remodelers counteract intrinsic histone-dna sequence...
TRANSCRIPT
Remodelers counteract intrinsic histone-DNA sequence preferences
Yuri Moshkin
Erasmus University Medical Center
1Y. Moshkin
ATP-dependentremodelers
ATP-dependent chromatin remodelers
(in vitro remodeling)
ATP
ADP + PiMNase
“naive” chromatin state (ordered)
“remodeled” chromatin state (disordered)
2Y. Moshkin
ATP-dependentremodeling
ATP-dependent chromatin remodelers
(in vitro transcription)
ATP
ADP + Pi
TF
TF: - -+ +
Remodeler: - +- +
chromatin template
3Y. Moshkin
ATP-dependent chromatin remodelers
(gene-centric model)
BRMMI2
NURD
ISWIINO80
INO80
BAP
PBAP
NURF
ACF
CHRAC
4Y. Moshkin
Q: How remodelers function in vivo?
Gene-centric type of questions:
• What genes remodelers bind?
• What is their impact on chromatin structure
and expression of the target genes?
5Y. Moshkin
ChIP-chip approach:
BRMMI2 ISWIINO80
NURD INO80BAP
PBAP
NURF
ACF
CHRAC
1 Remodeler/~15-20 nucleosomes7Y. Moshkin
• Remodelers are not enriched on genes (-)
BRM
MI2 ISWIINO80
Epigenetics view:
Q: Can histone code determine remodelers binding?
En. ?
9Y. Moshkin
Interband:
~500-2,000 bp
~2-10 nucleosomes
Band:
~5,000-100,000 bp
~25-500 nucleosomes
Remodeler
Interbands / Bands define two distinct
higher-order chromatin states (“open” / “closed”)
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Remodeler loci display characteristic sequence biasavera
ge A
T c
on
ten
t (%
)
BRMMI2 ISWIINO80
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• Remodelers are not enriched on genes (-)
• Remodeler loci do not show significant enrichment
in histone marks (+/-)
• Remodelers bind “open” chromatin and
recognize specific sequences (+)
15Y. Moshkin
Predicted propencity of remodeler loci
to bind nucleosomesN
uc
leo
so
me
sc
ore
#1
(Se
ga
l e
t a
l., 2
00
6)
Nu
cle
os
om
e
sc
ore
#2
(Lo
ck
e e
t a
l., 2
01
0)
BRMMI2 ISWIINO80
17Y. Moshkin
Remodelers counteract intrinsic histone-DNA
sequence preferencesavera
ge H
3 C
hIP
BRMMI2 ISWIINO80
score #1
score #2
S2 DMI2 S2 DBRM S2 DINO80 S2 DISWI
S2 RNAi
18Y. Moshkin
Remodelers counteract intrinsic histone-DNA
sequence preferences genome-wide
H3
Ch
IP
BRMMI2 ISWIINO80 SA SMC3S2
Nucleosome score #1
score #1
score #2
RNAi knockdown
1 Remodeler/~15-20 nucleosomes
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Nucleosome remodeling by “PUSH” and “PULL”
BRM
MI2 INO80 ISWI
“High affinity” “Low affinity”
sequence-dependent
“statistical”
“PULL” “PUSH”
20Y. Moshkin
DNA sequence determines nucleosome positioning
in replicating, but not differentiating cells H
3 C
hIP
Nucleosome score #1
no transcription zygotic transcription
MBT
0-1h 2-12h 21-24h larvae
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H3
Ch
IP
pro
mo
ters
MBT
TF TF
BRM
MI2
INO80
ISWI
Initiation of zygotic transcription may rely on
gradient distribution of TFs and “open” promoter configuration,
but not chromatin remodeling
0-1h 2-12h 21-24h larvae
22Y. Moshkin
OR
High nucleosome score:
GC - rich
High Stacking Energy
DG=DH-DST
In vitro
•Low T/ Low Histone conc.
In vivo
•De novo nucleosome assembly
In vitro
•High T / High Histone conc.
In vivo
•Nucleosome remodeling
Adapted from Wu, C., and Travers, A. (2005).
Relative affinities of DNA sequences
for the histone octamer
Low nucleosome score:
AT - rich
Low Stacking Energy
DG=DH-DST
23Y. Moshkin
Acknowledgments:
Department of Biochemistry, Erasmus MCGill Chalkley
Tsung Wei Kan
Peter Verrijzer
Erasmus MC Center for BiomicsWilfred van Ijcken
MRC Laboratory of Molecular Biology, Cambridge, UKAndrew Travers
24Y. Moshkin