Chromatin remodeling ATPases non-covalent change

Chromatin remodeling

ATPasesnon-covalent change

Lecture outline

Types of chromatin remodelers

complexes

protein domains

Activities of chromatin remodelers

on chromatin

in the organism

Chromatin remodeling ATPases

txn repression

txn

txnassemblyDNA methylation

exchange

repair

DNA methylation

heterochromationrecombination archealTBP

ISWI

CHD

SWI2/SNF2

INO80/SWR1

ATPase domain

Clapier and Cairns Ann. Rev. Biochem. 2009

Activities of chromatin remodeling ATPases

Clapier and Cairns, Annu. Rev. Biochem. 2009

Chromatin assembly

Dynamic Range of Chromatin Structure Created by ATP-

Dependent Chromatin Remodeling

Slide courtesy of Dr. Hua-Ying Fan

Shared characteristics of chromatin remodeling complexes

• bind nucleosomes

• are DNA-dependent ATPases

• recognize histone modifications

• ATPase activity can be regulated

• interact with other proteins

From Clapier and Cairns, Annu. Rev. Biochem. 2009

Assays for chromatin remodeling

Non-covalent alteration!

sliding

Assays for chromatin remodeling

Also MNAse qPCR or MNAse seq or MNAse H3 ChIP seq

Persistence

Proc. Natl. Acad. Sci. USAVol. 95, pp. 4947–4952, April 1998Perturbation of nucleosome core structure by the SWI/SNFcomplex persists after its detachment, enhancing subsequenttranscription factor bindingJACQUES COˆTE ,CRAIG L. PETERSON, AND JERRY L. WORKMAN

cold competitor oligonucleosomes

one remodeler per nucleosome

multiple enzymatic reactions destabilize 1 nucleosome

14 histone-DNA contacts

use ATP hydrolysis to break (ca. 1kcal/mol for each contact)

ATPases bind near center of nucleosomes (2 turns from dyad)

translocate along DNA 3’ to 5’

generate DNA loops, reposition nucleosome or destabilize

Chromatin remodeling

ISWI(SNF2H)

SMALL COMPLEXES (generally)

Yadon and Tsukiyama Cell Snapshot 2011

SMALL COMPLEXES (generally)

MANY COMPLEXES

Yadon and Tsukiyama

Roles of ISWI

nucleosome array formationchromatin assembly, replication

heterochromatin formation

reprogramming (nuclear transfer)

transcriptional regulationsome PolII, PolI

ISWI can position nucleosomes onto unfavorable DNA

ISWI: greenPolII: red

ISWI role in transcription

Deuring et al., Molecular Cell, Vol. 5, 355–365, February, 2000The ISWI Chromatin-Remodeling Protein Is Required for Gene Expression and the Maintenance of Higher Order Chromatin Structure In Vivo.

Female iswi mut. Male iswi mut.

Deuring et al., Molecular Cell, Vol. 5, 355–365, February, 2000The ISWI Chromatin-Remodeling Protein Is Required for Gene Expression and the Maintenance of Higher Order Chromatin Structure In Vivo.

ISWI: required for condensation of male X

Role of the domains

Blue + chargeRed - charge

Role of the domains

Yamada et al., Nature 2011

Role of the domains

SANT/HAND domain contacts histone tails

- charge: histone tail interaction

+ charge: DNA interaction

Slide domain linker DNA contact, ’measures’

distanceequal spacing of nucleosomes

ATPase domainnear dyad, motor, translocation

ROLE of ISWI domains

Loop propagation models

Yamada et al., Nature 2011

SWI/SNF

Isolated as sucrose-non-fermenting mutants in yeastsnf2, snf5, snf6

Isolated as mating type switch deficient mutants in yeastswi1, swi2, swi3

SNF2=SWI2

SWI2/SNF2 subfamily of chromatin-remodeling ATPases

LARGE COMPLEXES (generally)

Ca. 11 subunits, 2 MD in size Casten et al., Cell snapshot 2011

Core complex ATPase Snf2 (BRM/BRG1)

Snf5 (BAF47)Swi3 (BAF155/BAF170)

Function of some subunits not yet understoodATPase and core: sufficient in vitro, other subunits required in vivo

other subunitsSwp73 or BAF60 actin related proteins (ARP)BAF 57

SWI2/SNF2 complexes

Trends in Genetics 2007

Two types of complexes in most organisms

a,b

a,b

Clapier and Cairns, Annu. Rev. Biochem. 2009

Ho and Crabtree Nature 2010

BROMO domainbinds acetylated lysines on

histone tails

HSA domain protein interactions

actin/ARP transcription factors

ATPase domainnear dyad, motor, translocation

ROLE of SNF2/BRM domains

ROLE of SNF2/BRM domains

New SnAC domain required for remodeling activity

Sen et al., NAR 2011

Hopfner et al. COSB 2012

SNF2 ATPase activity

change nucleosome positionincreased regulatory

protein access!

change nucleosome conformation

eject histone octamer

displace H2A/H2B dimer

Roles of SWI2/SNF2

Inducible gene expression:transcription initiationtranscription elongation

Splicing

Repair

Roles in development and stress responses

sliding

ATP-dependentATP-dependentChromatin Remodeling ComplexChromatin Remodeling Complex

Cis-regulatory element

Activation or repression!

sliding

ATP-dependentATP-dependentChromatin Remodeling ComplexChromatin Remodeling Complex

Cis-regulatory element

Activation or repression!

Only a subset of genes depends on SWI2/SNF2

Holstege et al. (1998) Cell 95Whole genome expression analysis in S. cerevisiae

Role in activation and repression of transcription

Regulation of select genes

SWI2/SNF2 activities

Proc. Natl. Acad. Sci. USAVol. 95, pp. 4947–4952, April 1998Perturbation of nucleosome core structure by the SWI/SNFcomplex persists after its detachment, enhancing subsequenttranscription factor bindingJACQUES COˆTE ,CRAIG L. PETERSON, AND JERRY L. WORKMAN

cold competitor oligonucleosomes

Zhang et al.

The 2MD SWI/SNF complex fits around the entire nucleosome

Nature Structural & Molecular Biology 15, 1272 - 1277 (2008) Published online: 23 November 2008

http://www.nature.com/nsmb/journal/v15/n12/extref/nsmb.1524-S5.mov

RSC docks onto nucleosome

1 = ATPase

Casten et al., Cell snapshot 2011

Liu et al., MCB2011

CHD ATPases

CHD1: role in chromatin assembly; open chromatinin pluripotent cells

CHD3, 4HDAC complex subunits!NuRD complex

also contains Me-DNA binding protein (MBD2)complex connects deacetylation, chromatin remodeling and DNA methylation; repressive function

CHD7: together with PBAF; CHARGE syndrome

Together with SNF2: role in transcriptional elongation

Sims and Wade, Cell Snapshot 2011

Hopfner et al. COSB 2012

Sharma et al. JBC 2011

New insight into domains from crystal structure

CHROMO and PHD domainsbind methylated lysines on

histone tailsmodulate activity of remodelers

ATPase domainnear dyad, motor, translocation

ROLE of CHD ATPase domains

Hauk et al. Molec. Cell 2010

Chromodomains gate CHD1 activity

Role in chromatin assembly

Lusser et al., Nature Struc Mol Biol 2005

CHRHC

INO80chromatin assemblyDNA repairinteracts with phosphorylated H2A.X (gammaH2A.X)transcriptionexchange H2A.Z with H2A

SWR1

H2A exchange with H2A.ZBoundary to heterochromatin spreadingtranscriptionally poised promoters (together with H3.3)

Bao and Shen Cell Snapshot 2011

INO80/ SWR1

ATPase domain

Morrison and Shen, Nature reviews Mol Cell Biol, 2009

Role of INO80 complex

Biochem. Cell Biol vol 84 2006

Role of SWR complex

Instability of H2AZ allows high temperature to turn on genes in plants

Role of SWI2/SNF2

ATPases in the organism

Role of chromatin remodeling ATPasesin cancer

SWI2/SNF2 subgroup

*mouse BRG1 mutants develop tumors at high frequency (non-small lung carcinoma)Biallelic loss observed in prostrate, lung, breast and pancreatic cancer cell lines

*subunit hSNF5 (INI1) is tumor suppressorLOH in nearly all cases of pediatric rhabdoid sarcomarecapitulated in mouse models (conditional inactivationleas to lymphomas with 100% penentrance)

Role of chromatin remodeling ATPasesin cancer

Others

*dNURF: ISWI and p301 involved in neoplastic transformation

*NURD: CHD1/MI2 linked to certain breast cancers

Role in other diseases

* X-linked mental retardation

*William syndrome

*Cockayne syndrome

*Schimke immuno-osseous dysplasia

Why are they so important?

Maintenance and alteration of nucleosome

occupancy and positioning

Useful terminology

Specificity of chromatin remodelers

a. recruitment

ATP-DEPENDENT NUCLEOSOME REMODELINGPeter B. Becker and Wolfram HörzAnnu. Rev. Biochem. 2002. 71:247–73

CRM; chromatin remodeler

Transcription factor

Methyl -lysine

Polymerase

Acetyl-Lysine H3K14ac-RSC

H3K4me-ISWI

Nuclear hormone receptors-Brg1

Gal1promoter SNF2

H3K16 non ac - ISWI

Targeting of SWI/SNF

no DNA binding specificity

recruited by transcription factors in many organisms

yeast: SWI5, GCN4, GAL4, VP16Drosophila: Ikaros, hunchback, tramtrackhuman: EKLF, C/EBPB, GR, MyoDplants: LFY, TCP, MP

Regulation of SWI2/SNF2 activity

1. Post-translational modifications phosphorylation, acetylation, de-ubiquitylation

2. Complex compositionregulatory subunits (SWI5, Drososphila)tissue specific subunits (BAF60)

3. Interaction with small moleculesphosphatidyl inositol

Hogan and WeiszMutation Research 618 (2007) 41-51

Regulation by phosphorylation, acetylation

Clapier and Cairns, Ann. Rev. Biochem. 2009

Regulation of SWI2/SNF2 activity

1. Post-translational modifications phosphorylation, acetylation, de-ubiquitylation

2. Complex compositionregulatory subunits (SWI5, Drososphila)tissue specific subunits (BAF60)

3. Allosteric regulation by ATPase domains (CHD1)

4. Interaction with small molecules(phosphatidyl inositol)

Regulation by complex composition

Yoo and Crabtree, Nature 2010

Yoo et al., Nature 2009

Yoo et al., Nature 2009

Takeuchi and Bruneau Nature 2009

Can have instructive roles!

Role in many aspects of development

Ho and Crabtree Nature 2010

Nucleosome

from Horn and Peterson Science, 2002

me me

Ensure packaging of genomeEnable differential accessibility

of genome

H3K27me3DNA

methylation

Lecture summary

Types of chromatin remodelers

complexes

protein domains

Activities of chromatin remodelers

on chromatin

in the organism

Glossary and Summary I

Chromatin remodeler Families:ISWI; SWI/SNF; CHD; SWR1; INO80Others involved in repair and recombination

Remodeling Complexes ISWI: ACF, NURF, CHRACSWI/SNF: BAF, pBAFCHD: Mi2/NURD

Important domains:Bromodomain (SWI/SNF)SANT, Slide (ISWI; CHD)PHD, Chromodomain (CHD)

ATPase domain (all)

Glossary and Summary II

Activities of chromatin remodelers

properly space nucleosomes on chromatinafter replication, transcription, repair

alter nucleosome position or occupancyin response to exogenous or endogenous cues

In the organism

prevent loss of cell identity (cancer)role in pluripotency (ESC) and differentiationsurvival under stress