NDLI: Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

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Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Ma, Wenxiu Ay, Ferhat Lee, Choli Gulsoy, Gunhan Deng, Xinxian Cook, Savannah Hesson, Jennifer Cavanaugh, Christopher Ware, Carol B. Krumm, Anton Shendure, Jay Blau, Carl Anthony Disteche, Christine M. Noble, William S. Duan, Zhijun
Description	Country affiliation: United States Author Affiliation: Ma W ( Department of Genome Sciences, University of Washington, Seattle, Washington, USA.); Ay F ( Department of Genome Sciences, University of Washington, Seattle, Washington, USA.); Lee C ( Department of Genome Sciences, University of Washington, Seattle, Washington, USA.); Gulsoy G ( Department of Genome Sciences, University of Washington, Seattle, Washington, USA.); Deng X ( Department of Pathology, University of Washington, Seattle, Washington, USA.); Cook S ( 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.); Hesson J ( 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.); Cavanaugh C ( 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.); Ware CB ( 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.); Krumm A ( Department of Radiation Oncology, University of Washington, Seattle, Washington, USA.); Shendure J ( Department of Genome Sciences, University of Washington, Seattle, Washington, USA.); Blau CA ( 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Hematology, University of Washington, Seattle, Washington, USA.); Disteche CM ( Department of Pathology, University of Washington, Seattle, Washington, USA.); Noble WS ( Department of Genome Sciences, University of Washington, Seattle, Washington, USA.); Duan Z ( 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Hematology, University of Washington, Seattle, Washington, USA.)
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.
File Format	HTM / HTML
ISSN	15487091
e-ISSN	15487105
DOI	10.1038/nmeth.3205
Journal	Nature Methods
Issue Number	1
Volume Number	12
Language	English
Publisher	Nature Publishing Group
Publisher Date	2015-01-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Clinical Laboratory Techniques Chromatin Physiology Rna, Untranslated Genetics Chemistry Ultrastructure Chromosome Mapping Deoxyribonuclease I Metabolism Genome K562 Cells Protein Conformation Regulatory Elements, Transcriptional Research Support, N.i.h., Extramural Validation Studies
Content Type	Text
Resource Type	Article
Subject	Cell Biology Biochemistry Molecular Biology Biotechnology

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