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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 355-364 |
| Number of pages | 10 |
| Journal | Nature |
| Volume | 515 |
| Issue number | 7527 |
| DOIs | |
| State | Published - Nov 20 2014 |
ASJC Scopus subject areas
- General
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A comparative encyclopedia of DNA elements in the mouse genome. / Yue, Feng; Cheng, Yong; Breschi, Alessandra; Vierstra, Jeff; Wu, Weisheng; Ryba, Tyrone; Sandstrom, Richard; Ma, Zhihai; Davis, Carrie; Pope, Benjamin D.; Shen, Yin; Pervouchine, Dmitri D.; Djebali, Sarah; Thurman, Robert E.; Kaul, Rajinder; Rynes, Eric; Kirilusha, Anthony; Marinov, Georgi K.; Williams, Brian A.; Trout, Diane; Amrhein, Henry; Fisher-Aylor, Katherine; Antoshechkin, Igor; DeSalvo, Gilberto; See, Lei Hoon; Fastuca, Meagan; Drenkow, Jorg; Zaleski, Chris; Dobin, Alex; Prieto, Pablo; Lagarde, Julien; Bussotti, Giovanni; Tanzer, Andrea; Denas, Olgert; Li, Kanwei; Bender, M. A.; Zhang, Miaohua; Byron, Rachel; Groudine, Mark T.; McCleary, David; Pham, Long; Ye, Zhen; Kuan, Samantha; Edsall, Lee; Wu, Yi Chieh; Rasmussen, Matthew D.; Bansal, Mukul S.; Kellis, Manolis; Keller, Cheryl A.; Morrissey, Christapher S.; Mishra, Tejaswini; Jain, Deepti; Dogan, Nergiz; Harris, Robert S.; Cayting, Philip; Kawli, Trupti; Boyle, Alan P.; Euskirchen, Ghia; Kundaje, Anshul; Lin, Shin; Lin, Yiing; Jansen, Camden; Malladi, Venkat S.; Cline, Melissa S.; Erickson, Drew T.; Kirkup, Vanessa M.; Learned, Katrina; Sloan, Cricket A.; Rosenbloom, Kate R.; De Sousa, Beatriz Lacerda; Beal, Kathryn; Pignatelli, Miguel; Flicek, Paul; Lian, Jin; Kahveci, Tamer; Lee, Dongwon; Kent, W. James; Santos, Miguel Ramalho; Herrero, Javier; Notredame, Cedric; Johnson, Audra; Vong, Shinny; Lee, Kristen; Bates, Daniel; Neri, Fidencio; Diegel, Morgan; Canfield, Theresa; Sabo, Peter J.; Wilken, Matthew S.; Reh, Thomas A.; Giste, Erika; Shafer, Anthony; Kutyavin, Tanya; Haugen, Eric; Dunn, Douglas; Reynolds, Alex P.; Neph, Shane; Humbert, Richard; Hansen, R. Scott; De Bruijn, Marella; Selleri, Licia; Rudensky, Alexander; Josefowicz, Steven; Samstein, Robert; Eichler, Evan E.; Orkin, Stuart H.; Levasseur, Dana; Papayannopoulou, Thalia; Chang, Kai Hsin; Skoultchi, Arthur; Gosh, Srikanta; Disteche, Christine; Treuting, Piper; Wang, Yanli; Weiss, Mitchell J.; Blobel, Gerd A.; Cao, Xiaoyi; Zhong, Sheng; Wang, Ting; Good, Peter J.; Lowdon, Rebecca F.; Adams, Leslie B.; Zhou, Xiao Qiao; Pazin, Michael J.; Feingold, Elise A.; Wold, Barbara; Taylor, James; Mortazavi, Ali; Weissman, Sherman M.; Stamatoyannopoulos, John A.; Snyder, Michael P.; Guigo, Roderic; Gingeras, Thomas R.; Gilbert, David M.; Hardison, Ross C.; Beer, Michael A.; Ren, Bing.
In: Nature, Vol. 515, No. 7527, 20.11.2014, p. 355-364.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - A comparative encyclopedia of DNA elements in the mouse genome
AU - Yue, Feng
AU - Cheng, Yong
AU - Breschi, Alessandra
AU - Vierstra, Jeff
AU - Wu, Weisheng
AU - Ryba, Tyrone
AU - Sandstrom, Richard
AU - Ma, Zhihai
AU - Davis, Carrie
AU - Pope, Benjamin D.
AU - Shen, Yin
AU - Pervouchine, Dmitri D.
AU - Djebali, Sarah
AU - Thurman, Robert E.
AU - Kaul, Rajinder
AU - Rynes, Eric
AU - Kirilusha, Anthony
AU - Marinov, Georgi K.
AU - Williams, Brian A.
AU - Trout, Diane
AU - Amrhein, Henry
AU - Fisher-Aylor, Katherine
AU - Antoshechkin, Igor
AU - DeSalvo, Gilberto
AU - See, Lei Hoon
AU - Fastuca, Meagan
AU - Drenkow, Jorg
AU - Zaleski, Chris
AU - Dobin, Alex
AU - Prieto, Pablo
AU - Lagarde, Julien
AU - Bussotti, Giovanni
AU - Tanzer, Andrea
AU - Denas, Olgert
AU - Li, Kanwei
AU - Bender, M. A.
AU - Zhang, Miaohua
AU - Byron, Rachel
AU - Groudine, Mark T.
AU - McCleary, David
AU - Pham, Long
AU - Ye, Zhen
AU - Kuan, Samantha
AU - Edsall, Lee
AU - Wu, Yi Chieh
AU - Rasmussen, Matthew D.
AU - Bansal, Mukul S.
AU - Kellis, Manolis
AU - Keller, Cheryl A.
AU - Morrissey, Christapher S.
AU - Mishra, Tejaswini
AU - Jain, Deepti
AU - Dogan, Nergiz
AU - Harris, Robert S.
AU - Cayting, Philip
AU - Kawli, Trupti
AU - Boyle, Alan P.
AU - Euskirchen, Ghia
AU - Kundaje, Anshul
AU - Lin, Shin
AU - Lin, Yiing
AU - Jansen, Camden
AU - Malladi, Venkat S.
AU - Cline, Melissa S.
AU - Erickson, Drew T.
AU - Kirkup, Vanessa M.
AU - Learned, Katrina
AU - Sloan, Cricket A.
AU - Rosenbloom, Kate R.
AU - De Sousa, Beatriz Lacerda
AU - Beal, Kathryn
AU - Pignatelli, Miguel
AU - Flicek, Paul
AU - Lian, Jin
AU - Kahveci, Tamer
AU - Lee, Dongwon
AU - Kent, W. James
AU - Santos, Miguel Ramalho
AU - Herrero, Javier
AU - Notredame, Cedric
AU - Johnson, Audra
AU - Vong, Shinny
AU - Lee, Kristen
AU - Bates, Daniel
AU - Neri, Fidencio
AU - Diegel, Morgan
AU - Canfield, Theresa
AU - Sabo, Peter J.
AU - Wilken, Matthew S.
AU - Reh, Thomas A.
AU - Giste, Erika
AU - Shafer, Anthony
AU - Kutyavin, Tanya
AU - Haugen, Eric
AU - Dunn, Douglas
AU - Reynolds, Alex P.
AU - Neph, Shane
AU - Humbert, Richard
AU - Hansen, R. Scott
AU - De Bruijn, Marella
AU - Selleri, Licia
AU - Rudensky, Alexander
AU - Josefowicz, Steven
AU - Samstein, Robert
AU - Eichler, Evan E.
AU - Orkin, Stuart H.
AU - Levasseur, Dana
AU - Papayannopoulou, Thalia
AU - Chang, Kai Hsin
AU - Skoultchi, Arthur
AU - Gosh, Srikanta
AU - Disteche, Christine
AU - Treuting, Piper
AU - Wang, Yanli
AU - Weiss, Mitchell J.
AU - Blobel, Gerd A.
AU - Cao, Xiaoyi
AU - Zhong, Sheng
AU - Wang, Ting
AU - Good, Peter J.
AU - Lowdon, Rebecca F.
AU - Adams, Leslie B.
AU - Zhou, Xiao Qiao
AU - Pazin, Michael J.
AU - Feingold, Elise A.
AU - Wold, Barbara
AU - Taylor, James
AU - Mortazavi, Ali
AU - Weissman, Sherman M.
AU - Stamatoyannopoulos, John A.
AU - Snyder, Michael P.
AU - Guigo, Roderic
AU - Gingeras, Thomas R.
AU - Gilbert, David M.
AU - Hardison, Ross C.
AU - Beer, Michael A.
AU - Ren, Bing
N1 - Funding Information: Acknowledgements 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 andR01DK065806 (R.C.H.) from the National Institutes of Health, andBIO2011-26205 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. Publisher Copyright: © 2014 Macmillan Publishers Limited. All rights reserved.
PY - 2014/11/20
Y1 - 2014/11/20
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84911462077&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84911462077&partnerID=8YFLogxK
U2 - 10.1038/nature13992
DO - 10.1038/nature13992
M3 - Article
C2 - 25409824
AN - SCOPUS:84911462077
VL - 515
SP - 355
EP - 364
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7527
ER -