2024
High-resolution yeast actin structures indicate the molecular mechanism of actin filament stiffening by cations
Xu X, Cao W, Swift M, Pandit N, Huehn A, Sindelar C, De La Cruz E, Hanein D, Volkmann N. High-resolution yeast actin structures indicate the molecular mechanism of actin filament stiffening by cations. Communications Chemistry 2024, 7: 164. PMID: 39079963, PMCID: PMC11289367, DOI: 10.1038/s42004-024-01243-x.Peer-Reviewed Original ResearchActin filamentsVertebrate actinsActin structuresDNase I binding loopActin filament assemblyEukaryotic cell functionStructures of wild-typeNear-atomic resolution structuresPotential binding sitesActin subunitsFilament assemblyRegulatory proteinsDNase IA167ActinAdjacent subunitsRegulatory roleMolecular mechanismsVertebratesWild-typeGlutamic acidCell functionFilamentsSubunitResidues
2021
Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element
Baxter J, Johnson N, Tomczyk K, Gillespie A, Maguire S, Brough R, Fachal L, Michailidou K, Bolla M, Wang Q, Dennis J, Ahearn T, Andrulis I, Anton-Culver H, Antonenkova N, Arndt V, Aronson K, Augustinsson A, Becher H, Beckmann M, Behrens S, Benitez J, Bermisheva M, Bogdanova N, Bojesen S, Brenner H, Brucker S, Cai Q, Campa D, Canzian F, Castelao J, Chan T, Chang-Claude J, Chanock S, Chenevix-Trench G, Choi J, Clarke C, Collaborators N, Colonna S, Conroy D, Couch F, Cox A, Cross S, Czene K, Daly M, Devilee P, Dörk T, Dossus L, Dwek M, Eccles D, Ekici A, Eliassen A, Engel C, Fasching P, Figueroa J, Flyger H, Gago-Dominguez M, Gao C, García-Closas M, García-Sáenz J, Ghoussaini M, Giles G, Goldberg M, González-Neira A, Guénel P, Gündert M, Haeberle L, Hahnen E, Haiman C, Hall P, Hamann U, Hartman M, Hatse S, Hauke J, Hollestelle A, Hoppe R, Hopper J, Hou M, Investigators K, Investigators A, Ito H, Iwasaki M, Jager A, Jakubowska A, Janni W, John E, Joseph V, Jung A, Kaaks R, Kang D, Keeman R, Khusnutdinova E, Kim S, Kosma V, Kraft P, Kristensen V, Kubelka-Sabit K, Kurian A, Kwong A, Lacey J, Lambrechts D, Larson N, Larsson S, Le Marchand L, Lejbkowicz F, Li J, Long J, Lophatananon A, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Matsuo K, Mavroudis D, Mayes R, Menon U, Milne R, Taib N, Muir K, Muranen T, Murphy R, Nevanlinna H, O’Brien K, Offit K, Olson J, Olsson H, Park S, Park-Simon T, Patel A, Peterlongo P, Peto J, Plaseska-Karanfilska D, Presneau N, Pylkäs K, Rack B, Rennert G, Romero A, Ruebner M, Rüdiger T, Saloustros E, Sandler D, Sawyer E, Schmidt M, Schmutzler R, Schneeweiss A, Schoemaker M, Shah M, Shen C, Shu X, Simard J, Southey M, Stone J, Surowy H, Swerdlow A, Tamimi R, Tapper W, Taylor J, Teo S, Teras L, Terry M, Toland A, Tomlinson I, Truong T, Tseng C, Untch M, Vachon C, van den Ouweland A, Wang S, Weinberg C, Wendt C, Winham S, Winqvist R, Wolk A, Wu A, Yamaji T, Zheng W, Ziogas A, Pharoah P, Dunning A, Easton D, Pettitt S, Lord C, Haider S, Orr N, Fletcher O. Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element. American Journal Of Human Genetics 2021, 108: 1190-1203. PMID: 34146516, PMCID: PMC8322933, DOI: 10.1016/j.ajhg.2021.05.013.Peer-Reviewed Original ResearchConceptsBreast cancer risk lociCredible causal variantsCancer risk lociRegulatory elementsCausal variantsRisk lociCell type-specific transcriptionDeletion alleleTranscription factor binding regionsIdentified putative regulatory elementsChIP-seq dataPutative regulatory elementsCell type-specific expressionSignal 2ChIP-seqFunctional annotationStructural variantsDNase IBinding regionCRISPR assayIGFBP5 promoterEstrogen receptor-positive breast cancerReceptor-positive breast cancerRisk of estrogen receptor-positive breast cancerLoci
2008
Failure of Terminal Erythroid Differentiation in EKLF-Deficient Mice Is Associated with Cell Cycle Perturbation and Reduced Expression of E2F2
Pilon AM, Arcasoy MO, Dressman HK, Vayda SE, Maksimova YD, Sangerman JI, Gallagher PG, Bodine DM. Failure of Terminal Erythroid Differentiation in EKLF-Deficient Mice Is Associated with Cell Cycle Perturbation and Reduced Expression of E2F2. Molecular And Cellular Biology 2008, 28: 7394-7401. PMID: 18852285, PMCID: PMC2593440, DOI: 10.1128/mcb.01087-08.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell CycleCell DifferentiationE2F2 Transcription FactorEmbryo, MammalianErythropoiesisGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksKruppel-Like Transcription FactorsLiverMiceMice, KnockoutOligonucleotide Array Sequence AnalysisPromoter Regions, GeneticStem CellsTranscription, GeneticConceptsErythroid Krüppel-like factorTerminal erythroid differentiationEarly erythroid progenitor cellsErythroid progenitor cellsErythroid differentiationChromatin modifiersProgenitor cellsKrüppel-like transcription factorsNetwork of genesCell cycle regulationChromatin immunoprecipitation analysisKrüppel-like factorCell cycle progressionFailure of erythropoiesisS phase transitionEarly progenitor cellsTranscriptional activatorCycle regulationTranscriptional profilingTranscription factorsTarget genesImmunoprecipitation analysisDNase IErythroid cellsCycle progressionLocal and Distant Elements Regulate Tissue-Specific Expression of ANK-1 Gene Transcripts
Owen A, Laflamme K, Pilon A, Garrett L, Gallagher P, Bodine D. Local and Distant Elements Regulate Tissue-Specific Expression of ANK-1 Gene Transcripts. Blood 2008, 112: 2432. DOI: 10.1182/blood.v112.11.2432.2432.Peer-Reviewed Original ResearchNon-erythroid cellsHypersensitive sitesTransient transfection assaysConsensus sequenceChromatin loopsGATA-1NF-E2Promoter sequencesKb regionHistone acetylationErythroid transcription factor NF-E2Transfection assaysFirst exonDNase IErythroid cellsDevelopmental stage-specific patternsLocal chromatin architectureProtein-coding genesChromatin conformation captureANK-1 geneRNA Pol IITranscription initiation complexErythroid K562 cellsDNase hypersensitive sitesGATA-1 bindingPax5 and Linker Histone H1 Coordinate DNA Methylation and Histone Modifications in the 3′ Regulatory Region of the Immunoglobulin Heavy Chain Locus
Giambra V, Volpi S, Emelyanov AV, Pflugh D, Bothwell AL, Norio P, Fan Y, Ju Z, Skoultchi AI, Hardy RR, Frezza D, Birshtein BK. Pax5 and Linker Histone H1 Coordinate DNA Methylation and Histone Modifications in the 3′ Regulatory Region of the Immunoglobulin Heavy Chain Locus. Molecular And Cellular Biology 2008, 28: 6123-6133. PMID: 18644860, PMCID: PMC2547000, DOI: 10.1128/mcb.00233-08.Peer-Reviewed Original ResearchConceptsImmunoglobulin heavy chain locusHeavy chain locusHistone modificationsDNA methylationRegulatory regionsPalindromic regionMurine immunoglobulin heavy chain locusB-cell-specific transcription factor Pax5Chain locusLinker histone H1Multiple DNase IModular patternsTranscription factor Pax5Class switch recombinationMethylation-sensitive restriction sitesActive chromatinHeavy chain allelesHypersensitive sitesHistone H1B cell differentiationDNase ISwitch recombinationPotential insulatorsRestriction sitesHS4
2005
Chromatin Conformation and a Distal Regulatory Element Activate the Human Erythroid Ankyrin-1 Promoter.
Owen A, Liem R, Pilon A, Gallagher P, Bodine D. Chromatin Conformation and a Distal Regulatory Element Activate the Human Erythroid Ankyrin-1 Promoter. Blood 2005, 106: 803. DOI: 10.1182/blood.v106.11.803.803.Peer-Reviewed Original ResearchNon-erythroid cellsRegulatory elementsReporter geneErythroid cellsKb regionLuciferase reporter geneDNase IKb downstreamKb upstreamK562 cellsErythroid-specific transcription factorDNase I hypersensitive sitesE-box binding proteinGreen fluorescent protein (GFP) reporter geneCell typesChromatin conformation captureFluorescent protein reporter geneGFP reporter genePositive regulatory elementErythrocyte membrane skeletonConformation captureChromatin conformationChromatin loopsChromatin structureTranscription factorsGATA-1 and Oct-1 Are Required for Expression of the Human α-Hemoglobin-stabilizing Protein Gene*
Gallagher PG, Liem RI, Wong E, Weiss MJ, Bodine DM. GATA-1 and Oct-1 Are Required for Expression of the Human α-Hemoglobin-stabilizing Protein Gene*. Journal Of Biological Chemistry 2005, 280: 39016-39023. PMID: 16186125, DOI: 10.1074/jbc.m506062200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBinding SitesBlood ProteinsCell LineCloning, MolecularDNA, ComplementaryErythropoiesisGATA1 Transcription FactorGene ExpressionGlobinsHeLa CellsHumansMiceMice, TransgenicMolecular ChaperonesMolecular Sequence DataMutationOctamer Transcription Factor-1Promoter Regions, GeneticRecombinant ProteinsRNA, MessengerConceptsAlpha-hemoglobin-stabilizing proteinGATA-1AHSP promoterAHSP genePromoter/reporter plasmidsGel mobility shift assaysAHSP gene expressionChromatin immunoprecipitation assaysErythroid-specific expressionMobility shift assaysFurther genetic studiesHuman tissue culture cell linesErythroid proteinTissue culture cell linesErythroid promoterNonerythroid tissuesProtein geneImmunoprecipitation assaysRegulatory elementsShift assaysGene promoterReporter geneCandidate genesDNase IGene expression
2004
Human potassium chloride cotransporter 1 (SLC12A4) promoter is regulated by AP-2 and contains a functional downstream promoter element
Zhou GP, Wong C, Su R, Crable SC, Anderson KP, Gallagher PG. Human potassium chloride cotransporter 1 (SLC12A4) promoter is regulated by AP-2 and contains a functional downstream promoter element. Blood 2004, 103: 4302-4309. PMID: 14976052, DOI: 10.1182/blood-2003-01-0107.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsAcetylationBase SequenceCarcinoma, HepatocellularChromatinCloning, MolecularDNA-Binding ProteinsErythroid CellsHeLa CellsHumansK562 CellsMolecular Sequence DataPrecipitin TestsPromoter Regions, GeneticSp1 Transcription FactorSymportersTranscription Factor AP-2Transcription FactorsTranscription Initiation SiteConceptsDownstream promoter elementAP-2Gene promoterSp1 sitesK-Cl cotransportPromoter elementsKCC1 geneMammalian gene promotersElectrophoretic mobility shift assaysChromatin immunoprecipitation assaysFull promoter activityMobility shift assaysCore promoter regionReporter gene assayChloride cotransporter 1TATA boxImmunoprecipitation assaysInitiator elementShift assaysHeterologous cellsMutational analysisDNase IPromoter regionGenomic DNAPromoter activityProperties of Ets-1 Binding to Chromatin and Its Effect on Platelet Factor 4 Gene Expression
Lu J, Pazin MJ, Ravid K. Properties of Ets-1 Binding to Chromatin and Its Effect on Platelet Factor 4 Gene Expression. Molecular And Cellular Biology 2004, 24: 428-441. PMID: 14673175, PMCID: PMC303331, DOI: 10.1128/mcb.24.1.428-441.2004.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAnimalsChromatinDetergentsGene Expression RegulationHumansMegakaryocytesMiceNucleosomesPlatelet Factor 4Platelet Glycoprotein GPIb-IX ComplexPlatelet Membrane GlycoproteinsPromoter Regions, GeneticProto-Oncogene Protein c-ets-1Proto-Oncogene ProteinsProto-Oncogene Proteins c-etsRatsSarcosineTranscription FactorsConceptsEts-1 bindsPromoter activityLineage-specific factorsChromatin immunoprecipitation assaysEts-1 siteGlycoprotein IIbLineage-specific promotersNaked DNAGPIIb promoterTranscriptional regulationAccessory factorsPF4 promoterTranscription factorsHypersensitive sitesImmunoprecipitation assaysHematopoietic lineagesDNase IChromatinGene expressionPromoter activationPromoterProximal regionModel systemFactor 4ET-1
2003
Transcriptional Repression of Peri-Implantation EMX2 Expression in Mammalian Reproduction by HOXA10
Troy PJ, Daftary GS, Bagot CN, Taylor HS. Transcriptional Repression of Peri-Implantation EMX2 Expression in Mammalian Reproduction by HOXA10. Molecular And Cellular Biology 2003, 23: 1-13. PMID: 12482956, PMCID: PMC140663, DOI: 10.1128/mcb.23.1.1-13.2003.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCells, CulturedEmbryonic DevelopmentEndometriumEstradiolFemaleHomeobox A10 ProteinsHomeodomain ProteinsHumansMammalsMenstrual CycleMiceMutationOligonucleotides, AntisensePregnancyProgesteroneRecombinant ProteinsRegulatory Sequences, Nucleic AcidRepressor ProteinsReproductionTranscription FactorsTranscription, GeneticConceptsTranscriptional repressionMammalian reproductionNegative transcriptional regulationDivergent homeobox genesPossible evolutionary implicationsSite-directed mutagenesisTransient transfection assaysNegative regulatory relationshipDrosophila orthologUrogenital tract developmentDirection of regulationTranscriptional regulationEvolutionary implicationsGene relationshipsHomeobox genesTranscriptional activationTranscriptional targetsRegulatory regionsEmpty spiraclesRegulatory relationshipsDeletional analysisDNase IEMX2 mRNAConstitutive expressionNorthern analysis
2002
Erythroid Expression of the Human α-Spectrin Gene Promoter Is Mediated by GATA-1- and NF-E2-binding Proteins*
Boulanger L, Sabatino DE, Wong EY, Cline AP, Garrett LJ, Garbarz M, Dhermy D, Bodine DM, Gallagher PG. Erythroid Expression of the Human α-Spectrin Gene Promoter Is Mediated by GATA-1- and NF-E2-binding Proteins*. Journal Of Biological Chemistry 2002, 277: 41563-41570. PMID: 12196550, DOI: 10.1074/jbc.m208184200.Peer-Reviewed Original ResearchMeSH Keywords5' Flanking RegionAnimalsBase SequenceBinding SitesDNA, ComplementaryDNA-Binding ProteinsErythroid Precursor CellsErythroid-Specific DNA-Binding FactorsErythropoiesisGATA1 Transcription FactorHeLa CellsHumansK562 CellsMiceMice, TransgenicMolecular Sequence DataNF-E2 Transcription FactorNF-E2 Transcription Factor, p45 SubunitPromoter Regions, GeneticSpectrinTranscription FactorsConceptsGene promoterGATA-1Reporter genePromoter/reporter plasmidsAlpha-spectrinGel mobility shift assaysErythroid-specific expressionFull promoter activityAlpha-spectrin geneMobility shift assaysErythroid progenitor cellsHuman tissue culture cell linesTissue culture cell linesAdult reticulocytesErythroid promoterNonerythroid tissuesMembrane proteinsLow-level expressionRegulatory elementsShift assaysErythroid expressionCell shapeDNase IErythroid cellsPromoter activity
1999
Molecular Characterization of the PmrA Regulon*
Wösten M, Groisman E. Molecular Characterization of the PmrA Regulon*. Journal Of Biological Chemistry 1999, 274: 27185-27190. PMID: 10480935, DOI: 10.1074/jbc.274.38.27185.Peer-Reviewed Original ResearchMpl ligand enhances the transcription of the cyclin D3 gene: a potential role for Sp1 transcription factor.
Wang Z, Zhang Y, Lu J, Sun S, Ravid K. Mpl ligand enhances the transcription of the cyclin D3 gene: a potential role for Sp1 transcription factor. Blood 1999, 93: 4208-21. PMID: 10361118, DOI: 10.1182/blood.v93.12.4208.412k17_4208_4221.Peer-Reviewed Original ResearchConceptsProtein phosphatase 1Cyclin D3 promoterMpl ligandCyclin D3 geneTranscription factorsSp1-dependent genesD3 geneSp1 transcription factorForm of Sp1Basal promoter activityMegakaryocytic cell linesCyclin D3 proteinSp familySp1 proteinD3 gene expressionSp1 sitesPhosphatase 1Okadaic acidCyclin D3 gene expressionNuclear runSp1DNase IGene expressionPromoter activityPromoter regionA Human β-Spectrin Gene Promoter Directs High Level Expression in Erythroid but Not Muscle or Neural Cells*
Gallagher P, Sabatino D, Romana M, Cline A, Garrett L, Bodine D, Forget B. A Human β-Spectrin Gene Promoter Directs High Level Expression in Erythroid but Not Muscle or Neural Cells*. Journal Of Biological Chemistry 1999, 274: 6062-6073. PMID: 10037687, DOI: 10.1074/jbc.274.10.6062.Peer-Reviewed Original ResearchConceptsBeta-spectrin geneGene promoterHigh-level expressionGATA-1Regulatory elementsReporter geneErythroid tissuesPromoter/reporter plasmidsGel mobility shift assaysLevel expressionGATA-1 motifsFull promoter activityTissue-specific expressionMobility shift assaysAdditional regulatory elementsErythrocyte membrane proteinsHuman tissue culture cell linesTissue culture cell linesErythroid promoterMembrane proteinsShift assaysBeta spectrinHeterologous cellsCell shapeDNase I
1997
Parvovirus initiation factor PIF: a novel human DNA-binding factor which coordinately recognizes two ACGT motifs
Christensen J, Cotmore S, Tattersall P. Parvovirus initiation factor PIF: a novel human DNA-binding factor which coordinately recognizes two ACGT motifs. Journal Of Virology 1997, 71: 5733-5741. PMID: 9223459, PMCID: PMC191825, DOI: 10.1128/jvi.71.8.5733-5741.1997.Peer-Reviewed Original ResearchConceptsDNA-binding factorsACGT motifGel mobility shift assaysReplication initiation processMobility shift assaysHigher-order multimersParvovirus initiation factorSame cellular factorHeLa S3 cellsMouse genomeBinds DNADNA replicationACGT sequenceInitiation factorsOrigin sequencesShift assaysMinimal originMutant oligonucleotidesATP hydrolysisMobility shiftDNase ICellular factorsEssential cofactorMobility assaysSingle binding site
1996
Identification of tissue-specific DNase I hypersensitive sites in the rabbit flavin-containing monooxygenase form 2 gene.
Shehin-Johnson S, Palmer K, Hines R. Identification of tissue-specific DNase I hypersensitive sites in the rabbit flavin-containing monooxygenase form 2 gene. Drug Metabolism And Disposition 1996, 24: 891-898. PMID: 8869825, DOI: 10.1016/s0090-9556(25)07450-1.Peer-Reviewed Original ResearchConceptsDNase IHypersensitive sitesTissue-specific transcription factorsLambda EMBL3 genomic libraryPolyomavirus enhancer activator 3Base pairsTissue-specific DNase I hypersensitive siteDNase I hypersensitive sitesTissue-specific DNase IEMBL3 genomic libraryPrimer extension analysisTranscription start siteClassical TATA boxTissue-specific mannerHypersensitive domainGenomic clonesGenomic libraryMethylated regionsTranscription factorsCDNA sequenceKilobase pairsStart siteTATA boxExtension analysisType II cell populations
1995
Minute virus of mice transcriptional activator protein NS1 binds directly to the transactivation region of the viral P38 promoter in a strictly ATP-dependent manner
Christensen J, Cotmore S, Tattersall P. Minute virus of mice transcriptional activator protein NS1 binds directly to the transactivation region of the viral P38 promoter in a strictly ATP-dependent manner. Journal Of Virology 1995, 69: 5422-5430. PMID: 7636987, PMCID: PMC189388, DOI: 10.1128/jvi.69.9.5422-5430.1995.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAnimalsBase SequenceBinding SitesCell LineDeoxyribonuclease IDNA, ViralGenes, ViralGenetic VectorsGenome, ViralMinute virus of miceMolecular Sequence DataNucleopolyhedrovirusesPlasmidsPromoter Regions, GeneticRecombinant ProteinsSpodopteraTranscriptional ActivationTransfectionViral Nonstructural ProteinsViral ProteinsConceptsATP-dependent mannerGamma S-ATPTransactivation regionP38 promoterCognate sitesDNA fragmentsNS1 bindsCore DNA sequenceCarboxy-terminal peptidePotent transcriptional activatorMinute virusS-ATPTranscriptional activatorMVM genomeATP bindingTAR sequenceTATA boxDNA sequencesATP hydrolysisBiochemical stepsBp 5DNase INS1 polypeptideTAR bindingAntibodies
1993
Specific nuclear protein binding to a negative regulatory element on the human CYP1A1 gene
Boucher P, Ruch R, Hines R. Specific nuclear protein binding to a negative regulatory element on the human CYP1A1 gene. Journal Of Biological Chemistry 1993, 268: 17384-17391. PMID: 8349622, DOI: 10.1016/s0021-9258(19)85346-2.Peer-Reviewed Original ResearchConceptsNegative regulatory activityNuclear proteinsElectrophoretic mobility shift assaysCellular trans-acting factorsTrans-acting factorsRegulatory activityStrand-specific mannerCo-transfection studiesMethylation interference experimentsMobility shift assaysNegative regulatory elementSpecific nuclear proteinCytosine-rich sequencesHuman CYP1A1 genePromoter/enhancerRegulatory elementsShift assaysTransient expressionReporter geneDNase IChimeric plasmidsCYP1A1 promoterImportant sequencesCYP1A1 genePalindromes
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