title: Identification of biologically relevant enhancers in human erythroid cells.
abstract: Identification of cell type-specific enhancers is important for understanding the regulation of programs controlling cellular development and differentiation. Enhancers are typically marked by the co-transcriptional activator protein p300 or by groups of cell-expressed transcription factors. We hypothesized that a unique set of enhancers regulates gene expression in human erythroid cells, a highly specialized cell type evolved to provide adequate amounts of oxygen throughout the body. Using chromatin immunoprecipitation followed by massively parallel sequencing, genome-wide maps of candidate enhancers were constructed for p300 and four transcription factors, GATA1, NF-E2, KLF1, and SCL, using primary human erythroid cells. These data were combined with gene expression analyses, and candidate enhancers were identified. Consistent with their predicted function as candidate enhancers, there was statistically significant enrichment of p300 and combinations of co-localizing erythroid transcription factors within 1-50 kb of the transcriptional start site (TSS) of genes highly expressed in erythroid cells. Candidate enhancers were also enriched near genes with known erythroid cell function or phenotype. Candidate enhancers exhibited moderate conservation with mouse and minimal conservation with nonplacental vertebrates. Candidate enhancers were mapped to a set of erythroid-associated, biologically relevant, SNPs from the genome-wide association studies (GWAS) catalogue of NHGRI, National Institutes of Health. Fourteen candidate enhancers, representing 10 genetic loci, mapped to sites associated with biologically relevant erythroid traits. Fragments from these loci directed statistically significant expression in reporter gene assays. Identification of enhancers in human erythroid cells will allow a better understanding of erythroid cell development, differentiation, structure, and function and provide insights into inherited and acquired hematologic disease.
authors: Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520.
authors: Mack Y
authors: MY
authors: Su
authors: Department of Pediatrics, University of Rochester, Rochester, New York 14642.
authors: Laurie A
authors: LA
authors: Steiner
authors: Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520.
authors: Hannah
authors: H
authors: Bogardus
authors: Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802.
authors: Tejaswini
authors: T
authors: Mishra
authors: Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520.
authors: Vincent P
authors: VP
authors: Schulz
authors: Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802.
authors: Ross C
authors: RC
authors: Hardison
authors: Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520; Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520. Electronic address: patrick.gallagher@yale.edu.
authors: Patrick G
authors: PG
authors: Gallagher
mesh_terms: D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000378:metabolism / Q000502:physiology; D002478:Cells, Cultured; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D017124:Conserved Sequence; D050881:E1A-Associated p300 Protein / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D041905:Erythroid Cells / Q000378:metabolism*; D050982:GATA1 Transcription Factor / Q000378:metabolism / Q000502:physiology; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051741:Kruppel-Like Transcription Factors / Q000378:metabolism / Q000502:physiology; D049409:Luciferases, Firefly / Q000096:biosynthesis / Q000235:genetics; D058977:Molecular Sequence Annotation; D050984:NF-E2 Transcription Factor, p45 Subunit / Q000378:metabolism / Q000502:physiology; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D011518:Proto-Oncogene Proteins / Q000378:metabolism / Q000502:physiology; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; D059467:Transcriptome
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D002843:Chromatin; D050881:E1A-Associated p300 Protein; D050982:GATA1 Transcription Factor; D051741:Kruppel-Like Transcription Factors; D049409:Luciferases, Firefly; D050984:NF-E2 Transcription Factor, p45 Subunit; D011518:Proto-Oncogene Proteins; D012333:RNA, Messenger; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; C494688:GATA1 protein, human; C494692:NFE2 protein, human; C080774:erythroid Kruppel-like factor; C067143:TAL1 protein, human; C494360:EP300 protein, human