A comparative encyclopedia of DNA elements in the mouse genome
| Autor: | Ting Wang, Matthew D. Rasmussen, Dana N. Levasseur, Thomas A. Reh, Fidencio Neri, Tanya Kutyavin, Peter J. Good, Katrina Learned, Kate R. Rosenbloom, Lei Hoon See, Cedric Notredame, Ross C. Hardison, Chris Zaleski, Gerd A. Blobel, Dmitri D. Pervouchine, Shane Neph, Ali Mortazavi, Tamer Kahveci, Arthur I. Skoultchi, Peter J. Sabo, Jorg Drenkow, Alex Reynolds, Rebecca F. Lowdon, Marella F. T. R. de Bruijn, John A. Stamatoyannopoulos, Yin Shen, Richard Humbert, Anthony Kirilusha, Sherman M. Weissman, Roderic Guigó, James Taylor, Paul Flicek, Kristen Lee, Shinny Vong, Xiaoyi Cao, Douglas Dunn, Alessandra Breschi, Elise A. Feingold, Michael A. Beer, Piper M. Treuting, Igor Antoshechkin, Thomas R. Gingeras, Georgi K. Marinov, Tyrone Ryba, Jin Lian, Christine M. Disteche, Javier Herrero, Eric Rynes, Sheng Zhong, Weisheng Wu, Richard Sandstrom, Gilberto DeSalvo, Michael Snyder, Meagan Fastuca, Miguel Pignatelli, Mark Groudine, Sarah Djebali, Nergiz Dogan, Rajinder Kaul, Giovanni Bussotti, Henry Amrhein, Daniel Bates, Matthew S. Wilken, Alexander Dobin, Manolis Kellis, Licia Selleri, Diane Trout, Morgan Diegel, David M. Gilbert, Zhihai Ma, Jeff Vierstra, Xiao Qiao Zhou, Theresa K. Canfield, Venkat S. Malladi, Zhen Ye, Anthony Shafer, Tejaswini Mishra, Yiing Lin, Samantha Kuan, Anshul Kundaje, Thalia Papayannopoulou, Pablo Prieto, Robert E. Thurman, Long Pham, Cricket A. Sloan, Olgert Denas, Kathryn Beal, Erika Giste, Andrea Tanzer, Katherine I. Fisher-Aylor, Shin Lin, M. A. Bender, Stuart H. Orkin, Carrie A. Davis, Benjamin D. Pope, Rachel Byron, Srikanta Gosh, Beatriz Lacerda de Sousa, R. Scott Hansen, Brian A. Williams, Yong Cheng, Kanwei Li, Dongwon Lee, Yanli Wang, Evan E. Eichler, Camden Jansen, Feng Yue, Deepti Jain, Miaohua Zhang, David McCleary, W. James Kent, Melissa S. Cline, Kai Hsin Chang, Leslie B. Adams, Robert S. Harris, Ghia Euskirchen, Christapher S. Morrissey, Alexander Y. Rudensky, Philip Cayting, Drew T. Erickson, Eric Haugen, Michael J. Pazin, Vanessa M. Kirkup, Yi-Chieh Wu, Trupti Kawli, Mukul S. Bansal, Cheryl A. Keller, Lee Edsall, Robert M. Samstein, Bing Ren, Miguel Santos, Steven Z. Josefowicz, Barbara J. Wold, Julien Lagarde, Alan P. Boyle, Mitchell J. Weiss, Audra K. Johnson |
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| Přispěvatelé: | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Wu, Yi-Chieh, Rasmussen, Matthew D., Bansal, Mukul S., Kellis, Manolis |
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Epigenomics
DNA Replication Biology Regulatory Sequences Nucleic Acid ENCODE Genome Article Mice Species Specificity Animals Deoxyribonuclease I Humans Cell Lineage Gene Regulatory Networks Scaffold/matrix attachment region Gene ChIA-PET Conserved Sequence Genetics Multidisciplinary Mouse genome Molecular Sequence Annotation Genomics Chromatin Gene Expression Regulation RNA Human genome Transcriptome Genome-Wide Association Study Transcription Factors |
| Zdroj: | PMC Nature Recercat. Dipósit de la Recerca de Catalunya instname |
| Popis: | 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. This work is funded by grants R01HG003991 (B.R.), 1U54HG007004 (T.R.G.), 3RC2HG005602 (M.P.S.), GM083337 and GM085354 (D.M.G.), F31CA165863 (B.D.P.), RC2HG005573 and R01DK065806 (R.C.H.) from the National Institutes of Health, and BIO2011-26205 from the Spanish Plan Nacional and ERC 294653 (to R.G.). J.V. is supported by a National Science Foundation Graduate Research Fellowship under grant no. DGE-071824. K.B., M.P., J.H. and P.F. acknowledge the Wellcome Trust (grant number 095908), the NHGRI (grant number U01HG004695) and the European Molecular Biology Laboratory. We thank G. Hon for helping the analysis of high-throughput enhancer validation. L.S. is supported by R01HD043997-09. S.L. was supported by grants F32HL110473 and K99HL119617. |
| Databáze: | OpenAIRE |
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