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Chromatin
FromWikipedia,thefreeencyclopedia

Chromatinisacomplexofmacromoleculesfoundin
cells,consistingofDNA,protein,andRNA.The
primaryfunctionsofchromatinare1)topackage
DNAintoasmallervolumetofitinthecell,2)to
reinforcetheDNAmacromoleculetoallowmitosis,
3)topreventDNAdamage,and4)tocontrolgene
ThemajorstructuresinDNAcompaction:DNA,the
expressionandDNAreplication.Theprimaryprotein
nucleosome,the10nm"beadsonastring"fibre,the30nm
componentsofchromatinarehistonesthatcompact
chromatinfibreandthemetaphasechromosome.
theDNA.Chromatinisonlyfoundineukaryoticcells
(cellswithdefinednuclei).Prokaryoticcellshavea
differentorganizationoftheirDNA(theprokaryoticchromosomeequivalentiscalledgenophoreandislocalized
withinthenucleoidregion).
Thestructureofchromatindependsonseveralfactors.Theoverallstructuredependsonthestageofthecellcycle.
Duringinterphase,thechromatinisstructurallyloosetoallowaccesstoRNAandDNApolymerasesthat
transcribeandreplicatetheDNA.Thelocalstructureofchromatinduringinterphasedependsonthegenespresent
ontheDNA.DNAcodinggenesthatareactivelytranscribed("turnedon")ismorelooselypackagedand
associatedwithRNApolymerases(referredtoaseuchromatin)whileDNAcodinginactivegenes("turnedoff")is
morecondensedandassociatedwithstructuralproteins(heterochromatin).[1][2]Epigeneticchemicalmodification
ofthestructuralproteinsinchromatinalsoaltersthelocalchromatinstructure,inparticularchemicalmodifications
ofhistoneproteinsbymethylationandacetylation.Asthecellpreparestodivide,i.e.entersmitosisormeiosis,the
chromatinpackagesmoretightlytofacilitatesegregationofthechromosomesduringanaphase.Duringthisstage
ofthecellcyclethismakestheindividualchromosomesinmanycellsvisiblebyopticalmicroscope.
Ingeneralterms,therearethreelevelsofchromatinorganization:
1.DNAwrapsaroundhistoneproteinsformingnucleosomesthe"beadsonastring"structure(euchromatin).
2.Multiplehistoneswrapintoa30nmfibreconsistingofnucleosomearraysintheirmostcompactform
(heterochromatin).(Definitivelyestablishedtoexistinvitro,the30nanometerfibrewasnotseeninrecent
Xraystudiesofhumanmitoticchromosomes.[3])
3.HigherlevelDNApackagingofthe30nmfibreintothemetaphasechromosome(duringmitosisand
meiosis).
Thereare,however,manycellsthatdonotfollowthisorganisation.Forexample,spermatozoaandavianredblood
cellshavemoretightlypackedchromatinthanmosteukaryoticcells,andtrypanosomatidprotozoadonotcondense
theirchromatinintovisiblechromosomesformitosis.

Contents
1 Dynamicchromatinstructureandhierarchy
1.1 DNAstructure
1.2 Nucleosomesandbeadsonastring
1.3 30nanometerchromatinfibre
1.4 Spatialorganizationofchromatininthecellnucleus
1.5 Cellcycledependentstructuralorganization
2 Chromatinandburstsoftranscription
2.1 Alternativechromatinorganizations
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2.1 Alternativechromatinorganizations
Methodstoinvestigatechromatin
Chromatin:alternativedefinitions
NobelPrizes
Seealso
References
Otherreferences
Externallinks

Dynamicchromatinstructureandhierarchy
Chromatinundergoesvariousstructuralchangesduringacellcycle.Histoneproteinsarethebasicpackerand
arrangerofchromatinandcanbemodifiedbyvariousposttranslationalmodificationstoalterchromatinpacking
(Histonemodification).Mostofthemodificationsoccuronthehistonetail.Theconsequencesintermsof
chromatinaccessibilityandcompactiondependbothontheaminoacidthatismodifiedandthetypeof
modification.Forexample,Histoneacetylationresultsinlooseningandincreasedaccessibilityofchromatinfor
replicationandtranscription.Lysinetrimethylationcaneitherbecorrelatedwithtranscriptionalactivity(tri
methylationofhistoneH3Lysine4)ortranscriptionalrepressionandchromatincompaction(trimethylationof
histoneH3Lysine9or27).Severalstudiessuggestedthatdifferentmodificationscouldoccursimultaneously.For
example,itwasproposedthatabivalentstructure(withtrimethylationofbothLysine4and27onhistoneH3)was
involvedinmammalianearlydevelopment.[4]
Polycombgroupproteinsplayaroleinregulatinggenesthroughmodulationofchromatinstructure.[5]
Foradditionalinformation,seeHistonemodificationsinchromatinregulationandRNApolymerasecontrolby
chromatinstructure.

DNAstructure
Innature,DNAcanformthreestructures,A,B,andZDNA.
AandBDNAareverysimilar,formingrighthandedhelices,
whereasZDNAisalefthandedhelixwithazigzag
phosphatebackbone.ZDNAisthoughttoplayaspecificrole
inchromatinstructureandtranscriptionbecauseofthe
propertiesofthejunctionbetweenBandZDNA.
AtthejunctionofBandZDNA,onepairofbasesisflipped
outfromnormalbonding.Theseplayadualroleofasiteof
recognitionbymanyproteinsandasasinkfortorsionalstress
fromRNApolymeraseornucleosomebinding.

Nucleosomesandbeadsonastring

ThestructuresofA,B,andZDNA.

Mainarticles:Nucleosome,ChromatosomeandHistone
Thebasicrepeatelementofchromatinisthenucleosome,interconnectedbysectionsoflinkerDNA,afarshorter
arrangementthanpureDNAinsolution.

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Inadditiontothecorehistones,thereisthelinkerhistone,H1,whichcontactsthe
exit/entryoftheDNAstrandonthenucleosome.Thenucleosomecoreparticle,
togetherwithhistoneH1,isknownasachromatosome.Nucleosomes,withabout20
to60basepairsoflinkerDNA,canform,undernonphysiologicalconditions,an
approximately10nm"beadsonastring"fibre.(Fig.12)..

Acartoonrepresentation
ofthenucleosome
structure.FromPDB:
1KX5(http://www.rcsb.o
rg/pdb/explore/explore.d
o?structureId=1KX5).

ThenucleosomesbindDNAnonspecifically,asrequiredbytheirfunctioningeneral
DNApackaging.Thereare,however,largeDNAsequencepreferencesthatgovern
nucleosomepositioning.Thisisdueprimarilytothevaryingphysicalpropertiesof
differentDNAsequences:Forinstance,adenineandthyminearemorefavorably
compressedintotheinnerminorgrooves.Thismeansnucleosomescanbind
preferentiallyatonepositionapproximatelyevery10basepairs(thehelicalrepeatof
DNA)wheretheDNAisrotatedtomaximisethenumberofAandTbasesthatwill
lieintheinnerminorgroove.(SeemechanicalpropertiesofDNA.)

30nanometerchromatinfibre
WithadditionofH1,thebeadsonastringstructureinturncoilsintoa30nm
diameterhelicalstructureknownasthe30nmfibreorfilament.Theprecise
structureofthechromatinfibreinthecellisnotknownindetail,andthereis
stillsomedebateoverthis.[6]
Thislevelofchromatinstructureisthoughttobetheformofeuchromatin,
whichcontainsactivelytranscribedgenes.EMstudieshavedemonstratedthat
the30nmfibreishighlydynamicsuchthatitunfoldsintoa10nmfiber
("beadsonastring")structurewhentransversedbyanRNApolymerase
engagedintranscription.

Fourproposedstructuresofthe30nm
chromatinfilamentforDNArepeatlength
pernucleosomesrangingfrom177to207
bp.
LinkerDNAinyellowandnucleosomal
DNAinpink.

Twoproposedstructuresofthe
30nmchromatinfilament.
Left:1starthelix"solenoid"
structure.
Right:2startloosehelixstructure.
Note:thehistonesareomittedin
thisdiagramonlytheDNAis
shown.

Theexistingmodelscommonly
acceptthatthenucleosomeslie
perpendiculartotheaxisofthe
fibre,withlinkerhistones
arrangedinternally.Astable
30nmfibrereliesontheregular
positioningofnucleosomesalong
DNA.LinkerDNAisrelativelyresistanttobendingandrotation.This
makesthelengthoflinkerDNAcriticaltothestabilityofthefibre,
requiringnucleosomestobeseparatedbylengthsthatpermitrotation
andfoldingintotherequiredorientationwithoutexcessivestresstothe
DNA.Inthisview,differentlengthsofthelinkerDNAshouldproduce
differentfoldingtopologiesofthechromatinfiber.Recenttheoretical
work,basedonelectronmicroscopyimages[7]ofreconstitutedfibers
supportsthisview.[8]

Spatialorganizationofchromatininthecellnucleus
Thespatialarrangementofthechromatinwithinthenucleusisnotrandomspecificregionsofthechromatincan
befoundincertainterritories.Territoriesare,forexample,thelaminaassociateddomains(LADs),andthe
topologicalassociationdomains(TADs),whichareboundtogetherbyproteincomplexes.[9]Currently,polymer

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modelssuchastheStrings&BindersSwitch(SBS)model[10]andtheDynamicLoop(DL)model[11]areusedto
describethefoldingofchromatinwithinthenucleus.

Cellcycledependentstructuralorganization
1.Interphase:Thestructureofchromatinduringinterphaseofmitosisisoptimizedtoallowsimpleaccessof
transcriptionandDNArepairfactorstotheDNAwhilecompactingtheDNAintothenucleus.Thestructure
variesdependingontheaccessrequiredtotheDNA.GenesthatrequireregularaccessbyRNApolymerase
requirethelooserstructureprovidedbyeuchromatin.
2.Metaphase:Themetaphasestructureofchromatindiffersvastlyto
thatofinterphase.Itisoptimisedforphysicalstrengthand
manageability,formingtheclassicchromosomestructureseenin
karyotypes.Thestructureofthecondensedchromatinisthoughtto
beloopsof30nmfibretoacentralscaffoldofproteins.Itis,
however,notwellcharacterised.Thephysicalstrengthofchromatin
isvitalforthisstageofdivisiontopreventsheardamagetotheDNA
asthedaughterchromosomesareseparated.Tomaximisestrength
thecompositionofthechromatinchangesasitapproachesthe
centromere,primarilythroughalternativehistoneH1analogues.It
Karyogramofhumanmaleusing
shouldalsobenotedthat,duringmitosis,whilemostofthe
Giemsastaining,showingtheclassic
chromatinistightlycompacted,therearesmallregionsthatarenotas
metaphasechromatinstructure.
tightlycompacted.Theseregionsoftencorrespondtopromoter
regionsofgenesthatwereactiveinthatcelltypepriortoentryinto
chromatosis.Thelackofcompactionoftheseregionsiscalledbookmarking,whichisanepigenetic
mechanismbelievedtobeimportantfortransmittingtodaughtercellsthe"memory"ofwhichgeneswere
activepriortoentryintomitosis.[12]Thisbookmarkingmechanismisneededtohelptransmitthismemory
becausetranscriptionceasesduringmitosis.

Chromatinandburstsoftranscription
Chromatinanditsinteractionwithenzymeshasbeenresearched,andaconclusionbeingmadeisthatitisrelevant
andanimportantfactoringeneexpression.VincentG.Allfrey,aprofessoratRockefellerUniversity,statedthat
RNAsynthesisisrelatedtohistoneacetylation.[13]Thelysineaminoacidattachedtotheendofthehistonesis
positivelycharged.Theacetylationofthesetailswouldmakethechromatinendsneutral,allowingforDNA
access.
Whenthechromatindecondenses,theDNAisopentoentryofmolecularmachinery.Fluctuationsbetweenopen
andclosedchromatinmaycontributetothediscontinuityoftranscription,ortranscriptionalbursting.Otherfactors
areprobablyinvolved,suchastheassociationanddissociationoftranscriptionfactorcomplexeswithchromatin.
Thephenomenon,asopposedtosimpleprobabilisticmodelsoftranscription,canaccountforthehighvariabilityin
geneexpressionoccurringbetweencellsinisogenicpopulations[14]

Alternativechromatinorganizations
Duringmetazoanspermiogenesis,thespermatid'schromatinisremodeledintoamorespacedpackaged,widened,
almostcrystallikestructure.Thisprocessisassociatedwiththecessationoftranscriptionandinvolvesnuclear
proteinexchange.Thehistonesaremostlydisplaced,andreplacedbyprotamines(small,argininerichproteins).[15]

Methodstoinvestigatechromatin
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1.ChIPseq(Chromatinimmunoprecipitationsequencing),aimedagainstdifferenthistonemodifications,can
beusedtoidentifychromatinstatesthroughoutthegenome.Differentmodificationshavebeenlinkedto
variousstatesofchromatin.
2.DNaseseq(DNaseIhypersensitivesitesSequencing)usesthesensitivityofaccessibleregionsinthe
genometotheDNaseIenzymetomapopenoraccessibleregionsinthegenome.
3.FAIREseq(FormaldehydeAssistedIsolationofRegulatoryElementssequencing)usesthechemical
propertiesofproteinboundDNAinatwophaseseparationmethodtoextractnucleosomedepletedregions
fromthegenome.[16]
4.ATACseq(AssayforTransposableAccessibleChromatinsequencing)usestheTn5transposasetointegrate
(synthetic)transposonsintoaccessibleregionsofthegenomeconsequentiallyhighlightingthelocalisationof
nucleosomesandtranscriptionfactorsacrossthegenome.
5.DNAfootprintingisamethodaimedatidentifyingproteinboundDNA.Ituseslabelingandfragmentation
coupledtogelelectrophoresistoidentifyareasofthegenomethathavebeenboundbyproteins.[17]
6.MNaseseq(MicrococcalNucleasesequencing)usesthemicrococcalnucleaseenzymetoidentify
nucleosomepositioningthroughoutthegenome.[18][19]
7.Chromosomeconformationcapturedeterminesthespatialorganizationofchromatininthenucleus,by
inferringgenomiclocationsthatphysicallyinteract.

Chromatin:alternativedefinitions
Theterm,introducedbyWaltherFlemming,hasmultiplemeanings:
1.Simpleandconcisedefinition:ChromatinisamacromolecularcomplexofaDNAmacromoleculeand
proteinmacromolecules(andRNA).TheproteinspackageandarrangetheDNAandcontrolitsfunctions
withinthecellnucleus.
2.Abiochemistsoperationaldefinition:ChromatinistheDNA/protein/RNAcomplexextractedfrom
eukaryoticlysedinterphasenuclei.Justwhichofthemultitudinoussubstancespresentinanucleuswill
constituteapartoftheextractedmaterialpartlydependsonthetechniqueeachresearcheruses.Furthermore,
thecompositionandpropertiesofchromatinvaryfromonecelltypetotheanother,duringdevelopmentofa
specificcelltype,andatdifferentstagesinthecellcycle.
3.TheDNA+histone=chromatindefinition:TheDNAdoublehelixinthecellnucleusispackagedby
specialproteinstermedhistones.Theformedprotein/DNAcomplexiscalledchromatin.Thebasicstructural
unitofchromatinisthenucleosome.

NobelPrizes
ThefollowingscientistswererecognizedfortheircontributionstochromatinresearchwithNobelPrizes:

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Year

ChromatinWikipedia,thefreeencyclopedia

Who

Award

NobelPrizeinPhysiologyorMedicineforhisdiscoveryofthe
1910 AlbrechtKossel(UniversityofHeidelberg) fivenuclearbases:adenine,cytosine,guanine,thymine,and
uracil.
NobelPrizeinPhysiologyorMedicineforhisdiscoveriesof
ThomasHuntMorgan(CaliforniaInstitute theroleplayedbythegeneandchromosomeinheredity,based
1933
onhisstudiesofthewhiteeyedmutationinthefruitfly
ofTechnology)
Drosophila.[20]
FrancisCrick,JamesWatsonandMaurice
Wilkins(MRCLaboratoryofMolecular
1962
Biology,HarvardUniversityandLondon
Universityrespectively)

NobelPrizeinPhysiologyorMedicinefortheirdiscoveriesof
thedoublehelixstructureofDNAanditssignificancefor
informationtransferinlivingmaterial.

AaronKlug(MRCLaboratoryof
1982
MolecularBiology)

NobelPrizeinChemistry"forhisdevelopmentof
crystallographicelectronmicroscopyandhisstructural
elucidationofbiologicallyimportantnucleicacidprotein
complexes"

1993 RichardJ.RobertsandPhillipA.Sharp

NobelPrizeinPhysiology"fortheirindependentdiscoveries
ofsplitgenes,"inwhichDNAsectionscalledexonsexpress
proteins,andareinterruptedbyDNAsectionscalledintrons,
whichdonotexpressproteins.

2006 RogerKornberg(StanfordUniversity)

NobelPrizeinChemistryforhisdiscoveryofthemechanism
bywhichDNAistranscribedintomessengerRNA.

Seealso
Chromatid
Epigenetics
HistoneModifyingEnzymes
Positioneffectvariegation
Saltandpepperchromatin
Transcriptionalbursting
Activechromatinsequence

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Externallinks
Chromatin,Histones&Cathepsin(http://www.youtube.com/watch?v=eYrQ0EhVCYA)PMAPThe
ProteolysisMapanimation
[Recentchromatinpublicationsandnews]
ProtocolforinvitroChromatinAssembly(http://www.activemotif.com/documents/134.pdf)
ENCODEthreadsExplorer(http://www.nature.com/encode/#/threads/chromatinpatternsattranscriptionfac
torbindingsites)Chromatinpatternsattranscriptionfactorbindingsites.Nature(journal)
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