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, MA 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, James W 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, Scott R 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, and Bing Ren. 2014. “
A comparative encyclopedia of DNA elements in the mouse genome.” Nature, 515, 7527, Pp. 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.
Benjamin D Pope and David M Gilbert. 2014. “
Genetics: Up and down in Down's syndrome.” Nature, 508, 7496, Pp. 323-4.
Benjamin D Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue, Weisheng Wu, Olgert Denas, Daniel L Vera, Yanli Wang, Scott R Hansen, Theresa K Canfield, Robert E Thurman, Yong Cheng, Günhan Gülsoy, Jonathan H Dennis, Michael P Snyder, John A Stamatoyannopoulos, James Taylor, Ross C Hardison, Tamer Kahveci, Bing Ren, and David M Gilbert. 2014. “
Topologically associating domains are stable units of replication-timing regulation.” Nature, 515, 7527, Pp. 402-5.
AbstractEukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.