Occupancy maps of 208 chromatin-associated proteins in one human cell type.

Autor: Partridge EC; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA., Chhetri SB; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MA, USA., Prokop JW; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA., Ramaker RC; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA., Jansen CS; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA., Goh ST; Division of Biology, California Institute of Technology, Pasadena, CA, USA., Mackiewicz M; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA., Newberry KM; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA., Brandsmeier LA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA., Meadows SK; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA., Messer CL; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA., Hardigan AA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA., Coppola CJ; Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA., Dean EC; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA., Jiang S; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA., Savic D; Pharmaceutical Sciences Department, St Jude Children's Research Hospital, Memphis, TN, USA., Mortazavi A; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA., Wold BJ; Division of Biology, California Institute of Technology, Pasadena, CA, USA., Myers RM; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. rmyers@hudsonalpha.org., Mendenhall EM; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. eric.mendenhall@uah.edu.; Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA. eric.mendenhall@uah.edu.
Jazyk: angličtina
Zdroj: Nature [Nature] 2020 Jul; Vol. 583 (7818), pp. 720-728. Date of Electronic Publication: 2020 Jul 29.
DOI: 10.1038/s41586-020-2023-4
Abstrakt: Transcription factors are DNA-binding proteins that have key roles in gene regulation 1,2 . Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes 3-6 . However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiments using the human HepG2 cell line for 208 chromatin-associated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP-seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium.
Databáze: MEDLINE
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