center f dna curvature, melting, and flexibility - cbs · center f or biological sequence anal ysis...
TRANSCRIPT
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DNA curvature, melting, and flexibility
Dave UsseryComparative Microbial Genomics WorkshopPathumthani, Thailand8 March, 2005
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DNA curvature, melting, and flexibility
Dave UsseryComparative Microbial Genomics WorkshopPathumthani, Thailand8 March, 2005
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Outline
• Introduction & disclaimer
• DNA curvature
• DNA Flexibility
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MinorGroove
MajorGroove
1.12
3600= one helical
turn
10.5 bp per turn
34.30 twist angle
(rotation per residue)3.4A Axial Rise
Base Pair Tilt - 6o
Helix Pitch
35.7A
34.3o
Helix Diameter
20A
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Marini gel
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U2.1
200 bp
Straight DNA
A.
200 bp
Bent DNA
B.
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Agarose gel
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A=TA=T
2.5
Tilt Roll
A=T A=T
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Random Bends
Bends Phased at 10.5 bp
Bends Phased at 16 bp
2.6
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CCCAAAAATGTCAAAAAATAGGCAAAAAATGCCAAAAATCCCAAC
1
.
11
.
21
.
31
.
41
.
2.3
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katP >
espP >
L7028 >
L7031 >
etpD
>
etpE >
etpF >
etpL >
EHEC-hlyA >
EHEC-hlyB >
L7072
>
L70
81 >
L70
86 >
L70
91 >
L7095
>
traI >
EHEC-hlyC
EHEC
-hlyB
EHEC
-hlyA
L709
5
0k12.5k
25k
37.5k50k62
.5k
75k
GENOME ATLAS
Center for Biological Sequence Analysishttp://www.cbs.dtu.dk/
Genetica, 108:47-51, 2000
Intrinsic Curvaturedevavg
0.07 0.30
Stacking Energydevavg
-9.52 -6.40
Position Preferencedevavg
0.11 0.17
Annotations:
CDS +
CDS -
Direct Repeatsfixavg
5.00 7.50
Inverted Repeatsfixavg
5.00 7.50
Percent ATfixavg
0.30 0.70
Resolution: 19
E. coli pO157GenBank Acession AF074613 92,077 bp
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Promoter Structural profile
-10 “TATA box”-35“UP”
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!400 !200 0 200 400
!0.0
50.
000.
050.
100.
150.
200.
25Ecoli_K!12_W3110_Main: Stacking energy
Distance from translation start
Z!sc
ore
CURVATURE
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!400 !200 0 200 400
!0.0
50.
000.
050.
100.
150.
20
Ecoli_K!12_W3110_Main: Structural Profile
Distance from translation start
Z!sc
ore AT content
Position PreferenceStacking EnergyIntrinsic CurvatureDNAase sensitivity
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Promoter Structural profile
+1
CDS
DNA curvature,flexibility importanthere
meltsrigid
cruciform
-10-35
mRNACDS
β / β’-10
-35+1
σα
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2.10
"Refined" Junction Model
CCGG
Tilt
CGGC5' 3'
GGCC GCCG
A
T
5' 3'
AA A
AA
TT
Roll
+
Tilt
3' 5'
T TT
A
T
A
T
A
T
A
T
A
T
A
T
A
T
A
T
A
T
2.11
5'3'
5'3'
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nucleosomes
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chromatin
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Beads on a string
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Trimmed 1
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Trimmed 2
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trinuc. % Out AAT/ATT -0.280 AAA/TTT -0.274 CCA/TGG -0.246 AAC/GTT -0.205 ACT/AGT -0.183 CCG/CGG -0.136 ATC/GAT -0.110 AAG/CTT -0.081 CGC/GCG -0.077 AGG/CCT -0.057 GAA/TTC -0.037 ACG/CGT -0.033 ACC/GGT -0.032 GAC/GTC -0.013 CCC/GGG -0.012 ACA/TGT -0.006 CGA/TCG -0.003 GGA/TCC 0.013 CAA/TTG 0.015 AGC/GCT 0.017 GTA/TAC 0.025 AGA/TCT 0.027 CTC/GAG 0.031 CAC/GTG 0.040 TAA/TTA 0.068 GCA/TGC 0.076 CTA/TAG 0.090 GCC/GGC 0.107 ATG/CAT 0.134 CAG/CTG 0.175 ATA/TAT 0.182 TCA/TGA 0.194
“Travers” trinucleotide scale:
Satchwell,S.C., Drew,H.R., and Travers,A.A., "Sequence periodicities in chicken nucleosome core DNA" ,J. Mol. Biol. ,191 :659-675, (1986)
Baldi,P., Brunak,S., Chauvin,Y., and Krogh,A., "Naturally occurring nucleosome positioning signals in human exons and introns" ,J. Mol. Biol. ,263 :503-510, (1996). )
NOTE: we use a (slight) modification,in which the absolute value (magnitude) of the values is used to reflect trinucleotideswhich tend to exclude nucleosomes.
Low position pref.
Highposition pref.
Highposition pref.
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Spombe - 3 chromosomes
Nature, 415:871-880, (2002).
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S.pombe chr. 1
DNA Conformation and Transcription, chapt14, (edited by Takashi Ohyama, 2004).
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Spombe zoom
DNA Conformation and Transcription, chapt14, (edited by Takashi Ohyama, 2004).
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Terminus
Origin
rhsA
rhsB
rhsC
rhsD
rhsE
phnM ya
gF
rrsA
rrsB
rrsC
rrsD
rrsE
rrsG
rrsH
0M0.5M
1M1.5M
2M2.5M
3M3.
5M4M
GENOME ATLAS
Center for Biological Sequence Analysishttp://www.cbs.dtu.dk/
Intrinsic Curvaturedevavg
0.16 0.21
Stacking Energydevavg
-8.74 -7.63
Position Preferencedevavg
0.14 0.16
Annotations:
CDS +
CDS -
rRNA
tRNA
Watson Repeatsfixavg
5.00 7.50
Crick Repeatsfixavg
5.00 7.50
GC Skewfixavg
-0.03 0.03
Percent ATfixavg
0.45 0.55
Resolution: 1856
E. coli K-12isolate MG1655 4,639,221 bp
ygeG
rfaJ
rpoB
flu
ycgZ
rpsQ
b2651
phnI
rpsO
nohB
yagG
atpF
lpdA
ydfO
b0725
yjhA
yhiF
yi21_2
b037
3
0M0.5M
1M1.5M
2M2.5M
3M3.
5M4M
GENOME ATLAS
Center for Biological Sequence Analysishttp://www.cbs.dtu.dk/
Intrinsic Curvaturedevavg
0.16 0.21
Stacking Energydevavg
-8.66 -7.71
Position Preferencedevavg
0.14 0.16
Annotations:
CDS +
CDS -
rRNA
tRNA
Global Direct Repeatsfixavg
5.00 7.50
Global Inverted Repeatsfixavg
5.00 7.50
GC Skewdevavg
-0.05 0.05
Percent ATfixavg
0.20 0.80
Resolution: 1856
E. coli 4,639,221 bp
J. Mol. Biol, 299:907-930, (2000).
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J. Mol. Biol, 299:907-930, (2000).
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Histogram of log(affy.ex[, i])
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Highly Expressed Genes
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niceDogma
Comparative Microbial Genomics Group
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Summary
1. DNA sequence DNA structure Function
2. DNA curvature is caused mainly by phased A-tracts.
3. Where you are in the chromosome is important!