2023
Acetyl-methyllysine marks chromatin at active transcription start sites
Lu-Culligan W, Connor L, Xie Y, Ekundayo B, Rose B, Machyna M, Pintado-Urbanc A, Zimmer J, Vock I, Bhanu N, King M, Garcia B, Bleichert F, Simon M. Acetyl-methyllysine marks chromatin at active transcription start sites. Nature 2023, 622: 173-179. PMID: 37731000, PMCID: PMC10845139, DOI: 10.1038/s41586-023-06565-9.Peer-Reviewed Original ResearchConceptsPost-translational modificationsLysine residuesActive transcription start sitesTranscription start siteRange of speciesChromatin biologyChromatin proteinsLysine methylationActive chromatinProteins BRD2Transcriptional initiationLysine acetylationHistone H4Start siteMammalian tissuesHuman diseasesSame residuesMethylationAcetylationChromatinResiduesProteinBiological signalsHistonesBRD2Epigenetic markers and therapeutic targets for metastasis
Kravitz C, Yan Q, Nguyen D. Epigenetic markers and therapeutic targets for metastasis. Cancer And Metastasis Reviews 2023, 42: 427-443. PMID: 37286865, PMCID: PMC10595046, DOI: 10.1007/s10555-023-10109-y.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEpigenomic alterationsLineage integrityTherapeutic targetEpigenetic markersCancer cellsGenetic aberrationsCurrent knowledgeHuman tumorsMalignant cell cloneTumor progressionDNANumber of discoveriesCell clonesDisseminated diseaseCertain organsPrimary tumorTherapeutic responseMetastatic cancerEpigenomeChromatinHistonesLiquid biopsyAlterationsClonesTargetDOT1L promotes spermatid differentiation by regulating expression of genes required for histone-to-protamine replacement
Malla A, Rainsford S, Smith Z, Lesch B. DOT1L promotes spermatid differentiation by regulating expression of genes required for histone-to-protamine replacement. Development 2023, 150 PMID: 37082969, PMCID: PMC10259660, DOI: 10.1242/dev.201497.Peer-Reviewed Original ResearchConceptsHistone replacementMale sterilityProtamine exchangeSpermatid differentiationHistone H3 lysine 79Chromatin remodeling factorsRNA polymerase IIH3 lysine 79Expression of genesMature sperm headSperm headPostmeiotic germ cellsHistone methyltransferase DOT1LPolymerase IILysine 79Embryonic lethalityRemodeling factorsProtamine transitionProtamine replacementTranscriptional dysregulationMethyltransferase DOT1LIndispensable regulatorDOT1LHistonesGerm cellsGenome-Wide Association Study Points to Novel Locus for Gilles de la Tourette Syndrome
Tsetsos F, Topaloudi A, Jain P, Yang Z, Yu D, Kolovos P, Tumer Z, Rizzo R, Hartmann A, Depienne C, Worbe Y, Müller-Vahl K, Cath D, Boomsma D, Wolanczyk T, Zekanowski C, Barta C, Nemoda Z, Tarnok Z, Padmanabhuni S, Buxbaum J, Grice D, Glennon J, Stefansson H, Hengerer B, Yannaki E, Stamatoyannopoulos J, Benaroya-Milshtein N, Cardona F, Hedderly T, Heyman I, Huyser C, Mir P, Morer A, Mueller N, Munchau A, Plessen K, Porcelli C, Roessner V, Walitza S, Schrag A, Martino D, Group T, TSAICG T, Barr C, Batterson J, Berlin C, Budman C, Coppola G, Cox N, Darrow S, Dion Y, Freimer N, Grados M, Greenberg E, Hirschtritt M, Huang A, Illmann C, King R, Kurlan R, Leckman J, Lyon G, Malaty I, McMahon W, Neale B, Okun M, Osiecki L, Robertson M, Rouleau G, Sandor P, Singer H, Smit J, Sul J, Initiative T, Androutsos C, Basha E, Farkas L, Fichna J, Janik P, Kapisyzi M, Karagiannidis I, Koumoula A, Nagy P, Puchala J, Szejko N, Szymanska U, Tsironi V, Group T, Apter A, Ball J, Bodmer B, Bognar E, Buse J, Vela M, Fremer C, Garcia-Delgar B, Gulisano M, Hagen A, Hagstrøm J, Madruga-Garrido M, Pellico A, Ruhrman D, Schnell J, Silvestri P, Skov L, Steinberg T, Gloor F, Turner V, Weidinger E, Network T, Alexander J, Aranyi T, Buisman W, Buitelaar J, Driessen N, Drineas P, Fan S, Forde N, Gerasch S, van den Heuvel O, Jespersgaard C, Kanaan A, Möller H, Nawaz M, Nespoli E, Pagliaroli L, Poelmans G, Pouwels P, Rizzo F, Veltman D, van der Werf Y, Widomska J, Zilhäo N, Group T, Brown L, Cheon K, Coffey B, Fernandez T, Gilbert D, Hong H, Ibanez-Gomez L, Kim E, Kim Y, Kim Y, Koh Y, Kook S, Kuperman S, Leventhal B, Maras A, Murphy T, Shin E, Song D, Song J, State M, Visscher F, Wang S, Zinner S, Tischfield J, Heiman G, Willsey A, Dietrich A, Davis L, Crowley J, Mathews C, Scharf J, Georgitsi M, Hoekstra P, Paschou P. Genome-Wide Association Study Points to Novel Locus for Gilles de la Tourette Syndrome. Biological Psychiatry 2023, 96: 114-124. PMID: 36738982, PMCID: PMC10783199, DOI: 10.1016/j.biopsych.2023.01.023.Peer-Reviewed Original ResearchExpression quantitative trait lociGenome-wide significant lociWide association study dataComplex genetic architectureQuantitative trait lociAssociation study dataGenetic architectureTrait lociChromosome 5q15Significant lociSignificant enrichmentLociNovel insightsNeurodevelopmental disordersChildhood-onset neurodevelopmental disorderHistonesRNAsGenesPolygenic riskFuture studiesEnrichmentThe Histone Chaperone Network Is Highly Conserved in Physarum polycephalum
Poulet A, Rousselot E, Téletchéa S, Noirot C, Jacob Y, van Wolfswinkel J, Thiriet C, Duc C. The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum. International Journal Of Molecular Sciences 2023, 24: 1051. PMID: 36674565, PMCID: PMC9864664, DOI: 10.3390/ijms24021051.Peer-Reviewed Original ResearchConceptsHistone chaperonesEukaryotic treeChaperone networkBranching eukaryotesChaperone interactionsYeast complexCellular lifeDiverse proteinsPlant kingdomChaperone expressionRNA sequencingChaperonesKey residuesFunctional domainsHistonesCell cycleS phaseChromatinPhysarum polycephalumPlantsDistinct patternsEukaryotesOrthologuesCladeConserved
2022
The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication
Davarinejad H, Huang YC, Mermaz B, LeBlanc C, Poulet A, Thomson G, Joly V, Muñoz M, Arvanitis-Vigneault A, Valsakumar D, Villarino G, Ross A, Rotstein BH, Alarcon EI, Brunzelle JS, Voigt P, Dong J, Couture JF, Jacob Y. The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication. Science 2022, 375: 1281-1286. PMID: 35298257, PMCID: PMC9153895, DOI: 10.1126/science.abm5320.Peer-Reviewed Original ResearchConceptsTetratricopeptide repeat domainDNA polymerase thetaMulticellular eukaryotesHistone H3.1Replication forksChromatin maturationRepeat domainDNA repairGenomic instabilityPolymerase thetaPosition 31Amino acidsH3.1PlantsReplicationEukaryotesH3.3HistonesMonomethylationVariantsCommon strategyForkResiduesMaturationFunctionThe landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation
Miao L, Tang Y, Bonneau AR, Chan SH, Kojima ML, Pownall ME, Vejnar CE, Gao F, Krishnaswamy S, Hendry CE, Giraldez AJ. The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation. Molecular Cell 2022, 82: 986-1002.e9. PMID: 35182480, PMCID: PMC9327391, DOI: 10.1016/j.molcel.2022.01.024.Peer-Reviewed Original ResearchConceptsGenome activationChromatin openingTranscription factorsPioneer factor activityDifferent transcription factorsChromatin reprogrammingPioneer factorsNucleosome positionsActive enhancersIndividual genesCore histonesTriple mutantGene activationTF inputsDevelopmental transitionsSequence contextCell typesFactor activityHistonesPioneering activityEnhancerActivationSequence of eventsPou5f3Chromatin
2021
In Vitro Characterization of Histone Chaperones using Analytical, Pull-Down and Chaperoning Assays.
Bobde R, Saharan K, Baral S, Gandhi S, Samal A, Sundaram R, Kumar A, Singh A, Datta A, Vasudevan D. In Vitro Characterization of Histone Chaperones using Analytical, Pull-Down and Chaperoning Assays. Journal Of Visualized Experiments 2021 PMID: 35037657, DOI: 10.3791/63218.Peer-Reviewed Original ResearchConceptsHistone chaperonesH3/H4 tetramersNucleosome assembly processH3/H4H2A/H2BCore histones H2APull-down assaysAnalytical size exclusion chromatographyEukaryotic chromatinH4 tetramersHistone H2AH2A/Core histonesHistone octamerSingle copyChaperonesHistonesCellular cytoplasmDiverse classChromatinProteinDNAH2BH4Non-specific interactions
2018
Epigenetic Changes and Epigenetic Targets in Head and Neck Cancer
Peri S, Andrews A, Bhatia A, Mehra R. Epigenetic Changes and Epigenetic Targets in Head and Neck Cancer. Current Cancer Research 2018, 327-352. DOI: 10.1007/978-3-319-78762-6_12.Peer-Reviewed Original ResearchEpigenetic changesRepression of genesEpigenetic control systemsGene expression patternsModification of DNAEpigenetic controlEpigenetic regulationEpigenetic modificationsEpigenetic targetsTranscriptional activityKey proteinsExpression patternsGene expressionDNASelective inductionDisease pathologySpatial conformationHistonesRepressionGenesProteinTumor DNARegulationModificationExpression
2017
Ubiquitination-Deficient Mutations in Human Piwi Cause Male Infertility by Impairing Histone-to-Protamine Exchange During Spermiogenesis
Gou L, Kang J, Dai P, Wang X, Li F, Zhao S, Zhang M, Hua M, Lu Y, Zhu Y, Li Z, Chen H, Wu L, Li D, Fu X, Li J, Shi H, Liu M. Ubiquitination-Deficient Mutations in Human Piwi Cause Male Infertility by Impairing Histone-to-Protamine Exchange During Spermiogenesis. Obstetrical & Gynecological Survey 2017, 72: 540-541. DOI: 10.1097/ogx.0000000000000482.Peer-Reviewed Original Research
2016
Dual Genetic Encoding of Acetyl‐lysine and Non‐deacetylatable Thioacetyl‐lysine Mediated by Flexizyme
Xiong H, Reynolds NM, Fan C, Englert M, Hoyer D, Miller SJ, Söll D. Dual Genetic Encoding of Acetyl‐lysine and Non‐deacetylatable Thioacetyl‐lysine Mediated by Flexizyme. Angewandte Chemie International Edition 2016, 55: 4083-4086. PMID: 26914285, PMCID: PMC4789153, DOI: 10.1002/anie.201511750.Peer-Reviewed Original ResearchConceptsPost-translational modificationsHistone H3Post-translational protein modificationImportant post-translational protein modificationHuman histone H3Non-histone proteinsFull-length proteinTranscriptional regulationLysine acetylationDNA replicationProtein acetylationDNA repairProtein modificationGenetic encodingLysine residuesAcetyl lysineAcetylationHistonesLysine positionsH3ProteinFlexizymesCrosstalkPowerful toolResidues
2014
Histones to the cytosol: exportin 7 is essential for normal terminal erythroid nuclear maturation
Hattangadi SM, Martinez-Morilla S, Patterson HC, Shi J, Burke K, Avila-Figueroa A, Venkatesan S, Wang J, Paulsen K, Görlich D, Murata-Hori M, Lodish HF. Histones to the cytosol: exportin 7 is essential for normal terminal erythroid nuclear maturation. Blood 2014, 124: 1931-1940. PMID: 25092175, PMCID: PMC4168348, DOI: 10.1182/blood-2013-11-537761.Peer-Reviewed Original ResearchConceptsMost nuclear proteinsExportin-7Nuclear proteinsLate erythroblastsNuclear protein exportTerminal erythroid maturationFetal liver erythroblastsNuclear export proteinErythroid nucleiProtein exportTerminal erythropoiesisHistone H2AChromatin condensationErythroid differentiationExport proteinErythroid maturationNuclear condensationProteomic examinationProteinXPO7HistonesHemoglobin accumulationSevere inhibitionErythroblastsFetal liver
2011
Diet-induced Lethality Due to Deletion of the Hdac3 Gene in Heart and Skeletal Muscle
Sun Z, Singh N, Mullican SE, Everett LJ, Li L, Yuan L, Liu X, Epstein JA, Lazar MA. Diet-induced Lethality Due to Deletion of the Hdac3 Gene in Heart and Skeletal Muscle. Journal Of Biological Chemistry 2011, 286: 33301-33309. PMID: 21808063, PMCID: PMC3190900, DOI: 10.1074/jbc.m111.277707.Peer-Reviewed Original ResearchConceptsNutritional environmentProper mitochondrial functionHistone deacetylase 3Bioenergetic genesSkeletal muscleNucleosomal histonesHDAC3 geneGene expressionCovalent modificationHuman diseasesHDAC3Mitochondrial functionEmbryonic deletionCardiac mitochondriaGenesLipid metabolismDeletionMilder phenotypePhenotypeMajor cardiomyopathiesLethalityEpigenomeGenomeHistonesMouse modelRapid Cellular Turnover in Adipose Tissue
Rigamonti A, Brennand K, Lau F, Cowan C. Rapid Cellular Turnover in Adipose Tissue. PLOS ONE 2011, 6: e17637. PMID: 21407813, PMCID: PMC3047582, DOI: 10.1371/journal.pone.0017637.Peer-Reviewed Original ResearchConceptsCellular turnoverAdipocyte populationsRapid cellular turnoverGreen fluorescent proteinIndependent experimental approachesIncorporation of BrdUFluorescent proteinMurine adipose tissueRapid turnoverTissue turnoverPossible new avenuesTurnoverAdipose tissueExperimental approachNew avenuesHistones
2009
Functional pathways analyses to identify candidate therapeutic targets in triple-negative breast cancer
Andre F, Dessen P, Job B, Delaloge S, Pusztai L, Lazar V. Functional pathways analyses to identify candidate therapeutic targets in triple-negative breast cancer. Journal Of Clinical Oncology 2009, 27: 569-569. DOI: 10.1200/jco.2009.27.15_suppl.569.Peer-Reviewed Original ResearchGene gainPathway analysisHigh resolution CGH arrayBRB-Array ToolsFunctional pathway analysisChromosome organizationTargetable pathwaysTriple-negative breast cancerMolecular classesGene setsCDNA arraysNotch pathwayCandidate therapeutic targetGenomic aberrationsNegative breast cancerCGH arrayHistonesPathway dysregulationPathwayGenesDifferential pathwaysVEGFA geneTherapeutic targetDysregulationHedgehogComplex developmental patterns of histone modifications associated with the human β-globin switch in primary cells
Hsu M, Richardson CA, Olivier E, Qiu C, Bouhassira EE, Lowrey CH, Fiering S. Complex developmental patterns of histone modifications associated with the human β-globin switch in primary cells. Experimental Hematology 2009, 37: 799-806.e4. PMID: 19460472, PMCID: PMC2748252, DOI: 10.1016/j.exphem.2009.04.006.Peer-Reviewed Original ResearchConceptsHistone modificationsGene expressionBeta-globin switchDimethyl lysine 9Beta-globin locusΒ-globin switchGamma geneImportant histone modificationsBone marrow cellsGamma gene expressionSuch histonesComplex developmental patternLysine 9Chromatin immunoprecipitationHistone H3Gene suppressionPrimary fetalMarrow cellsUnexpressed genesGamma-globinGenesHistonesDevelopmental stagesBone marrow erythroblastsPrimary cells
2007
The Site-Specific Installation of Methyl-Lysine Analogs into Recombinant Histones
Simon MD, Chu F, Racki LR, de la Cruz CC, Burlingame AL, Panning B, Narlikar GJ, Shokat KM. The Site-Specific Installation of Methyl-Lysine Analogs into Recombinant Histones. Cell 2007, 128: 1003-1012. PMID: 17350582, PMCID: PMC2932701, DOI: 10.1016/j.cell.2006.12.041.Peer-Reviewed Original ResearchConceptsLysine methylationChromatin structureRecombinant histonesContext of chromatinHistone lysine methylationHistone lysine residuesSpecific lysine methylationNucleosome remodelingEffector proteinsPosttranslational modificationsDegree of methylationRecombinant proteinsHistonesLysine residuesMethyl lysineMethylationBiochemical mechanismsSite-specific installationProteinRapid generationNatural counterpartsChromatinPowerful toolAdaptorResiduesLinking the epigenetic 'language' of covalent histone modifications to cancer.
Hake S, Xiao A, Allis C. Linking the epigenetic 'language' of covalent histone modifications to cancer. British Journal Of Cancer 2007, 96 Suppl: r31-9. PMID: 17393583.Peer-Reviewed Original ResearchCovalent histone modificationsHistone modificationsMethylation of DNAEpigenetic languageChromatin reorganisationEpigenetic modulationCovalent modificationHuman biologyHuman cancersMultistep processMethylationRecent findingsChromatinHuman healthHistonesPhosphorylationBiologyAcetylationDNAModificationPotential therapyCarcinogenesisMajor partCancer
2006
New Role for hPar-1 Kinases EMK and C-TAK1 in Regulating Localization and Activity of Class IIa Histone Deacetylases
Dequiedt F, Martin M, Von Blume J, Vertommen D, Lecomte E, Mari N, Heinen MF, Bachmann M, Twizere JC, Huang MC, Rider MH, Piwnica-Worms H, Seufferlein T, Kettmann R. New Role for hPar-1 Kinases EMK and C-TAK1 in Regulating Localization and Activity of Class IIa Histone Deacetylases. Molecular And Cellular Biology 2006, 26: 7086-7102. PMID: 16980613, PMCID: PMC1592903, DOI: 10.1128/mcb.00231-06.Peer-Reviewed Original ResearchMeSH Keywords14-3-3 ProteinsActive Transport, Cell NucleusAmino Acid SequenceAnimalsBinding SitesCell NucleusCells, CulturedChlorocebus aethiopsCOS CellsCytoplasmHeLa CellsHistone DeacetylasesHumansMolecular Sequence DataPhosphorylationPhosphoserineProtein Serine-Threonine KinasesProtein TransportSubstrate SpecificityConceptsMicrotubule affinity-regulating kinaseClass IIa HDACsN-terminal serine residueClass IIa histoneIIa HDACsC-TAK1IIa histoneSerine residuesMajor developmental programsMARK/ParVariety of kinasesHierarchical phosphorylationRepressive activityNuclear exportRepressive functionDevelopmental programSubcellular localizationNuclear exclusionConstitutive phosphorylationSophisticated regulationPhosphorylationKinaseSpecific signalsHDACsHistones
2005
Symplekin and multiple other polyadenylation factors participate in 3′-end maturation of histone mRNAs
Kolev NG, Steitz JA. Symplekin and multiple other polyadenylation factors participate in 3′-end maturation of histone mRNAs. Genes & Development 2005, 19: 2583-2592. PMID: 16230528, PMCID: PMC1276732, DOI: 10.1101/gad.1371105.Peer-Reviewed Original ResearchConceptsTail elongationU7 small nuclear ribonucleoproteinCommon molecular machineryMammalian cell extractsCleavage stimulation factorPolyadenylation specificity factorSmall nuclear ribonucleoproteinMolecular machineryHistone mRNAProtein complexesMRNA cleavageSpecificity factorPolyadenylation factorsTranslational activationNuclear ribonucleoproteinSymplekinReconstitution experimentsCell extractsHeat-labile factorMessenger RNAHistonesMRNAStimulation factorSubunitsCytoplasmic
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