title: FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells.
abstract: Promoters and enhancers establish precise gene transcription patterns. The development of functional approaches for their identification in mammalian cells has been complicated by the size of these genomes. Here we report a high-throughput functional assay for directly identifying active promoter and enhancer elements called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), which we used to simultaneously assess over 80,000 DNA fragments derived from nucleosome-free regions within the chromatin of embryonic stem cells (ESCs) and identify 6,364 active regulatory elements. Many of these represent newly discovered ESC-specific enhancers, showing enriched binding-site motifs for ESC-specific transcription factors including SOX2, POU5F1 (OCT4) and KLF4. The application of FIREWACh to additional cultured cell types will facilitate functional annotation of the genome and expand our view of transcriptional network dynamics.
authors.affiliation: Department of Microbiology, New York University School of Medicine, New York, New York, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Murtha
authors.affiliation: Department of Microbiology, New York University School of Medicine, New York, New York, USA.
authors.forename: Zeynep
authors.initials: Z
authors.lastname: Tokcaer-Keskin
authors.affiliation: Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA.
authors.forename: Zuojian
authors.initials: Z
authors.lastname: Tang
authors.affiliation: Department of Biology and Biological Sciences, Yale University, New Haven, Connecticut, USA.
authors.forename: Francesco
authors.initials: F
authors.lastname: Strino
authors.affiliation: Department of Biology, New York University, New York, New York, USA.
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Microbiology, New York University School of Medicine, New York, New York, USA.
authors.forename: Yatong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Microbiology, New York University School of Medicine, New York, New York, USA.
authors.forename: Xiangmei
authors.initials: X
authors.lastname: Xi
authors.affiliation: Department of Microbiology, New York University School of Medicine, New York, New York, USA.
authors.forename: Claudio
authors.initials: C
authors.lastname: Basilico
authors.affiliation: Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA.
authors.forename: Stuart
authors.initials: S
authors.lastname: Brown
authors.affiliation: 1] Department of Biology, New York University, New York, New York, USA. [2] Department of Computer Science, Courant Institute of Mathematical Sciences, New York, New York, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
authors.affiliation: Department of Biology and Biological Sciences, Yale University, New Haven, Connecticut, USA.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Kluger
authors.affiliation: Department of Microbiology, New York University School of Medicine, New York, New York, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Dailey
mesh_terms: D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry; D019295:Computational Biology; D003850:Deoxyribonuclease I / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000166:cytology; D004742:Enhancer Elements, Genetic; D005434:Flow Cytometry; D005786:Gene Expression Regulation; D015723:Gene Library; D017930:Genes, Reporter; D005821:Genetic Techniques; D016678:Genome; D049452:Green Fluorescent Proteins / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D000090062:Kruppel-Like Factor 4; D016086:Lentivirus / Q000235:genetics / Q000378:metabolism; D008156:Luciferases / Q000378:metabolism; D051379:Mice; D010957:Plasmids / Q000378:metabolism; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic; D019076:Transgenes
chemical_list: D002843:Chromatin; C000715468:Klf4 protein, mouse; D000090062:Kruppel-Like Factor 4; D049452:Green Fluorescent Proteins; D008156:Luciferases; D003850:Deoxyribonuclease I