A comparative encyclopedia of DNA elements in the mouse genome

• Type of Material: Article
• Authors: Feng Yue, Ludwig Institute for Cancer Research; Yong Cheng, Stanford University; Alessandra Breschi, Center for Genomic Regulation, Barcelona, Catalunya, Spain; Jeff Vierstra, University of Washington; Weisheng Wu, Pennsylvania State University; Tyrone Ryba, Florida State University; Richard Sandstrom, University of Washington; Zhihai Ma, Stanford University; Robert Harris, Emory University; Bing Ren, Emory University
• Language: English
• Date: 2014-11-20
• Publisher: Nature Publishing Group
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2014 Macmillan Publishers Limited. All rights reserved.
• Final Published Version (URL): http://dx.doi.org/10.1038/nature13992
• Title of Journal or Parent Work: Nature
• Volume: 515
• Issue: 7527
• Start Page: 355
• End Page: +
• Grant/Funding Information: BIO2011-26205 from the Spanish Plan Nacional; KB, MP, JH and PF acknowledge the Wellcome Trust (grant number 095908), the NHGRI (grant number U01HG004695) and the European Molecular Biology Laboratory; J.V. is supported by a National Science Foundation Graduate Research Fellowship under grant no. DGE-071824.; Grants R01HG003991 (B.R.), 1U54HG007004 (T.R.G.), 3RC2HG005602 (M.P.S), GM083337 and GM085354 (D.M.G), F31CA165863(BDP), RC2HG005573 and R01DK065806 (R.C.H.) from the National Institutes of Health; ERC 294653 (to R.G.); S.L. was supported by grants F32HL110473 and K99HL119617; L.S. is supported by R01HD043997-09
• Keywords: GENE; PERVASIVE TRANSCRIPTION; TRANSPOSABLE ELEMENTS; EXPRESSION; Science & Technology; TRANSCRIPTION FACTOR-BINDING; EVOLUTIONARY DYNAMICS; EMBRYONIC STEM-CELLS; LANDSCAPE; CHROMATIN INTERACTIONS; Multidisciplinary Sciences; Science & Technology - Other Topics; ENCODE DATA
• Research Categories: Health Sciences, Oncology; Biology, Genetics

Abstract

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.