title: Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.
abstract: High-throughput methods based on chromosome conformation capture have greatly advanced our understanding of the three-dimensional (3D) organization of genomes but are limited in resolution by their reliance on restriction enzymes. Here we describe a method called DNase Hi-C for comprehensively mapping global chromatin contacts. DNase Hi-C uses DNase I for chromatin fragmentation, leading to greatly improved efficiency and resolution over that of Hi-C. Coupling this method with DNA-capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of 998 large intergenic noncoding RNA (lincRNA) promoters in two human cell lines. Our results revealed that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the Polycomb repressive complex. Our results provide the first glimpse of the cell type-specific 3D organization of lincRNA genes.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Wenxiu
authors.initials: W
authors.lastname: Ma
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Ferhat
authors.initials: F
authors.lastname: Ay
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Choli
authors.initials: C
authors.lastname: Lee
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Gunhan
authors.identifier: 0000000184822930
authors.initials: G
authors.lastname: Gulsoy
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, USA.
authors.forename: Xinxian
authors.initials: X
authors.lastname: Deng
authors.affiliation: 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Comparative Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Savannah
authors.initials: S
authors.lastname: Cook
authors.affiliation: 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Comparative Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hesson
authors.affiliation: 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Comparative Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Cavanaugh
authors.affiliation: 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Comparative Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Carol B
authors.initials: CB
authors.lastname: Ware
authors.affiliation: Department of Radiation Oncology, University of Washington, Seattle, Washington, USA.
authors.forename: Anton
authors.initials: A
authors.lastname: Krumm
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Hematology, University of Washington, Seattle, Washington, USA.
authors.forename: Carl Anthony
authors.initials: CA
authors.lastname: Blau
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, USA.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Disteche
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: William S
authors.initials: WS
authors.lastname: Noble
authors.affiliation: 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Hematology, University of Washington, Seattle, Washington, USA.
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Duan
mesh_terms: D002843:Chromatin / Q000737:chemistry / Q000502:physiology* / Q000648:ultrastructure; D002874:Chromosome Mapping; D003850:Deoxyribonuclease I / Q000378:metabolism; D016678:Genome; D006801:Humans; D020014:K562 Cells; D011487:Protein Conformation; D022661:RNA, Untranslated / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional / Q000235:genetics
chemical_list: D002843:Chromatin; D022661:RNA, Untranslated; D003850:Deoxyribonuclease I