title: Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.
abstract: It is currently not possible to resolve the genome-wide relationship of transcription factors (TFs) and nucleosomes at the level of individual chromatin templates despite rapidly increasing data on TF and nucleosome occupancy in the human genome. Here we describe DNase I-released fragment-length analysis of hypersensitivity (DNase-FLASH), an approach that directly couples mapping of TF occupancy, via quantification of DNA microfragments released from individual TF recognition sites in regulatory DNA, to the surrounding nucleosome architecture, via analysis of larger DNA fragments, in a single assay. DNase-FLASH enables coupling of individual TF footprints to nucleosome occupancy, identifying TFs that precisely demarcate the regulatory DNA-nucleosome interface.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Jeff
authors.initials: J
authors.lastname: Vierstra
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Sam
authors.initials: S
authors.lastname: John
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Sandstrom
authors.affiliation: 1] Department of Genome Sciences, University of Washington, Seattle, Washington, USA. [2] Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000032:analysis / Q000737:chemistry; D003850:Deoxyribonuclease I / Q000737:chemistry* / Q000378:metabolism; D044127:Epigenesis, Genetic; D057890:Epigenomics; D005347:Fibroblasts / Q000378:metabolism; D015894:Genome, Human; D005881:Gingiva / Q000378:metabolism; D006801:Humans; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D014157:Transcription Factors; D004247:DNA; D003850:Deoxyribonuclease I