2023
Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin
Pownall M, Miao L, Vejnar C, M'Saad O, Sherrard A, Frederick M, Benitez M, Boswell C, Zaret K, Bewersdorf J, Giraldez A. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023, 381: 92-100. PMID: 37410825, PMCID: PMC10372697, DOI: 10.1126/science.ade5308.Peer-Reviewed Original ResearchConceptsZygotic genome activationTranscriptional elongationExpansion microscopyRNA polymerase IIChromatin regulatory factorsEnhancer-promoter contactsGenome activationChromatin organizationNuclear organizationPolymerase IIPol IIFactor NanogTranscription factorsGene expressionRegulatory factorsChromatinNanoscale organizationNanogTranscriptionElongationNucleosomesUniversal processPromoterEmbryosEnhancer
2022
MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles
He L, Gao M, Pratt H, Weng Z, Struhl K. MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles. PLOS ONE 2022, 17: e0264799. PMID: 35482762, PMCID: PMC9049301, DOI: 10.1371/journal.pone.0264799.Peer-Reviewed Original ResearchBromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs
Kenworthy C, Haque N, Liou S, Chandris P, Wong V, Dziuba P, Lavis L, Liu W, Singer R, Coleman R. Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs. Biophysical Journal 2022, 121: 1738-1752. PMID: 35364106, PMCID: PMC9117891, DOI: 10.1016/j.bpj.2022.03.027.Peer-Reviewed Original ResearchConceptsChromatin remodelersChromatin statePBAF chromatin-remodeling complexSingle-molecule fluorescence microscopy studiesDifferent chromatin statesChromatin-remodeling complexRNA polymerase IIChromatin hubTranscriptional burstingPolymerase IIAcetylated nucleosomesFluorescence microscopy studiesPBAFBromodomainsNucleosomesChromatin stabilityLive cellsStable engagementRemodelersDynamic targetingDirect roleChromatinImaging revealsTargetingGenome
2021
Extrusion of chromatin loops by a composite loop extrusion factor
Yan H, Surovtsev I, Williams JF, Bailey MLP, King MC, Mochrie SGJ. Extrusion of chromatin loops by a composite loop extrusion factor. Physical Review E 2021, 104: 024414. PMID: 34525654, PMCID: PMC9112126, DOI: 10.1103/physreve.104.024414.Peer-Reviewed Original Research
2020
Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin
Miron E, Oldenkamp R, Brown JM, Pinto DMS, Xu CS, Faria AR, Shaban HA, Rhodes JDP, Innocent C, de Ornellas S, Hess HF, Buckle V, Schermelleh L. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin. Science Advances 2020, 6: eaba8811. PMID: 32967822, PMCID: PMC7531892, DOI: 10.1126/sciadv.aba8811.Peer-Reviewed Original ResearchChromatin domainsThree-dimensional chromatin organizationFunctional nuclear organizationMammalian genome functionActive histone modificationsSingle-cell levelInterchromatin compartmentGenome functionChromatin organizationGenome organizationRepressive modificationsHistone modificationsNuclear organizationEuchromatic regionsSomatic cellsCohesinChromatinFunctional modulesKey roleNucleosomesDomainRNACompartmentsModificationCells
2019
Targeting the epigenome of pancreatic cancer for therapy: challenges and opportunities
Baretti M, Ahuja N, Azad N. Targeting the epigenome of pancreatic cancer for therapy: challenges and opportunities. Annals Of Pancreatic Cancer 2019, 2: 18-18. DOI: 10.21037/apc.2019.10.01.Peer-Reviewed Original ResearchEpigenetic modulatory drugsEpigenetic alterationsGene expressionImmediate translational implicationsProgression of PAADEpigenetic regulationHeritable differencesEpigenetic abnormalitiesPrimary sequenceTumor microenvironmentNucleosomesEssential roleCurrent knowledgeTranslational applicationsComplex seriesDNATranslational implicationsNew therapeutic approachesExpressionPancreatic adenocarcinomaEpigenomeChromatinEpigeneticsSubsequent interactionAlterationsMolecular recognition of nucleosomes by binding partners
Kale S, Goncearenco A, Markov Y, Landsman D, Panchenko A. Molecular recognition of nucleosomes by binding partners. Current Opinion In Structural Biology 2019, 56: 164-170. PMID: 30991239, PMCID: PMC6656623, DOI: 10.1016/j.sbi.2019.03.010.Peer-Reviewed Original ResearchConceptsEpigenetic signaling pathwaysChromatin factorsEukaryotic cellsHistone tailsChromatin packingInteraction landscapeLinker DNAMolecular recognitionNucleosomesHistone coreIntrinsic disorderSignaling pathwaysBroad repertoireFurther complexityBasic mechanismsChromatinDNARegulationPathwayRepertoireCellsPartnersTailLandscape
2017
Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome
Nodelman IM, Bleichert F, Patel A, Ren R, Horvath KC, Berger JM, Bowman GD. Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome. Molecular Cell 2017, 65: 447-459.e6. PMID: 28111016, PMCID: PMC5308885, DOI: 10.1016/j.molcel.2016.12.011.Peer-Reviewed Original ResearchConceptsChromatin remodelersDNA gyresATPase motorChd1 chromatin remodelerDNA-binding domainDomain-domain communicationNucleosome assemblyNucleosome spacingNucleosomal DNAInterdomain communicationChd1 remodelerNucleosomesGenomic DNARemodelersDomain arrangementNucleosome coreDNAUnique organizationChromodomainDomain
2016
Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection
Clapier CR, Kasten MM, Parnell TJ, Viswanathan R, Szerlong H, Sirinakis G, Zhang Y, Cairns BR. Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. Molecular Cell 2016, 62: 453-461. PMID: 27153540, PMCID: PMC5291166, DOI: 10.1016/j.molcel.2016.03.032.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateBinding SitesBiological TransportCell Cycle ProteinsChromatin Assembly and DisassemblyDNA-Binding ProteinsDNA, FungalHydrolysisMicrofilament ProteinsMutationNuclear ProteinsNucleosomesProtein BindingProtein Interaction Domains and MotifsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTime FactorsTranscription Factors
2015
Histone reader BRWD1 targets and restricts recombination to the Igk locus
Mandal M, Hamel KM, Maienschein-Cline M, Tanaka A, Teng G, Tuteja JH, Bunker JJ, Bahroos N, Eppig JJ, Schatz DG, Clark MR. Histone reader BRWD1 targets and restricts recombination to the Igk locus. Nature Immunology 2015, 16: 1094-1103. PMID: 26301565, PMCID: PMC4575638, DOI: 10.1038/ni.3249.Peer-Reviewed Original Research
2013
Probing Allostery Through DNA
Kim S, Broströmer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su XD, Sun Y, Xie XS. Probing Allostery Through DNA. Science 2013, 339: 816-819. PMID: 23413354, PMCID: PMC3586787, DOI: 10.1126/science.1229223.Peer-Reviewed Original ResearchMeSH KeywordsAllosteric RegulationBase SequenceBinding SitesDNA-Binding ProteinsDNA-Directed RNA PolymerasesDNA, B-FormEscherichia coliGene ExpressionGene Expression Regulation, BacterialLac RepressorsMolecular Dynamics SimulationNucleosomesProtein BindingProtein Structure, TertiaryReceptors, GlucocorticoidTranscription FactorsViral Proteins
2012
Rules of engagement for base excision repair in chromatin
Odell ID, Wallace SS, Pederson DS. Rules of engagement for base excision repair in chromatin. Journal Of Cellular Physiology 2012, 228: 258-266. PMID: 22718094, PMCID: PMC3468691, DOI: 10.1002/jcp.24134.Peer-Reviewed Original ResearchConceptsBase excision repairSingle-strand break repairNucleotide excision repairHomology-directed repairExcision repairCheckpoint activationCell cycle checkpoint activationStrand break repair pathwaysDouble-strand break repair pathwayStrand break repairBreak repair pathwayOxidative damage resultsNucleosome disruptionDNA replicationBreak repairRepair pathwaysDNA segmentsChromatinEfficient repairNumerous DNAOxidative DNA damageRegulatory factorsHuman cellsNucleosomesDNA damage
2011
Nucleosome Disruption by DNA Ligase III-XRCC1 Promotes Efficient Base Excision Repair
Odell ID, Barbour JE, Murphy DL, Della-Maria JA, Sweasy JB, Tomkinson AE, Wallace SS, Pederson DS. Nucleosome Disruption by DNA Ligase III-XRCC1 Promotes Efficient Base Excision Repair. Molecular And Cellular Biology 2011, 31: 4623-4632. PMID: 21930793, PMCID: PMC3209256, DOI: 10.1128/mcb.05715-11.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDeoxyribonuclease (Pyrimidine Dimer)DNADNA DamageDNA GlycosylasesDNA Ligase ATPDNA LigasesDNA Polymerase betaDNA RepairDNA-(Apurinic or Apyrimidinic Site) LyaseDNA-Binding ProteinsHumansLytechinusNucleosomesPoly-ADP-Ribose Binding ProteinsReactive Oxygen SpeciesXenopusXenopus ProteinsX-ray Repair Cross Complementing Protein 1ConceptsBase excision repairNucleosome disruptionApurinic endonucleaseExcision repairEfficient base excision repairNucleated human cellsDNA polymerase βNucleosome substratesRibosomal DNASingle base gapHuman cellsNucleosomesDNA ligasePolymerase βPol βRate-limiting stepHNTH1Ternary complexDNAUnique roleChromatinLigaseDisruptionEndonucleaseLesions formThe RSC chromatin remodelling ATPase translocates DNA with high force and small step size
Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang Y. The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. The EMBO Journal 2011, 30: 2364-2372. PMID: 21552204, PMCID: PMC3116276, DOI: 10.1038/emboj.2011.141.Peer-Reviewed Original ResearchConceptsATP-dependent chromatinHigh-resolution optical tweezersDNA-histone interactionsBp/sDNA translocation processRSC chromatinATPase domainTranslocase systemDiverse functionsATP hydrolysisBare DNATranslocation processBiophysical knowledgeDNAChromatinNucleosomesMechanical forcesBPForce generationRemodellersTranslocaseProcessivityTranslocationATPaseOptical tweezers
2004
A BAF-centred view of the immune system
Chi T. A BAF-centred view of the immune system. Nature Reviews Immunology 2004, 4: 965-977. PMID: 15573131, DOI: 10.1038/nri1501.Peer-Reviewed Original ResearchConceptsChromatin-remodelling complexBAF complexRepressive chromatin structureStructure of chromatinHistone-DNA contactsTranscription factor complexPost-translational modificationsTranscriptional start siteIFN-β geneTranscriptional machineryChromatin structureTranscriptional activatorTranscriptional repressorHuman genesResponsive genesExpression of CIITAStart siteDNA sequencesFactor complexHistone octamerNucleosomesOwn replicationGene expressionGenomic DNAIFN-β expression
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply