacco wheat rice and spruce approximately 3 g of material were 408

ground to a fine powder and homogenized for 15 min in histone extraction buffer [025 409

M sucrose 1 mM CaCl2 15 mM NaCl 60 mM KCl 5 mM MgCl2 15 mM PIPES pH 410

70 05 Triton X-100 including protease inhibitors cocktail (Roche) and 10 mM 411

sodium butyrate] After centrifugation for 20 min at 4degC and 4500timesg pellets were 412

dissolved in 01 M H2SO4 After further centrifugation for 10 min at 17000timesg total 413

histones were precipitated from the supernatant with concentrated Trichloroacetic acid 414

to a final concentration of 33 The histone pellet was washed twice with acetone-01 415

HCl air dried dissolved either in 1times Laemmli buffer and subjected to SDS-PAGE 416

followed by protein immunoblotting using anti-H3 (cat no 07-690 UpstateMillipore) 417

and anti-H3K36ac (cat no 39379 ActiveMotif) antibodies or fractionated by RP-418

HPLC 419

420

Histone fractionation by RP-HPLC and PTM identification by tandem mass 421

spectrometry 422

Bulk histones from cauliflower were prepared as described above The pellet was 423

dissolved in 100 μl of water sonicated for 1 min and centrifuged for 1 min at 10000timesg 424

The supernatant was gently aspirated by pipetting and loaded on an ECLIPS XDB-C8 425

(46times150 mm) (Agilent) connected to an Agilent HP1100 binary HPLC system Histone 426

variants were separated and eluted according to (Tweedie-Cullen et al 2009) The 427

fractions containing H3 were combined dried and dissolved in 50 mM ammonium 428


19

bicarbonate pH 80 After reduction with dithiothreitol (DTT 10 mM) and alkylation 429

with iodoacetamide (IAA 40 mM) histones H3 were digested for 2 h at 37degC with 430

Chymotrypsin (enzymesubstrate ratio 150 (ww)) (Promega Switzerland) or with 431

Arg_C (150 (ww)) (Roche Switzerland) Samples were desalted with C18 ZipTips 432

(Millipore Switzerland) following the manufacturerrsquos recommendations and dried 433

Peptides were resolubilized in 10 μl of 5 acetonitrile 01 trifluoracetic acid and 434

were analyzed by LC-MSMS on an LTQ-Orbitrap XL-ETD mass spectrometer 435

(Thermo Fischer Scientific Bremen Germany) coupled to an Eksigent-Nano-HPLC 436

system (Eksigent Technologies Dublin CA USA) Solvent composition at the two 437

channels was 02 formic acid 1 acetonitrile for channel A and 02 formic acid 438

80 acetonitrile for channel B Peptides were resolubilized in 10μl of 5 acetonitrile 439

and 01 formic acid and loaded on a self-made tip column (75 microm times 70 mm) packed 440

with reverse-phase C18 material (AQ 3 μm 200 Aring Bischoff GmbH Leonberg 441

Germany) Elution was performed with a flow rate of 200 nl min by a gradient from 3 442

to 10 of B in 6 min 35 B in 38 min 97 B in 45 min One scan cycle comprised of 443

a full-scan MS survey spectrum followed by up to 6 sequential CID and ETD MSMS 444

scans on the 3 most intense signals above a threshold of 500 Full-scan MS spectra 445

(300minus2000 mz) were acquired in the FT-Orbitrap with a resolution of 60 000 at 400 mz 446

after accumulation to a target value of 200000 while CID and ETD MSMS spectra 447

were recorded in the linear ion trap (target value of 1e4 for ion trap MSn scans) The 448

ETD anion target value was set at 3e5 and activation time at 50 ms Supplementary 449

activation was employed to enhance the fragmentation efficiency for 2+ precursors and 450

charge state dependent ETD time enabled The ETD reaction time was 120 ms and 451

isolation width was 3 mz Charge state screening was enabled and singly charge states 452


20

were rejected Precursor masses selected twice for MSMS were excluded for further 453

selection for 120 s Samples were acquired using internal lock mass calibration set on 454

mz 4290887 and 4451200 455

MS raw-files were converted into Mascot generic files (mgf) with Mascot 456

Distiller software 2420 (Matrix Science Ltd London UK) Peak lists were searched 457

using Mascot Server 23 against the Arabidopsis TAIR10 protein database Search 458

parameters were requirement for chymotryptic or ArgC ends one missed cleavage 459

allowed peptide tolerance plusmn 6 ppm MSMS tolerance plusmn 05 Da Carbamidomethylation 460

of cysteine was set as fixed modification while oxidation (methionine) acetylation (N-461

term protein lysine) mono- di- and tri-methylation (arginine lysine) were set as 462

variable To assess the location of the post-translational modification sites we used the 463

site localization analysis provided by Mascot The presence of modification sites was 464

further validated by manual inspection of spectra 465

466

Chromatin Immunopreciptation and ChIP-seq 467

Native and cross-linked chromatin immunoprecipitation (N-ChIP and X-ChIP) assays 468

were performed as described (Bernatavichute et al 2008 Exner et al 2009) using 469

gene-specific primers (Supplemental Tab S3) See supplemental information for 470

details For ChIP-seq leaf number six of plants grown for 35 days under short-day 471

conditions (8 h light) was harvested at zeitgeber time ZT=7 and used for nuclei 472

isolation Supplemental Table S2 gives a summary of the ChIP-seq experiments 473

474

Bioinformatics and ChIP-seq data analysis 475


21

Illumina reads were mapped to the Arabidopsis reference TAIR10 genome using 476

bowtie2 (version 21) (Langmead et al 2012) SAM file output from bowtie was 477

converted to BAM format using SAMTOOLS (version 14) (Li et al 2009) and 478

imported into R (version 2152) (httpwwwR-projectorg) using functions from the 479

Rsamtools package All subsequent analysis was performed in R Identical reads present 480

more than 25 times were considered as PCR artifacts and filtered out using the 481

filterDuplReads function from package HtSeqTools Replicates were pooled samples 482

normalization to identical sequencing depth and H3K36ac signals were normalized to 483

histone signals to control for variable nucleosome density using functions from package 484

nucleR (Flores et al 2011) H3K4me3 H3K36me2 H3K36me3 and H2AZ data were 485

taken from the literature (Oh et al 2008 Zilberman et al 2008) Gene expression data 486

are from (Shu et al 2012) and match cultivation conditions plant age harvest time and 487

tissue used here for ChIP-seq The expression cutoff to consider a gene as active was a 488

value of 6 in the microarray data from (Shu et al 2012) resulting in a set of 12102 489

active protein coding genes Heat maps were generated using the open source tool 490

deepTools (Ramirez et al 2014) 491

492

Constructs and recombinant protein expression and purification 493

The coding region for the amino-terminal tail of H3 (amino acids 1-50) was amplified 494

by PCR from Arabidopsis cDNA using primers LH1625 (CTATTC-495

TCTTAAAGCAACAGTTCC forward) and LH1626 (CACCATGGCTCGTACCAA 496

reverse) The PCR product was cloned into vector pET100-D-TOPO according to the 497

manufacturerrsquos recommendations (Invitrogen) pGEX4T1 was obtained from 498

(Amersham Life Science Stockholm Sweden) pQE30-GCN5 was previously 499


22

described (Benhamed et al 2006) Recombinant amino-terminal 6xHis tagged H31-50 500

was expressed in Escherichia coli BL21pLys Rosetta cells and purified on TALON 501

metal affinity resin (Clontech Stockholm Sweden) according to manufacturerrsquos 502

recommendations Recombinant GST and GST-GCN5 were expressed in BL21pLys 503

Rosetta and purified with Glutathione Sepharose 4B resin according to the 504

manufacturerrsquos recommendations (Amersham Life Science) Purified proteins were 505

stored at -20degC until use in HAT activity assays 506

507

Histone acetyl transferase activity assays 508

HAT assays using recombinant GST-GCN5 expressed in E coli were performed as 509

follows 1 microg of purified His-tagged histone H31-50 was mixed with purified 510

recombinant GST-GCN5 or with GST alone in HAT buffer [025 μgμl Acetyl-CoA 511

(Sigma-Aldrich) 50 mM Tris-HCl (pH 80) 10 glycerol (vv) 1 mM dithiothreitol 512

complete EDTA‐free protease inhibitor (Roche Indianapolis IN USA) and 10 mM 513

sodium butyrate] Acetylation reactions were incubated for 60 min at 30degC with gentle 514

shaking and terminated by addition of 2times SDS Laemmli sample buffer followed by 515

heating for 5 min to 100degC The reaction products were electrophoretically resolved on 516

15 SDS-PAGE gels and subjected to protein immunoblotting using anti-H3K36ac 517

(cat no 39379 Active Motif) and anti-H3 (cat no 07-690 UpstateMillipore) 518

antibodies 519

520

RNA isolation and RT-qPCR 521


23

RNA extraction and reverse transcription were performed as described previously 522

(Alexandre et al 2009) using gene-specific primers (Supplemental Tab S3) See 523

supplemental information for details 524

525

Immunostaining 526

Immunostaining was performed as described previously (Jasencakova et al 2000) with 527

some modifications See supplemental information for details 528

529

Accession numbers 530

Sequencing reads are deposited in Gene Expression Omnibus (GSE74841) 531


24

Supplemental Material 532

533

Supplemental_Materialpdf contains 534

- Supplemental Methods (RNA isolation and RT-qPCR ChIP and ChIP-seq 535

Immunostaining Sequence alignment of H3 amino-terminal tails) 536

- Supplemental Figures 537

Figure S1 Histone separation by RP-HPLC 538

Figure S2 Identification of H3K36me2 539


Figure S4 Genome-wide distribution of H3K36ac on the Arabidopsis genome 541

Figure S5 H3K36ac is a qualitative mark for transcriptional activity 542

Figure S6 Dependency of histone marks on gene length 543

Figure S7 H3K36ac positively correlates with H3K4me3 H3K36me3 and 544

H2AZ 545

Figure S8 HDA6 does not affect H3K36ac steady state levels on AT3G04720 or 546

AT3G28060 547

Figure S9 Expression levels of Norway spruce genes used for ChIP 548

- Supplemental Tables 549

Table S1 List of histone H3 modifications that were identified in B oleracea 550

Table S2 Summary of ChIP-seq experiments 551

Table S3 Lists of primers used 552

553

554

Acknowledgments 555


25

We thank Cecilia Waumlrdig for technical help We thank Keqiang Wu Craig Pikaard and 556

Dao-Xiu Zhou for kindly providing seeds of HDA19-RNAi1 35SFlag-HDA6 gcn5-1 557

and the pQE30-GCN5 construct respectively We thank the FGCZ for Illumina 558

sequencing This work was supported by grants from the Swiss National Science 559

Foundation the Swedish Science Foundation VR and the Knut-and-Alice-Wallenberg 560

Foundation 561

562

Author contributions 563

WM JM MN and SH performed the experiments WM MT SH PH and LH analyzed 564

data WM CK and LH planned the experiments WM MT CK WG and LH wrote the 565

manuscript 566

567


26

Figure legends 568

569

Figure 1 Identification of H3K36ac in cauliflower MSMS fragmentation spectrum 570

of the [M+2H]2+ parent ion at mz 15048474 This peptide was identified as the H3 571

peptide (histone H3 amino acids 27ndash40) derived from ArgC digested RP-HPLC-572

purified cauliflower H3 The position of acetylation at Lysine 36 is displayed the scale 573

for the y-axis represents the relative abundance of the parent ion Above the spectrum is 574

the peptide sequence in which predicted c-type ions which contain the aminoterminus 575

of the peptide are immediately above the sequence Predicted z-type ions which 576

contain the carboxyterminus are immediately below the sequence ions observed in the 577

spectrum which represent masses associated with the fragmented peptides from the 578

MSMS analyses are underlined 579

580

Figure 2 Detection of H3K36ac in Arabidopsis (A) Acid-extracted histones from 581

Arabidopsis inflorescences were resolved on a 15 SDS-PAGE gel followed by 582

protein immunoblotting using anti-H3 and anti-H3K36ac antibodies (B-D) Localization 583

of H3K36ac in root tip nuclei Root tip interphase nuclei of Arabidopsis plants were 584

stained with DAPI (B) and analyzed for immunofluorescence using an anti-H3K36ac 585

antibody (C) (D) The overlay of DAPI and H3K36ac signal The line indicates a 586

section through the nucleus that was analyzed using ImageJ software (E) Quantitative 587

line profiles of DAPI (blue) and H3K36ac (red) florescence intensities Scale bars 5 588

μm (F) X-ChIP assays were performed using IgG anti-H3 and anti-H3K36ac 589

antibodies with primers against the active ACTIN7 gene and the silent Ta2 transposable 590

element 591


27

592

Figure 3 H3K36ac distribution across genes (A) Metagene plots of H3K36ac 593

enrichment around the TSS (left panel) and TTS (right panel) The highest enrichment 594

was detected within the first 500 bp distal to the TSS (B) H3K36ac enrichment is 595

independent of gene length Metagene plots are shown for the first (black) second (red) 596

third (green) and forth (blue) length quartile where the black line represents the 25 597

shortest genes (C) Distribution of gene-specific H3K36ac scores defined as the mean 598

H3K36ac signal within a window of 35 bp to 516 bp distal to the TSS Note the two 599

separate populations of genes with scores of less or more than 27 respectively (D) 600

Relation between H3K36ac score and transcriptional state H3K36ac scores are shown 601

for the 10 genes with lowest (red) and highest (green) mRNA levels respectively (E) 602

H3K36ac metagene plot around the TSS for the 10 genes with lowest (red) and 603

highest (green) mRNA levels respectively Only active genes have the characteristic 604

H3K36ac peak within the first 500 bp Expression data are from (Shu et al 2012) 605

606

Figure 4 Metagene plots of active chromatin marks around the TSS Phased 607

enrichment of H3 modifications and the histone variant H2AZ around the TSS The 608

peak of enrichment is indicated for each profile Data are from (Reed et al 1996 609

Zilberman et al 2008) and from this study 610

611

Figure 5 H3K36ac and H3K36me3 distribution across transcribed genes (A B) 612

H3K36ac enrichment along transcribed genes is shown on an absolute scale from 2 kb 613

upstream to 4 kb downstream of the TSS (A) and on a relative scale from TSS to TTS 614

(B) H3K36ac was mainly found in the first 500 bp of the gene body The enrichments 615


28

are similar in level and breadth irrespective of the length and the fraction of the gene 616

being covered (C D) H3K36me3 enrichment along transcribed genes is shown on an 617

absolute scale from 2 kb upstream to 4 kb downstream of the TSS (C) and on a relative 618

scale from TSS to TTS (D) H3K36me3 localizes close to the TSS and expands further 619

towards the 3rsquo-end Longer genes have higher and wider levels of H3K36me3 Genes 620

were ordered by length 621

622

Figure 6 GCN5 is required for H3K36 acetylation (A) H3K36ac levels on 623

AT3G04720 and AT3G28060 depend on GCN5 10 days old seedlings were used for X-624

ChIP with anti-H3 and anti-H3K36ac antibodies The enrichment of H3K36ac relative 625

to H3 is shown as mean plusmn SEM (B) H3K36ac acetyltransferase activity of GCN5 626

Left Recombinant GST and GST-GCN5 were purified with Glutathione Sepharose 4B 627

resin blotted and probed with anti-GST antibodies M weight marker Right HAT 628

assays were performed using recombinant His-H3 as substrate The reaction products 629

were resolved on a 15 SDS-PAGE gel transferred to PVDF membrane and probed 630

with anti-H3K36ac antibodies Anti-H3 was used as control 631

632

Figure 7 Competing modifications of H3K36 by GCN5 and SGD8 (A) Gain of 633

H3K36ac along genes in the sdg8-2 background (D) Gain of H3K36me3 along genes in 634

the gcn5-1 background Shaded areas represent 95 confidence intervals 635

636

Figure 8 HDA19 affects H3K36ac levels H3K36ac levels on AT3G04720 and 637

AT3G28060 are affected by HDA19 downregulation Ten-day-old seedlings were used 638

for X-ChIP with anti-H3 and anti-H3K36ac antibodies The enrichment of H3K36ac 639


29

relative to H3 is shown as mean plusmn SEM 640

641

Figure 9 H3K36ac is conserved in seed plants (A) Amino acid alignment of the 642

amino-terminal tails of H3 from mouse yeast and several plants shows conservation of 643

lysine 36 (B) Acid-extracted histones prepared from tobacco (Nicotiana tabacum) 644

wheat (Triticum aestivum) rice (Oryza sativa) and Norway spruce (Picea abies) were 645

resolved on 15 SDS-PAGE gels followed by immunoblotting using anti-H3K36ac 646

antibodies (C) H3K36ac X-ChIP in Norway spruce Shown are mean plusmn SEM (n=3) 647

H3K36ac is found downstream (downstr) of the TSS on transcribed genes 648

649

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Cell Res 21 381-395 658

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36

802


Figure 1 Identification of H3K36ac in cauliflower MSMS fragmentation spectrum of the [M+2H]2+ parent ion at mz 15048474 This peptide was identified as the H3 peptide (histone H3 amino acids 27ndash40) derived from ArgC digested RP-HPLC-purified cauliflower H3 The position of acetylation at Lysine 36 is displayed the scale for the y-axis represents the relative abundance of the parent ion Above the spectrum is the peptide sequence in which predicted c-type ions which contain the aminoterminus of the peptide are immediately above the sequence Predicted z-type ions which contain the carboxyterminus are immediately below the sequence ions observed in the spectrum which represent masses associated with the fragmented peptides from the MSMS analyses are underlined

200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+

K27 S A P T T G G V K36ac K P H R40

c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+


Figure 2 Detection of H3K36ac in Arabidopsis (A) Acid-extracted histones from Arabidopsis inflorescences were resolved on a 15 SDS-PAGE gel followed by protein immunoblotting using anti-H3 and anti-H3K36ac antibodies (B-D) Localization of H3K36ac in root tip nuclei Root tip interphase nuclei of Arabidopsis plants were stained with DAPI (B) and analyzed for immunofluorescence using an anti-H3K36ac antibody (C) (D) The overlay of DAPI and H3K36ac signal The line indicates a section through the nucleus that was analyzed using ImageJ software (E) Quantitative line profiles of DAPI (blue) and H3K36ac (red) florescence intensities Scale bars 5 μm (F) X-ChIP assays were performed using IgG anti-H3 and anti-H3K36ac antibodies with primers against the active ACTIN7 gene and the silent Ta2 transposable element

010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac


Figure 3 H3K36ac distribution across genes (A) Metagene plots of H3K36ac enrichment around the TSS (left panel) and TTS (right panel) The highest enrichment was detected within the first 500 bp distal to the TSS (B) H3K36ac enrichment is independent of gene length Metagene plots are shown for the first (black) second (red) third (green) and forth (blue) length quartile where the black line represents the 25 shortest genes (C) Distribution of gene-specific H3K36ac scores defined as the mean H3K36ac signal within a window of 35 bp to 516 bp distal to the TSS Note the two separate populations of genes with scores of less or more than 27 respectively (D) Relation between H3K36ac score and transcriptional state H3K36ac scores are shown for the 10 genes with lowest (red) and highest (green) mRNA levels respectively (E) H3K36ac metagene plot around the TSS for the 10 genes with lowest (red) and highest (green) mRNA levels respectively Only active genes have the characteristic H3K36ac peak within the first 500 bp Expression data are from (Shu et al 2012)

minus500 0 500 1000 1500 2000

2040

6080

Distance from TSS (bp)

Aver

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36ac

sco

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active genesinactive genes

leng

th

A

B C

D E


Figure 4 Metagene plots of active chromatin marks around the TSS Phased enrichment of H3 modifications and the histone variant H2AZ around the TSS The peak of enrichment is indicated for each profile Data are from (Oh et al 2004 Zilberman et al 2008) and from this study

195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

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08


Aver

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cove

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H2AZH3K4me3H3K36me2H3K36me3



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac



Figure 5 H3K36ac and H3K36me3 distribution across transcribed genes (A B) H3K36ac enrichment along transcribed genes is shown on an absolute scale from 2 kb upstream to 4 kb downstream of the TSS (A) and on a relative scale from TSS to TTS (B) H3K36ac was mainly found in the first 500 bp of the gene body The enrichments are similar in level and breadth irrespective of the length and the fraction of the gene being covered (C D) H3K36me3 enrichment along transcribed genes is shown on an absolute scale from 2 kb upstream to 4 kb downstream of the TSS (C) and on a relative scale from TSS to TTS (D) H3K36me3 localizes close to the TSS and expands further towards the 3rsquo end Longer genes have higher and wider levels of the trimethylation Genes were ordered by length

A B C D


Figure 6 GCN5 is required for H3K36 acetylation (A) H3K36ac levels on AT3G04720 and AT3G28060 depend on GCN5 10 days old seedlings were used for X-ChIP with anti-H3 and anti-H3K36ac antibodies The enrichment of H3K36ac relative to H3 is shown as mean plusmn SEM (B) H3K36ac acetyltransferase activity of GCN5 Left Recombinant GST and GST-GCN5 were purified with Glutathione Sepharose 4B resin blotted and probed with anti-GST antibodies M weight marker Right HAT assays were performed using recombinant His-H3 as substrate The reaction products were resolved on a 15 SDS-PAGE gel transferred to PVDF membrane and probed with anti-H3K36ac antibodies Anti-H3 was used as control

AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B


Figure 7 Competing modifications of H3K36 by GCN5 and SGD8 (A) Gain of H3K36ac along genes in the sdg8-2 background (D) Gain of H3K36me3 along genes in the gcn5-1 background Shaded areas represent 95 confidence intervals

minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4

Distance from TTS (Kb)

H3K36me3 gcn5minuswt

minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt


Figure 8 HDA19 affects H3K36ac levels H3K36ac levels on AT3G04720 and AT3G28060 are affected by HDA19 downregulation 10 days old seedlings were used for X-ChIP with anti-H3 and anti-H3K36ac antibodies The enrichment of H3K36ac relative to H3 is shown as mean plusmn SEM

AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1


Figure 9 H3K36ac is conserved in seed plants (A) Amino acid alignment of the amino-terminal tails of H3 from mouse yeast and several plants shows conservation of lysine 36 (B) Acid-extracted histones prepared from tobacco (Nicotiana tabacum) wheat (Triticum aestivum) rice (Oryza sativa) and Norway spruce (Picea abies) were resolved on 15 SDS-PAGE gels followed by immunoblotting using anti-H3K36ac antibodies (C) H3K36ac X-ChIP in Norway spruce Shown are mean plusmn SEM (n=3) H3K36ac is found downstream (downstr) of the TSS on transcribed genes


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Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

2

Abstract 23

In eukaryotic cells histones are subject to a large number of post-translational 24

modifications whose sequential or combinatorial action affects chromatin structure and 25

genome function We have identified acetylation at lysine 36 in histone H3 (H3K36ac) 26

as a new chromatin modification in plants The H3K36ac modification is evolutionary 27

conserved in seed plants including the gymnosperm Norway spruce and the 28

angiosperms rice tobacco and Arabidopsis thaliana In Arabidopsis H3K36ac is highly 29

enriched in euchromatin but not in heterochromatin Genome-wide ChIP-seq 30

experiments revealed that H3K36ac peaks at the 5rsquo end of genes mainly on the two 31

nucleosomes immediately distal to the transcription start site independently of gene 32

length H3K36ac overlaps with H3K4me3 and the H2AZ histone variant The histone 33

acetyl transferase GCN5 and the histone deacetylase HDA19 are required for H3K36ac 34

homeostasis H3K36ac and H3K36me3 show negative crosstalk which is mediated by 35

GCN5 and the histone methyl transferase SDG8 Although H3K36ac is associated with 36

gene activity we did not find a linear relationship between H3K36ac and transcript 37

levels suggesting that H3K36ac is a binary indicator of transcription 38

39

40

One sentence summary 41

Profiling of histone H3 modifications by MSMS identified H3K36ac which is 42

introduced at the first 500 bp of active Arabidopsis genes by GCN5 and is conserved in 43

gymnosperms and angiosperms 44

45

Introduction 46


3

47


















2011) 65







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Results 114






6











modifications 129

130













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154













8




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13






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14







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15


























16


























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exist 385

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Plant material 388
















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420


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19


























20



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466








474



21

















492









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507












antibodies 519

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23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

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Acknowledgments 555


25






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manuscript 566

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26

Figure legends 568

569











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element 591


27

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606





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Cell Res 21 381-395 658







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6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



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34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



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+

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+

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+ c(10

)+

[M+

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[M+

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c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

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cove

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minus500 0 500 1000 1500 2000

2040

6080

100

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50 100 150 200

010

0020

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00


050

100

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H3K

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minus500 0 500 1000 1500 2000

050

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Aver

age

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rage


leng

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A

B C

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195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

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rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

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GST

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anti H3K36ac

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minus5

0

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20

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iffer

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Distance from TSS

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Distance from TSS

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Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

3

47


















2011) 65







4
















et al 2002) 86










5



















113

Results 114






6











modifications 129

130













7













154













8




169


genes 171




















9


























10


















al 2008) 231




235



11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

4
















et al 2002) 86










5



















113

Results 114






6











modifications 129

130













7













154













8




169


genes 171




















9


























10


















al 2008) 231




235



11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

5



















113

Results 114






6











modifications 129

130













7













154













8




169


genes 171




















9


























10


















al 2008) 231




235



11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

6











modifications 129

130













7













154













8




169


genes 171




















9


























10


















al 2008) 231




235



11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

7













154













8




169


genes 171




















9


























10


















al 2008) 231




235



11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

8




169


genes 171




















9


























10


















al 2008) 231




235



11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

9


























10


















al 2008) 231




235



11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

10


















al 2008) 231




235



11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

11



















255







12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

12















275











13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

13






290




















14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

14







315

Discussion 316


















15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

15


























16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

16


























17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

17





exist 385

386


Plant material 388
















2008) 404


18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

18

405














HPLC 419

420


spectrometry 422








19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

19


























20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

20



mz 4290887 and 4451200 455











466








474



21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

21

















492









22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

22








507












antibodies 519

520



23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

23




525

Immunostaining 526



529




24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

24


533












H2AZ 545


AT3G28060 547






553

554

Acknowledgments 555


25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

25






Foundation 561

562




manuscript 566

567


26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

26

Figure legends 568

569











580











element 591


27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

27

592














606





611






28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

28







622










632




636





29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

29


641








649









Cell Res 21 381-395 658







30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

30



Proteome Res 6 3655-3668 666













20 1283-1293 679










31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

31












DNA J Biol Chem 268 305-314 699






2100 705





6518 710


32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

32







480-485 717


Methods 9 357-359 719





Biol 61 395-420 724



3 727



136 730




33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

33




















81-120 752





34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

34








Plant Cell 26 2351-2366 763




403 41-45 767



Acad Sci U S A 101 9528-9533 770




104 2086-2091 774





35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

35















Nat Cell Biol 7 1156-1160 792






129 798



2632 801


36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

36

802



200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


200 400 600 800 1000 1200 1400mz

0

25

50

75

100

Rel

ativ

eA

bund

ance

37739

67521

49744

746004243875465

6226847605

2612115916 9867571740616865215035311 9123982539 13498423319 30297 127584100664 14922612119811142414616 144880

z+1(

4)2+

z+2(

4)2+

z+1(

5)2+

z+2(

5)2+

z+1(

6)2+

z+2(

6)2+

z+1(

7)2+

z+2(

7)2+

z+1(

8)2+

z+2(

8)2+

z+1(

9)2+

z+2(

9)2+

z+1(

10)2+

z+2(

10)2+

z+2(

11)2+

z+1(

12)2+

z+2(

12)2+

z+1(

7)+

z+2(

7)+

z+2(

6)+

z+2(

4)+

z+1(

1)+

c(2)

+

c(5)

+

c(6)

+

c(7)

+

c(8)

+

c(9)

+ c(10

)+

[M+

4H]4+

[M+

4H]2+bullbull

c(6)

2+


c(2)+ c(5)+ c(6)+ c(7)+ c(8)+ c(9)+ c(10)+c(6)2+

z+1(1)+z+1(4)2+

z+2(4)2+

z+1(5)2+

z+2(5)2+z+2(6)+z+1(6)2+

z+2(6)2+

z+1(7)+z+2(7)+z+1(7)2+

z+2(7)2+

z+1(8)2+

z+2(8)2+z+1(9)2+

z+2(9)2+z+1(10)2+

z+2(10)2+z+2(11)2+z+1(12)2+

z+2(12)2+



010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


010203040506070

Inte

nsity

DAPIH3K36ac

A

B C D

E

F

Inpu

t

IgG

H3

H3K

36ac

ACTIN 7

Ta2

α-H3 α-H3K36ac



minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


minus500 0 500 1000 1500 2000

2040

6080


Aver

age

cove

rage

minus400 minus200 0 200 400

2040

6080


Aver

age

cove

rage

minus500 0 500 1000 1500 2000

2040

6080

100

120


Aver

age

cove

rage

H3K36acminusscore

Freq

uenc

y

50 100 150 200

010

0020

0030

00


050

100

150

200

H3K

36ac

sco

re

minus500 0 500 1000 1500 2000

050

100

150


Aver

age

cove

rage


leng

th

A

B C

D E



195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


195

bp25

2 bp

368

bp62

9 bp

minus500 0 500 1000 1500 2000 2500

00

04

08


Aver

age

cove

rage H3K36ac




A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


A B C D



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

l

00

02

04

06

08WSgcn5-1

AT3G28060

IgG H3K36ac00

01

02WSgcn5-1

M

GST

-GC

N5

GST

anti H3K36ac

anti H3

H31 GST GST-GCN5

A

B



minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


minus5

0

10

20

30D

iffer

ence

ina v

erag

e co

vera

ge

minus2 0 2 4

Distance from TSS

minus2 0 2 4



minus2 0 2 4

Distance from TSS

minus2 0 2 4


H3K36ac sdg8minuswt



AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations


AT3G04720

IgG H3K36ac

Rel

H3K

36ac

leve

ls

00

02

04

06

08 ColHDA19 RNAi1

AT3G28060

IgG H3K36ac00

02

04

06 ColHDA19 RNAi1







































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations






































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Parsed Citations

active genes walid mahrez , minerva susana trejo arellano · 24 in eukaryotic cells, ... 74 and has...

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