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
