Chromatin dynamics in cellular function

156 Pages·2006·2.419 MB·English

by  Brehon Curtis Laurent

Results and Problems in Cell Differentiation
41
Series Editors
D. Richter, H. Tiedge

BrehonC.Laurent (Ed.)
Chromatin Dynamics
in Cellular Function
With14Figuresand1Table
123
BrehonC.Laurent,PhD
DepartmentofOncologicalSciences
MountSinaiSchoolofMedicine
OneGustaveL.LevyPlace
Box1130
NewYork,NY10029
USA
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Contents
StructureandFunctionofProteinModulesinChromatinBiology
K.L.Yap,M.-M.Zhou . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2 HistoneLysineAcetylationRecognition
bytheBromodomain . . . . . . . . . . . . . . . . . . . . . . 2
3 HistoneLysineMethylationRecognition . . . . . . . . . . . 4
4 ChromosomalDNA/HistoneBinding . . . . . . . . . . . . . 8
5 ChromosomalProtein–ProteinInteractions . . . . . . . . . 11
6 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
7 FutureDirections . . . . . . . . . . . . . . . . . . . . . . . . 17
8 ConcludingRemarks . . . . . . . . . . . . . . . . . . . . . . 17
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
TheGenerationandRecognitionofHistoneMethylation
M.S.Torok,P.A.Grant . . . . . . . . . . . . . . . . . . . . . . . . . 25
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2 TheNucleosomeandChromatinStructure . . . . . . . . . . 26
2.1 ChromatinDomains . . . . . . . . . . . . . . . . . . . . . . 27
2.2 HistoneModifications . . . . . . . . . . . . . . . . . . . . . 27
3 HistoneMethylation . . . . . . . . . . . . . . . . . . . . . . 28
3.1 LysineMethylation . . . . . . . . . . . . . . . . . . . . . . . 29
3.2 ArginineMethylation . . . . . . . . . . . . . . . . . . . . . . 31
3.3 HistoneDemethylation . . . . . . . . . . . . . . . . . . . . . 32
4 HistoneModificationBindingProteins . . . . . . . . . . . . 33
4.1 Chromodomains . . . . . . . . . . . . . . . . . . . . . . . . 33
4.2 TudorandMalignantBrainTumorDomains . . . . . . . . . 35
4.3 WD40Domain . . . . . . . . . . . . . . . . . . . . . . . . . 36
5 HistoneModificationCrosstalkwithMethylation . . . . . . 36
6 ConclusionsandFuturePerspectives . . . . . . . . . . . . . 38
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
VI Contents
HistoneUbiquitylationandtheRegulationofTranscription
M.A.Osley,A.B.Fleming,C.-F.Kao . . . . . . . . . . . . . . . . . . 47
1 RegulationofHistoneUbiquitylation . . . . . . . . . . . . . 47
1.1 TheUbiquitinConjugatingPathway . . . . . . . . . . . . . . 49
1.2 FactorsRegulatingHistoneUbquitylation . . . . . . . . . . 50
2 RelationshipBetweenHistoneH2BUbiquitylation
andHistoneH3Methylation . . . . . . . . . . . . . . . . . . 55
3 RoleofHistoneUbiquitylationinGeneExpression . . . . . . 57
3.1 UbiquitylatedH2B . . . . . . . . . . . . . . . . . . . . . . . 57
3.2 UbiquitylatedH2A . . . . . . . . . . . . . . . . . . . . . . . 63
3.3 UbiquitylatedH4 . . . . . . . . . . . . . . . . . . . . . . . . 65
4 AdditionalCellularRolesofUbiquitylatedHistones . . . . . 66
5 SummaryandPerspectives . . . . . . . . . . . . . . . . . . . 66
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
HistoneDynamicsDuringTranscription:
ExchangeofH2A/H2BDimersandH3/H4Tetramers
DuringPolIIElongation
C.Thiriet,J.J.Hayes . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
1 ABriefHistoryofChromatinandTranscription . . . . . . . 77
2 RNAPolymeraseActivityInducesHistoneExchange
withFreePools . . . . . . . . . . . . . . . . . . . . . . . . . 79
3 HistoneExchangeMaybeDuetoRNAPolIIElongation
ThroughNucleosomes . . . . . . . . . . . . . . . . . . . . . 80
4 ExchangeofH3/H4TetramersDuringTranscription . . . . . 82
5 H2A/H2BvsH3/H4Exchange . . . . . . . . . . . . . . . . . 83
6 Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
TheRolesofChromatinRemodellingFactorsinReplication
A.Neves-Costa,P.Varga-Weisz. . . . . . . . . . . . . . . . . . . . . 91
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 91
2 HistoneModificationsandDNAReplication . . . . . . . . . 94
3 HistoneChaperonesandDNAReplication . . . . . . . . . . 94
4 ATP-DependentRemodellingFactors
andChromatinDynamicsinDNAReplication . . . . . . . . 97
4.1 Energy-DependentChromatinRemodellersHaveRoles
inDNARepair . . . . . . . . . . . . . . . . . . . . . . . . . 97
4.2 ISWIComplexesFacilitateDNAReplicationinChromatin . . 98
4.3 ISWIComplexeshaveRoles
intheReplicationofChromatinStructures . . . . . . . . . . 99
4.4 ISWIComplexesTargetReplicationSites . . . . . . . . . . . 100
5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Contents VII
ChromatinModificationsinDNARepair
A.J.Morrison,X.Shen . . . . . . . . . . . . . . . . . . . . . . . . . . 109
1 OverviewofChromatinModifications . . . . . . . . . . . . . 109
1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 109
1.2 ChromatinModifications . . . . . . . . . . . . . . . . . . . . 110
2 HistoneModificationsinDNARepair . . . . . . . . . . . . . 111
2.1 H2AandH2B . . . . . . . . . . . . . . . . . . . . . . . . . . 111
2.2 H3andH4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
3 Chromatin-ModifyingComplexesinDNARepair . . . . . . 115
3.1 Histone-ModifyingComplexes . . . . . . . . . . . . . . . . . 115
3.2 Chromatin-RemodelingComplexes . . . . . . . . . . . . . . 115
4 FutureDirections . . . . . . . . . . . . . . . . . . . . . . . . 117
4.1 AdditionalChromatinModifiersinDNARepair . . . . . . . 117
4.2 RecruitmentandFunctionofChromatinModifiers
inDNARepair . . . . . . . . . . . . . . . . . . . . . . . . . 118
4.3 ChromatinModificationsandCancer . . . . . . . . . . . . . 120
4.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
MechanismsforNucleosomeMovement
byATP-dependentChromatinRemodelingComplexes
A.Saha,J.Wittmeyer,B.R.Cairns . . . . . . . . . . . . . . . . . . . 127
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 127
2 NucleosomeSpecialization . . . . . . . . . . . . . . . . . . . 128
3 TheNucleosome:ABiophysicalChallengeforRemodelers . 129
3.1 RemodelerFamilies:Discovery,Functions,andProperties. . 130
3.2 RemodelersElicitDNA-
and/orNucleosome-dependentATPaseActivity . . . . . . . 132
3.3 NucleosomeSlidingandAccessibility . . . . . . . . . . . . . 133
3.4 TheSWI/SNFandISWIRemodelers
areATP-dependentDirectionalDNATranslocases . . . . . . 134
4 RemodelersResembleDNAHelicases/Translocases . . . . . 135
4.1 DNATranslocationfromanInternalNucleosomalSite . . . . 136
4.2 Helicases/TranslocasesProvideModels
forDNATranslocationbyRemodelers. . . . . . . . . . . . . 137
4.3 ApplyingPrinciplesofTranslocases
toRemodelNucleosomes . . . . . . . . . . . . . . . . . . . . 138
4.4 DNATranslocationMayUnderlieDNATwisting . . . . . . . 141
5 ChromatinRemodeling
EnablesSpecializedBiologicalFunctions . . . . . . . . . . . 142
5.1 NucleosomeAssemblyandSpacing . . . . . . . . . . . . . . 142
VIII Contents
5.2 HistoneOctamerTransfer . . . . . . . . . . . . . . . . . . . 143
5.3 NucleosomeEjection . . . . . . . . . . . . . . . . . . . . . . 143
6 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
SubjectIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
ResultsProblCellDiffer(41)
L.Brehon:ChromatinDynamicsinCellularFunction
DOI10.1007/010/Published online:17February2006
© Springer-VerlagBerlinHeidelberg2006
StructureandFunctionofProteinModules
inChromatinBiology
KyokoL.Yap·Ming-MingZhou((cid:1))
StructuralBiologyProgram,DepartmentofPhysiologyandBiophysics,
MountSinaiSchoolofMedicine,NewYorkUniversity,1425MadisonAvenue,
NewYork,NY10029-6574USA
[email protected]
Abstract Chromatin-mediated gene transcription or silencing is a dynamic process in
which binding of various proteins or protein complexes can displace nucleosomal his-
tones from DNA to relieve repression or drive the gene into a highly repressed, silent
state.CovalentmodificationstoDNAandhistonesassociatedwithchromatinstructural
change play a crucial role in transcriptional regulation, with particular modifications
on certain residues associated with a specific transcriptional outcome. In recent years
a number of structural domains have been identified within chromatin-associated pro-
teins,includingDNAorRNAbindingdomains,protein-proteininteractiondomainsand
domainsthatrecognizespecificcovalentmodificationstohistonetails.Inthisreviewwe
discussthestructuralfeaturesoftheseproteinmodulesandthefunctionalrolestheyplay
inchromatinbiology.
1
Introduction
Gene transcriptional regulation at the chromatin level is coordinated by
a number of proteins and protein complexes that interact with nucleosomal
DNA and histone proteins. The addition and removal of covalent modifica-
tions to chromatin allow for another level of transcriptional controlbeyond
thegeneticcode.Toattainthisgoal,oneneedstounderstandthemechanisms
underlying the regulation and transduction of genetic information. Grow-
ing evidence supports the view that a genome-wide epigenetic mechanism,
imposedatthelevelofgenomicDNA-packinghistoneproteinsthroughpost-
translational amino acid modifications including acetylation, methylation,
phosphorylation,andubiquitination, playsafundamentalroleincontrolling
thecapacityofthegenomeforinformationstorageandretrievalinresponse
to physiological and environmental stimuli, and for inheritable changes of
gene function and expression. Site- and state-specific modifications on cer-
tain amino acid residues within nucleosomal histones have been associated
with a specific transcriptional outcome, e.g. gene repression or activation.
Indeed, the “histone code hypothesis” (Strahl and Allis 2000; Turner 2002)
postulates that different combinations of modifications, either in combina-