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

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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?

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polII / BRM polII / ISWI

Cheap approach:

Remodelers do not co-localize with RNA polII

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ChIP-chip approach:

BRMMI2 ISWIINO80

NURD INO80BAP

PBAP

NURF

ACF

CHRAC

1 Remodeler/~15-20 nucleosomes7Y. Moshkin

Remodelers are not particularly enriched on genes

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• Remodelers are not enriched on genes (-)

BRM

MI2 ISWIINO80

Epigenetics view:

Q: Can histone code determine remodelers binding?

En. ?

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Remodeler sites show only a moderate enrichment

in histone marks

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DNA-Histone / MI2

Remodelers preferentially localize to interbands

(“open chromatin”)

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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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BRM / MI2 ISWI / MI2

MI2 co-localize with BRM, but not with ISWI

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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 (+)

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Sequence properties of remodeler loci

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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

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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

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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”

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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

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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

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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

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BRMMI2 ISWIINO80

Nucleosome turnover at remodelers loci

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