2023
KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic
Zhang S, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. Advances In Experimental Medicine And Biology 2023, 1433: 113-137. PMID: 37751138, DOI: 10.1007/978-3-031-38176-8_6.ChaptersConceptsPlant homeodomainFamily proteinsKey epigenetic markCell fate determinationHistone methylation marksCancer type-dependent mannerKetoglutarate-dependent dioxygenasesSelective KDM5 inhibitorsTumor suppressive functionType-dependent mannerEpigenetic marksTumor suppressive roleFate determinationJumonji CLysine 4Active chromatinMethylation marksHistone H3Lysine demethylasesCatalytic coreKDM5 inhibitorsDrug targetsKDM5Cancer metastasisSuppressive roleDOT1L bridges transcription and heterochromatin formation at mammalian pericentromeres
Malla A, Yu H, Farris D, Kadimi S, Lam T, Cox A, Smith Z, Lesch B. DOT1L bridges transcription and heterochromatin formation at mammalian pericentromeres. EMBO Reports 2023, 24: embr202256492. PMID: 37317657, PMCID: PMC10398668, DOI: 10.15252/embr.202256492.Peer-Reviewed Original ResearchConceptsMouse embryonic stem cellsBurst of transcriptionMajor satellite repeatsLong-term silencingRepetitive DNA elementsEmbryonic stem cellsSatellite transcriptionHeterochromatin stabilityHeterochromatin formationHeterochromatin structureChromatin stateSatellite repeatsGenome stabilityGenome integrityPericentromeric repeatsPericentromeric heterochromatinGenome featuresDNA elementsHistone H3Transcriptional activationHistone methyltransferaseRepetitive elementsDOT1L lossRepeat elementsTranscript production
2022
Histone H3 proline 16 hydroxylation regulates mammalian gene expression
Liu X, Wang J, Boyer J, Gong W, Zhao S, Xie L, Wu Q, Zhang C, Jain K, Guo Y, Rodriguez J, Li M, Uryu H, Liao C, Hu L, Zhou J, Shi X, Tsai Y, Yan Q, Luo W, Chen X, Strahl B, von Kriegsheim A, Zhang Q, Wang G, Baldwin A, Zhang Q. Histone H3 proline 16 hydroxylation regulates mammalian gene expression. Nature Genetics 2022, 54: 1721-1735. PMID: 36347944, PMCID: PMC9674084, DOI: 10.1038/s41588-022-01212-x.Peer-Reviewed Original ResearchConceptsPost-translational modificationsHistone post-translational modificationsMammalian gene expressionGene expressionHistone H3Mammalian cellsDNA-templated processesTranscriptome-wide analysisTarget gene expressionHydroxylation of prolineWnt/β-cateninChromatin recruitmentHistone codeTarget genesRegulatory marksLysine residuesDirect bindingTriple-negative breast cancerΒ-cateninResidues 16H3ExpressionH3K4me3TrimethylationGenome
2021
AP-2α Regulates S-Phase and Is a Marker for Sensitivity to PI3K Inhibitor Buparlisib in Colon Cancer
Beck AC, Cho E, White JR, Paemka L, Li T, Gu VW, Thompson DT, Koch KE, Franke C, Gosse M, Wu VT, Landers SR, Pamatmat AJ, Kulak MV, Weigel RJ. AP-2α Regulates S-Phase and Is a Marker for Sensitivity to PI3K Inhibitor Buparlisib in Colon Cancer. Molecular Cancer Research 2021, 19: 1156-1167. PMID: 33753551, PMCID: PMC8254761, DOI: 10.1158/1541-7786.mcr-20-0867.Peer-Reviewed Original ResearchMeSH KeywordsAminopyridinesAnimalsBiomarkers, TumorCell Line, TumorCell SurvivalColonic NeoplasmsGene Expression ProfilingGene Expression Regulation, NeoplasticGene Knockout TechniquesHCT116 CellsHumansMiceMorpholinesPhosphoinositide-3 Kinase InhibitorsRNA InterferenceRNA-SeqS PhaseTranscription Factor AP-2Xenograft Model Antitumor AssaysConceptsAP-2αPI3K inhibitorsColon cancer cell linesCell cycleS phasePrimary gene targetsK inhibitorsChromatin immunoprecipitation sequencingCancer cell linesPI3K cascadeProlonged S phaseCell linesActivation of AktShort hairpin RNAPhosphorylation of AktHistone H3Immunoprecipitation sequencingRNA sequencingPI3K inhibitionTarget genesK cascadeGene targetsTumor suppressorHairpin RNAColon cancer
2020
H3K4me1 Distribution Predicts Transcription State and Poising at Promoters
Bae S, Lesch BJ. H3K4me1 Distribution Predicts Transcription State and Poising at Promoters. Frontiers In Cell And Developmental Biology 2020, 8: 289. PMID: 32432110, PMCID: PMC7214686, DOI: 10.3389/fcell.2020.00289.Peer-Reviewed Original ResearchGerm cellsGene regulatory statesDifferent epigenetic marksTranscription start siteEmbryonic stem cellsMouse germ cellsGene expression levelsTranscription stateChromatin stateEpigenetic memoryEpigenetic stateEpigenetic marksLysine 4Histone H3Somatic cellsDistal enhancerStart siteActive promotersH3K4me1Transcriptional activityPromoter regionH3K4me3Possible rolePromoterCell types
2018
EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells
Zhang L, Ettou S, Khalid M, Taglienti M, Jain D, Jung YL, Seager C, Liu Y, Ng KH, Park PJ, Kreidberg JA. EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells. Development 2018, 145: dev157149. PMID: 29945864, PMCID: PMC6514390, DOI: 10.1242/dev.157149.Peer-Reviewed Original ResearchConceptsNephron progenitor cellsGene expressionProgenitor cellsNephron differentiationSelf-renewing stem cellsThousands of nephronsRole of PRC2Expression of genesDifferentiation of stemMutant micePolycomb groupH3K27me3 marksProgenitor stateEpigenetic regulationPRC2 complexHistone H3Progenitor populationsEnhancer sitesRenal vesiclesNonredundant componentMammalian kidneyCrucial rolePhysiological homeostasisGenesStem cells
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
Structural insight into autoinhibition and histone H3-induced activation of DNMT3A
Guo X, Wang L, Li J, Ding Z, Xiao J, Yin X, He S, Shi P, Dong L, Li G, Tian C, Wang J, Cong Y, Xu Y. Structural insight into autoinhibition and histone H3-induced activation of DNMT3A. Nature 2014, 517: 640-644. PMID: 25383530, DOI: 10.1038/nature13899.Peer-Reviewed Original Research
2013
Serum‐mediated transgenerational effects on sperm: Evidence for lamarckian inheritance?
Seki Y, Groszmann R, Iwakiri Y, Taddei T. Serum‐mediated transgenerational effects on sperm: Evidence for lamarckian inheritance? Hepatology 2013, 57: 1663-1665. PMID: 23568276, DOI: 10.1002/hep.26240.Peer-Reviewed Original ResearchPeroxisome proliferator-activated receptor gLiver fibrosisCells exposed to conditioned mediumRemodeling of DNA methylationLiver damageMild liver fibrosisTrimethylation of histone H3Histone variant H2A.ZHepatic wound healingWound healingNaive ratsCultured ratSevere fibrosisSperm chromatinHepatic insultProfibrogenic factorsSerum transferVariant H2A.ZMale ratsDNA methylationConditioned mediumHistone H3Histone acetylationTGF-b1Epigenetic signatures
2012
Structural Insight into Coordinated Recognition of Trimethylated Histone H3 Lysine 9 (H3K9me3) by the Plant Homeodomain (PHD) and Tandem Tudor Domain (TTD) of UHRF1 (Ubiquitin-like, Containing PHD and RING Finger Domains, 1) Protein*
Cheng J, Yang Y, Fang J, Xiao J, Zhu T, Chen F, Wang P, Li Z, Yang H, Xu Y. Structural Insight into Coordinated Recognition of Trimethylated Histone H3 Lysine 9 (H3K9me3) by the Plant Homeodomain (PHD) and Tandem Tudor Domain (TTD) of UHRF1 (Ubiquitin-like, Containing PHD and RING Finger Domains, 1) Protein*. Journal Of Biological Chemistry 2012, 288: 1329-1339. PMID: 23161542, PMCID: PMC3543016, DOI: 10.1074/jbc.m112.415398.Peer-Reviewed Original ResearchConceptsTandem Tudor domainHistone H3 lysine 9Plant homeodomainH3 lysine 9Tudor domainHistone methylationLysine 9DNA methylationStructural insightsDNA replication forksCoordinated recognitionImportant epigenetic regulatorsUnmodified histone H3Unmodified H3UHRF1 proteinReplication forksHistone H3Epigenetic regulatorsLys-9Autoubiquitination activityLys-4H3K9me3UHRF1Linker regionBiochemical experiments
2009
Complex 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
2004
Multiple Defects in Erythroid Gene Expression in Erythroid Krupple-Like Factor (EKLF) Target Genes in EKLF-Deficient Mice.
Gallagher P, Pilon A, Arcasoy M, Bodine D. Multiple Defects in Erythroid Gene Expression in Erythroid Krupple-Like Factor (EKLF) Target Genes in EKLF-Deficient Mice. Blood 2004, 104: 1602. DOI: 10.1182/blood.v104.11.1602.1602.Peer-Reviewed Original ResearchDNaseI hypersensitive sitesSubtractive hybridizationHypersensitive sitesΒ-globin geneHistone H3Transcription factorsTarget genesFetal liver cellsΒ-spectrinGene expressionΒ-globinErythroid gene expressionMouse Genome 430 2.0 ArrayAffymetrix GeneChip Mouse Genome 430 2.0 ArrayFactor target genesAHSP gene expressionChromatin immunoprecipitation analysisBand 3Mature erythroid progenitorsAHSP promoterRBC membrane proteinsErythroid genesChromatin upstreamChromatin modulatorsRegulated genesChromatin Remodeling of the Mouse AHSP Gene Requires EKLF.
Pilon A, Wong C, Garrett-Beal L, Weiss M, Gallagher P, Bodine D. Chromatin Remodeling of the Mouse AHSP Gene Requires EKLF. Blood 2004, 104: 375. DOI: 10.1182/blood.v104.11.375.375.Peer-Reviewed Original ResearchAlpha-Hemoglobin Stabilizing ProteinDNase I hypersensitive sitesAHSP geneAHSP gene expressionHypersensitive sitesWild typeΓ-globin mRNAFetal liver cellsHistone H3Human γ-globin genesGene expressionStrong DNase I hypersensitive siteIntron 1Wild-type chromatinChromatin Remodeling ComplexErythroid-specific proteinΓ-globin genePutative promoter sequencesTranscription factor EKLFExon 1Non-coding exonsΑ-globin mRNAPosition-independent expressionMRNA initiation siteRNase protection analysisB cell–specific loss of histone 3 lysine 9 methylation in the VH locus depends on Pax5
Johnson K, Pflugh DL, Yu D, Hesslein DG, Lin KI, Bothwell AL, Thomas-Tikhonenko A, Schatz DG, Calame K. B cell–specific loss of histone 3 lysine 9 methylation in the VH locus depends on Pax5. Nature Immunology 2004, 5: 853-861. PMID: 15258579, PMCID: PMC1635547, DOI: 10.1038/ni1099.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceB-LymphocytesCell LineageCells, CulturedDNA-Binding ProteinsFlow CytometryGene Rearrangement, B-LymphocyteHematopoietic Stem CellsHistonesImmunoglobulin Heavy ChainsImmunoglobulin Variable RegionLysineMethylationMiceModels, ImmunologicalMolecular Sequence DataPAX5 Transcription FactorPrecipitin TestsReverse Transcriptase Polymerase Chain ReactionTranscription FactorsConceptsH3-K9 methylationDJH recombinationVH locusHistone 3 lysine 9 methylationLysine 9 methylationFunction of Pax5Non-B lineage cellsB cell-specific lossB cell commitmentHistone exchangeInactive chromatinLysine 9Histone H3Transcription factorsCell commitmentCell-specific lossInhibitory modificationMethylationLineage cellsLociPAX5B cellsHeavy chain rearrangementRecombinationChain rearrangement
1987
Both Conserved Signals on Mammalian Histone Pre-mRNAs Associate with Small Nuclear Ribonucleoproteins During 3′ end Formation in Vitro
Mowry K, Steitz J. Both Conserved Signals on Mammalian Histone Pre-mRNAs Associate with Small Nuclear Ribonucleoproteins During 3′ end Formation in Vitro. Molecular And Cellular Biology 1987, 7: 1663-1672. DOI: 10.1128/mcb.7.5.1663-1672.1987.Peer-Reviewed Original ResearchSmall nuclear ribonucleoproteinEnd formationNuclear ribonucleoproteinSequence elementsSm small nuclear ribonucleoproteinsMouse histone genesHeLa cell nuclear extractsHistone H3 transcriptsHuman histone H3Trimethylguanosine cap structureCell nuclear extractsHistone pre-mRNAHairpin loop structureH3 transcriptsHistone genesConserved signalU RNAHistone H3MRNA substratesPre-mRNACap structureNuclear extractsRNA fragmentsProcessing reactionsProtein determinantsBoth conserved signals on mammalian histone pre-mRNAs associate with small nuclear ribonucleoproteins during 3' end formation in vitro.
Mowry KL, Steitz JA. Both conserved signals on mammalian histone pre-mRNAs associate with small nuclear ribonucleoproteins during 3' end formation in vitro. Molecular And Cellular Biology 1987, 7: 1663-1672. PMID: 2955216, PMCID: PMC365266, DOI: 10.1128/mcb.7.5.1663.Peer-Reviewed Original ResearchConceptsSmall nuclear ribonucleoproteinEnd formationNuclear ribonucleoproteinSequence elementsSm small nuclear ribonucleoproteinsMouse histone genesHeLa cell nuclear extractsHistone H3 transcriptsHuman histone H3Trimethylguanosine cap structureCell nuclear extractsHistone pre-mRNAHairpin loop structureH3 transcriptsHistone genesMammalian histonesU RNAHistone H3MRNA substratesPre-mRNACap structureMRNA associatesNuclear extractsRNA fragmentsProcessing reactions
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