• Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Tyrone Ryba, Richard Sandstrom, Zhihai Ma, Carrie Davis, Benjamin D Pope, Yin Shen, Dmitri D Pervouchine, Sarah Djebali, Robert E Thurman, Rajinder Kaul, Eric Rynes, Anthony Kirilusha, Georgi K Marinov, Brian A Williams, Diane Trout, Henry Amrhein, Katherine Fisher-Aylor, Igor Antoshechkin, Gilberto DeSalvo, Lei-Hoon See, Meagan Fastuca, Jorg Drenkow, Chris Zaleski, Alex Dobin, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer, Olgert Denas, Kanwei Li, M A Bender, Miaohua Zhang, Rachel Byron, Mark T Groudine, David McCleary, Long Pham, Zhen Ye, Samantha Kuan, Lee Edsall, Yi-Chieh Wu, Matthew D Rasmussen, Mukul S Bansal, Manolis Kellis, Cheryl A Keller, Christapher S Morrissey, Tejaswini Mishra, Deepti Jain, Nergiz Dogan, Robert S Harris, Philip Cayting, Trupti Kawli, Alan P Boyle, Ghia Euskirchen, Anshul Kundaje, Shin Lin, Yiing Lin, Camden Jansen, Venkat S Malladi, Melissa S Cline, Drew T Erickson, Vanessa M Kirkup, Katrina Learned, Cricket A Sloan, Kate R Rosenbloom, Beatriz Lacerda de Sousa, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian, Tamer Kahveci, Dongwon Lee, W James Kent, Miguel Ramalho Santos, Javier Herrero, Cedric Notredame, Audra Johnson, Shinny Vong, Kristen Lee, Daniel Bates, Fidencio Neri, Morgan Diegel, Theresa Canfield, Peter J Sabo, Matthew S Wilken, Thomas A Reh, Erika Giste, Anthony Shafer, Tanya Kutyavin, Eric Haugen, Douglas Dunn, Alex P Reynolds, Shane Neph, Richard Humbert, R Scott Hansen, Marella De Bruijn, Licia Selleri, Alexander Rudensky, Steven Josefowicz, Robert Samstein, Evan E Eichler, Stuart H Orkin, Dana Levasseur, Thalia Papayannopoulou, Kai-Hsin Chang, Arthur Skoultchi, Srikanta Gosh, Christine Disteche, Piper Treuting, Yanli Wang, Mitchell J Weiss, Gerd A Blobel, Xiaoyi Cao, Sheng Zhong, Ting Wang, Peter J Good, Rebecca F Lowdon, Leslie B Adams, Xiao-Qiao Zhou, Michael J Pazin, Elise A Feingold, Barbara Wold, James Taylor, Ali Mortazavi, Sherman M Weissman, John A Stamatoyannopoulos, Michael P Snyder, Roderic Guigo, Thomas R Gingeras, David M Gilbert, Ross C Hardison, Michael A Beer, Bing Ren, and Mouse ENCODE Consortium.
• 1] Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA.
• Nature. 2014 Nov 20;515(7527):355-64.

AbstractThe 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.

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