Chromatinloopcontactsrevealdistalregulatoryelementsandstructuraldomains.Genomicpositionsoflong-rangechromatincontactsaremeasuredgenome-widebymassivelyparallelsequencingacollectionofDNAfragmentsgeneratedbyproximityligation.Intactchromatiniscross-linkedtophysicallylinkgenomicallydistalnucleosomesthatareadjacentin3-dimensionalspace.Cross-linkedchromatinisenzymaticallydigestedandtheresultingDNAendlabeledwithbiotinandsubjectedtoproximityligation.LigatedDNAisshearedbysonicationorenzymaticdigestionandtheligatedjunctionsenrichedbystreptavidinpull-down.TheresultingDNAispurified,subjectedlibraryconstruction,clonallysequenced,andalignedtoareferencegenome.DigestLigateendsAddlinkersSequenceandanalyzeAddlinkersSequenceandanalyze3DchromatincaptureNucleosome-depletedregionsareenrichedinregulatoryelements.Genomicpositionsofopenchromatinaremeasuredgenome-widebymassivelyparallelsequencingofacollectionofDNAfragmentsliberatedfromintactchromatinbyeithertransposoninsertion,enzymaticdigestion,orsonication.TheresultingDNAfragmentsaresubjectedtosizeselectionorphenol-chloroformextractiontodepletenucleosome-associatedDNA.TheresultingDNAispurified,subjectedtolibraryconstruction,clonallysequenced,andalignedtoareferencegenome.DigestspecifictoopenregionsTransposonatopenregionsSizeselectOpenchromatinanalysisShearDNAEnrichRemovehistoneandaddlinkersSequenceandanalyzeChromatinimmunoprecipitationsequencingSonicateSonicateDigestEnrichwithstreptavidinpull-downBiotinDigestHistonesaredecoratedwithchemicalmodifications.Genomicpositionsofmodifiedhistonesaremeasuredgenome-widebychromatinimmunoprecipitationfollowedbymassivelyparallelsequencing(ChIP-seq).Histonescanbeliberatedfromthegenomebysonication,enzymaticdigestion,orbytransposoninsertion(notshown).Ifsonicationisused,chromatinmustfirstbechemicallycross-linked(seeStep4).Followinghistoneliberation,specificchemicalmodificationsareenrichedbyimmuno-absorption.DNAassociatedwithenrichedhistonesispurified,subjectedtolibraryconstruction,clonallysequenced,andalig...
