ZHANG ZHIZHUOMAY 2010

Nucleosome Positioning& Transcription Factor Identification

Outline

Basic ConceptNucleosome Positioning and Gene Regulation

General Transcription Mechanism Genomic Organization of Nucleosomes The Organization of Nucleosomes on Genes Control of DNA Access

Nucleosome Related TF Identification Enhancer Identification Integrating Histone Information to Predict TF binding

sites

Basic Concept

Histone

Nucleosome

Basic Concept

HistoneNucleosomeLinker-DNA

DNA between two nucleosomesRNA PolyII

An enzyme catalyzes the transcription of DNATBP

TATA binding protein and a necessary component of RNA polymerase

General Transcription Mechanism

”Bridge”

Chromatinremodelling

General Transcription Mechanism

Genomic Organization of Nucleosomes

Deposition of histones on DNA during DNA replication occurs at random positions?

Not Really!

Genomic Organization of Nucleosomes

 Highly phased or a random continuous distribution

Genomic Organization of Nucleosomes

Highly phased or a random continuous distribution

Facing inwards or outwards

Distance between Positioned nucleosomes

Tend to be fixed distanceshort stretches of linker DNA

 165 bp (18 bp linker) in S. cerevisiae 175 bp (28 bp linker) in D. melanogaste 185 bp (38 bp linker) in humans

ISWI complex models the spacingLinkers might have regulatory functions

The organization of nucleosomes on genes

Nucleosome numbering

The organization of nucleosomes on genes

Nucleosome numberingH2A.Z levels, acetylation, H3K4 methylation

and phasing

Nucleosome Positions

Independent positioningStatistical Positioning

Analog to Roulette wheel

Nucleosome-Free Region(NFR)

Poly(dA:dT) tracts contribute to rigidity We thought promoter regions would be

occluded by nucleosomes except when they were activated.

But in fact, NFRs demonstrated that open promoter states are stable and common, even at genes that are transcribed so infrequently.

Nucleosome-Free Region(NFR)

Low basal levels of leaky transcription might have a general housekeeping function

Open architecture of the 5' NFR is necessary for the initial 'pioneering' polymerase or whether transcription itself establishes the NFR from the closed state (after the last transcription)

Transcription start site selection by nucleosomes?

Most promoters seem to lack core promoter elements, including a TATA box, the TFIIB recognition element (BRE), INR, downstream promoter element (DPE) or motif ten element (MTE)

Control of DNA Access

DNA accessibility without catalysis thermal fluctuation energetically less favourable towards the midpoint of

the nucleosome Binding of one factor might stabilize a partially

disassembled state

Control of DNA Access

DNA accessibility without catalysisDNA accessibility and remodelling complexes

Control of DNA Access

DNA accessibility without catalysisDNA accessibility and remodelling complexesNucleosome eviction

Nucleosome dynamics define transcriptional enhancers. Nat Genet 42:343-347.

Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol 11:R7.

Nucleosome Related TF Identification

Nucleosome Dynamics Define Transcriptional Enhancers

Monomethylated H3K4 (H3K4me) : enhancers, Trimethylated H3K4 (H3K4me3) :TSS, Dimethylated H3K4 (H3K4me2) : both the TSS and

enhancers

H3K4me2 are destabilized at AR binding site, but better positioning at flanking loci.

FOXA1 as pioneer factor to stabilize the nucleosomes.

Motif Analysis in the Paired Nucleosome Regions

Identify Nucleosome

Motif Analysis in the Paired Nucleosome Regions

Identify NucleosomeIdentify Enhancer Region

Motif Analysis in the Paired Nucleosome Regions

Identify NucleosomeIdentify Enhancer RegionMotif Analysis in Enhancer Region

Genome-wide prediction of transcription factor binding sites using an integrated model

Eight chromatin marks (H3, H3K4me1, H3K4me2, H3K4me3, H3K9me3, H3K36me3, H3K20me3, and H3K27me3) 

Genome-wide prediction of transcription factor binding sites using an integrated model

Future work

Finding candidate nucleosome organizing factors

Better understand nucleosome positioning

Reference

I) NUCLEOSOME POSITIONING.II) NUCLEOSOME REMODELING. BCH 6415. http://www.med.ufl.edu/biochem/tyang/

http://www.uio.no/studier/emner/matnat/molbio/MBV4230/ Nucleosome dynamics define transcriptional enhancers, Nature

genetics 42 (4): 343-7, 2010 Apr Nucleosome positioning and gene regulation: advances through

genomics, Nature reviews. Genetics 10 (3): 161-72, 2009 Mar Inducible gene expression: diverse regulatory mechanisms,

Nature reviews. Genetics , 2010 Apr 27 Genome-wide prediction of transcription factor binding sites

using an integrated model, Genome biology 11 (1): R7, 2010 Jan 22

http://en.wikipedia.org/wiki/Histone

Q&A