2023
Identification of a Novel Gene Regulatory Element in Human Erythroid Progenitor Cells
Schulz V, Lezon-Geyda K, Shan P, Papoin J, Narla M, Steiner L, Blanc L, Palis J, Gallagher P. Identification of a Novel Gene Regulatory Element in Human Erythroid Progenitor Cells. Blood 2023, 142: 9. DOI: 10.1182/blood-2023-186046.Peer-Reviewed Original ResearchErythroid progenitor cellsActive enhancersEarly erythropoiesisChIP-seqRegulatory elementsGene expressionATAC-seqRUNX motifsGATA motifSingle nucleotide polymorphismsProgenitor cellsGATA1 bindingDisease genesEnhancer regionErythroid lineageTissue-specific transcription factorsNovel gene regulatory elementsNovel enhancer regionErythrocyte traitsGenome-wide association studiesDirect tissue-specific expressionNovel regulatory elementGene regulatory elementsHuman erythroid progenitor cellsTerminal erythroid differentiation
2011
Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation
Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, Anderson SM, Mullikin J, Gallagher P, Hardison R, Margulies E, Bodine D. Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. Blood 2011, 118: e139-e148. PMID: 21900194, PMCID: PMC3208289, DOI: 10.1182/blood-2011-05-355107.Peer-Reviewed Original ResearchConceptsErythroid Kruppel-like factorKruppel-like factorChIP-seqTranscription factorsGenome-wide ChIP-seqProgenitor cellsMouse erythroid progenitor cellsCell cycle regulatory pathwaysErythroid transcription factorsGeneral cell growthRNA-seq analysisErythroid progenitor cellsTranscriptional activatorGATA factorsIntragenic regionsErythrocyte differentiationRegulatory pathwaysNuclear distributionPromoter regionParallel sequencingInteractomeDifferentiated erythroblastsCell growthTAL1Little overlap
2010
A Common Regulatory Signature Associated with Barrier Insulators in Human Primary Erythroid Cells
Steiner L, Maksimova Y, Schulz V, Gallagher P. A Common Regulatory Signature Associated with Barrier Insulators in Human Primary Erythroid Cells. Blood 2010, 116: 3868. DOI: 10.1182/blood.v116.21.3868.3868.Peer-Reviewed Original ResearchGenome-wide mapsPrimary erythroid cellsErythroid cellsProximal promoterChromatin domainsBarrier insulatorsChIP-seqRegulatory signaturesMammalian cellsGene promoterEnhancer-blocking insulator activityTissue-specific gene expressionUpstream stimulatory factor proteinsHeterochromatin-mediated geneGenome-wide occupancyRole of CTCFRecruitment of enzymesΒ-globin locusHistone methyltransferase activityHuman primary erythroid cellsSpecific transcription factorsChicken β-globin locusProximal promoter regionProtein CTCFChromatin boundaries
2009
Genome-Wide ChIP-Seq Reveals a Dramatic Shift in the EKLF Binding Profile Between Erythroid Progenitors and Erythroblasts.
Pilon A, Ajay S, Abaan H, Margulies E, Gallagher P, Bodine D. Genome-Wide ChIP-Seq Reveals a Dramatic Shift in the EKLF Binding Profile Between Erythroid Progenitors and Erythroblasts. Blood 2009, 114: 565. DOI: 10.1182/blood.v114.22.565.565.Peer-Reviewed Original ResearchTarget genesChIP-seqNearest geneSimultaneous genome-wide analysisC2H2 zinc finger transcription factorGenome-wide ChIP-seqErythroid Kruppel-like factorZinc finger transcription factorErythroid progenitorsTranscription factor occupancyBeta-globin locusGenome-wide analysisCell cycle control factorsProtein-DNA interactionsFinger transcription factorChIP-seq dataS-phase entryNon-repetitive regionsKruppel-like factorEKLF geneEKLF proteinFetal liverCell cycle S-phase entryChromatin remodelingFactor occupancy
2008
Genome-Wide Analysis of EKLF Occupancy in Erythroid Chromatin Reveals 5′, 3′ and Intragenic Binding Sites in EKLF Target Genes
Pilon A, Margulies E, Abaan H, Allen A, Townes T, Frederick A, Zhou D, Gallagher P, Bodine D. Genome-Wide Analysis of EKLF Occupancy in Erythroid Chromatin Reveals 5′, 3′ and Intragenic Binding Sites in EKLF Target Genes. Blood 2008, 112: 283. DOI: 10.1182/blood.v112.11.283.283.Peer-Reviewed Original ResearchCell cycle networkChIP-seqIngenuity Pathway AnalysisTranscription factorsEKLF geneWide analysisIntragenic sitesTarget genesChIP-PCRErythroid cellsMapping protein-DNA interactionsErythroid Kruppel-like factorFetal liver erythroid cellsGenome-wide scaleBeta-globin locusGenome-wide analysisCell cycle control networkProtein-DNA interactionsChIP-seq resultsTerminal erythroid maturationDNase hypersensitive sitesKnowledge of genesChIP-seq librariesChIP-seq dataFL cells