2013
Enhancers and Super Enhancers Are Associated With Genes That Control Phenotypic Traits In Primary Human Erythroid Cells
Schulz V, Lezon-Geyda K, Maksimova Y, Gallagher P. Enhancers and Super Enhancers Are Associated With Genes That Control Phenotypic Traits In Primary Human Erythroid Cells. Blood 2013, 122: 1200. DOI: 10.1182/blood.v122.21.1200.1200.Peer-Reviewed Original ResearchTranscriptional start siteRegulation of programsSuper enhancersErythroid cellsGene expressionErythroid enhancerTF motifsTranscription factorsHistone H3 lysine 4 monomethylationSpecific enhancersH3K27ac modificationGWAS catalogGene locusHistone H3 lysine 27 acetylationCell type-specific enhancersPrimary human erythroid cellsH3 lysine 27 acetylationAlpha-globin gene clusterDisease-associated genetic variantsGenome-wide mapsNHGRI GWAS catalogSubset of enhancersHundreds of kilobasesLysine 27 acetylationSpecialized cell typesIdentification of Biologically Relevant Enhancers in Human Erythroid Cells*
Su MY, Steiner LA, Bogardus H, Mishra T, Schulz VP, Hardison RC, Gallagher PG. Identification of Biologically Relevant Enhancers in Human Erythroid Cells*. Journal Of Biological Chemistry 2013, 288: 8433-8444. PMID: 23341446, PMCID: PMC3605659, DOI: 10.1074/jbc.m112.413260.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBasic Helix-Loop-Helix Transcription FactorsCells, CulturedChromatinChromatin ImmunoprecipitationConserved SequenceE1A-Associated p300 ProteinEnhancer Elements, GeneticErythroid CellsGATA1 Transcription FactorGene Expression RegulationGenes, ReporterHigh-Throughput Nucleotide SequencingHumansKruppel-Like Transcription FactorsLuciferases, FireflyMolecular Sequence AnnotationNF-E2 Transcription Factor, p45 SubunitOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotidePromoter Regions, GeneticProtein BindingProto-Oncogene ProteinsRNA, MessengerSequence Analysis, DNAT-Cell Acute Lymphocytic Leukemia Protein 1TranscriptomeConceptsHuman erythroid cellsCandidate enhancersTranscriptional start siteErythroid cellsTranscription factorsGenome-wide association study catalogCell type-specific enhancersPrimary human erythroid cellsRegulation of programsGenome-wide mapsErythroid transcription factorsErythroid cell developmentSpecialized cell typesIdentification of enhancersGene expression analysisErythroid traitsMinimal conservationChromatin immunoprecipitationModerate conservationStart siteRelevant enhancersCellular developmentGenetic lociExpression analysisReporter gene
2012
Identification of Biologicaly Relevant Enhancers in Human Erythroid Cells
Su M, Steiner L, Bogardus H, Schulz V, Hardison R, Gallagher P. Identification of Biologicaly Relevant Enhancers in Human Erythroid Cells. Blood 2012, 120: 368. DOI: 10.1182/blood.v120.21.368.368.Peer-Reviewed Original ResearchTranscriptional start siteHuman erythroid cellsCell type-specific enhancersErythroid transcription factorsErythroid-specific genesTranscription factorsErythroid cellsCandidate enhancersSpecific enhancersSignificant enrichmentGene expressionPrimary human erythroid cellsRegulation of programsDisease-associated genetic variantsGenome-wide mapsHundreds of kilobasesSpecialized cell typesTranscription factor sitesKb of genesGene expression analysisParallel gene expression analysisGenomic vicinityGenomic methodologiesEvolutionary analysisHigh conservation
2009
Chromatin Architecture and Transcription Factor Binding Regulate Expression of Erythrocyte Membrane Protein Genes
Steiner LA, Maksimova Y, Schulz V, Wong C, Raha D, Mahajan MC, Weissman SM, Gallagher PG. Chromatin Architecture and Transcription Factor Binding Regulate Expression of Erythrocyte Membrane Protein Genes. Molecular And Cellular Biology 2009, 29: 5399-5412. PMID: 19687298, PMCID: PMC2756878, DOI: 10.1128/mcb.00777-09.Peer-Reviewed Original ResearchMeSH KeywordsBasic Helix-Loop-Helix Transcription FactorsChromatinErythrocyte MembraneErythrocytesGATA1 Transcription FactorGene Expression RegulationHeLa CellsHistone DeacetylasesHumansMembrane ProteinsNF-E2 Transcription Factor, p45 SubunitNuclear ProteinsProto-Oncogene ProteinsRepressor ProteinsT-Cell Acute Lymphocytic Leukemia Protein 1Transcription FactorsConceptsErythrocyte membrane protein genesMembrane protein geneNF-E2 bindingGATA-1Protein geneChromatin architectureFOG-1Nonerythroid cellsBinding motifDynamic chromatin architectureHistone H3 trimethylationNF-E2Numerous candidate regionsTranscription factor bindingGATA-1 bindingTranscriptional start siteComplex genetic lociParallel DNA sequencingGenomic organizationLocus structureLysine 4H3 trimethylationGene regulationChromatin immunoprecipitationStart site
2008
Chromatin Architecture and Transcription Factor Occupancy of Erythrocyte Membrane Genes Studied by Chromatin Immunoprecipitation on Microarrays (ChIP-chip)
Steiner L, Maksimova Y, Wong C, Schulz V, Gallagher P. Chromatin Architecture and Transcription Factor Occupancy of Erythrocyte Membrane Genes Studied by Chromatin Immunoprecipitation on Microarrays (ChIP-chip). Blood 2008, 112: 2436. DOI: 10.1182/blood.v112.11.2436.2436.Peer-Reviewed Original ResearchErythrocyte membrane protein genesNF-E2 siteMembrane protein geneGATA-1 sitesTranscriptional start siteChromatin architectureTranscription factor bindingPrimary erythroid cellsGATA-1Protein geneChromatin immunoprecipitationTranscription factorsErythroid cellsH3K4me3 enrichmentFlanking DNAFactor bindingDNA sequencesK562 cellsErythroid transcription factor GATA-1Mapping protein-DNA interactionsNon-erythroid cell linesTranscription factor GATA-1Quantitative ChIP analysisTranscription factor occupancyGenome-wide scale
2006
Identification of a Novel Core Promoter Element That Enhances Transcription: Application to Ankyrin Promoters for Globin Gene Therapy.
Laflamme K, Elnitski L, Owen A, Gallagher P, Bodine D. Identification of a Novel Core Promoter Element That Enhances Transcription: Application to Ankyrin Promoters for Globin Gene Therapy. Blood 2006, 108: 3261. DOI: 10.1182/blood.v108.11.3261.3261.Peer-Reviewed Original ResearchGC-rich promoterLocus control regionΓ-globin expressionHematopoietic stem cellsTG dinucleotideErythroid cellsNovel core promoter elementΑ-globinDifferent tissue-specific promotersLike globin genesBinding regionsΓ-globin transcriptionANK-1 geneTranscription initiation complexΓ-globin geneErythroid K562 cellsConsensus promoter sequenceTranscriptional start siteCore promoter elementsRNA virus vectorMouse erythroid cellsK562 cellsStable transfection assaysWild-type promoterTissue-specific promoters