Principles of regulatory information conservation between mouse and human

Cheng, Yong; Ma, Zhihai; Kim, Bong-Hyun; Wu, Weisheng; Cayting, Philip; Boyle, Alan P.; Sundaram, Vasavi; Xing, Xiaoyun; Dogan, Nergiz; Li, Jingjing; Euskirchen, Ghia; Lin, Shin; Lin, Yiing; Visel, Axel; Kawli, Trupti; Yang, Xinqiong; Patacsil, Dorrelyn; Keller, Cheryl A.; Giardine, Belinda; Kundaje, Anshul; Wang, Ting; Pennacchio, Len A.; Weng, Zhiping; Hardison, Ross C.; Snyder, Michael P.

doi:10.1038/nature13985

Title: Principles of regulatory information conservation between mouse and human

Journal Article · Wed Nov 19 00:00:00 EST 2014 · Nature (London)

DOI:https://doi.org/10.1038/nature13985· OSTI ID:1257363

Cheng, Yong ^[1]; Ma, Zhihai ^[1]; Kim, Bong-Hyun ^[2]; Wu, Weisheng ^[3]; Cayting, Philip ^[1]; Boyle, Alan P. ^[1]; Sundaram, Vasavi ^[4]; Xing, Xiaoyun ^[4]; Dogan, Nergiz ^[5]; Li, Jingjing ^[1]; Euskirchen, Ghia ^[1]; Lin, Shin ^[1]; Lin, Yiing ^[6]; Visel, Axel ^[7]; Kawli, Trupti ^[1]; Yang, Xinqiong ^[1]; Patacsil, Dorrelyn ^[1]; Keller, Cheryl A. ^[5]; Giardine, Belinda ^[5]; Kundaje, Anshul ^[1] more »

Stanford Univ., Stanford, CA (United States)
Univ. of Massachusetts Medical School, Worcester, MA (United States)
Pennsylvania State Univ., University Park, PA (United States); Univ. of Michigan, Ann Arbor, MI (United States)
Washington Univ. School of Medicine, St. Louis, MO (United States)
Pennsylvania State Univ., University Park, PA (United States)
Stanford Univ., Stanford, CA (United States); Washington Univ. School of Medicine, St. Louis, MO (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); DOE Joint Genome Institute, Walnut Creek, CA (United States); Univ. of California, Merced, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); DOE Joint Genome Institute, Walnut Creek, CA (United States)

To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human–mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here we deduce several evolutionary principles of gene regulatory features operating since the mouse and human lineages diverged. The genomic distribution profiles, primary binding motifs, chromatin states, and DNA methylation preferences are well conserved for TF-occupied sequences. However, the extent to which orthologous DNA segments are bound by orthologous TFs varies both among TFs and with genomic location: binding at promoters is more highly conserved than binding at distal elements. Notably, occupancy-conserved TF-occupied sequences tend to be pleiotropic; they function in several tissues and also co-associate with many TFs. Lastly, single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE

Contributing Organization:: The Mouse ENCODE Consortium

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1257363

Journal Information:: Nature (London), Vol. 515, Issue 7527; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 188 works

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Genome-Wide Identification of Target Genes for the Key B Cell Transcription Factor Ets1 Saelee, Prontip; Kearly, Alyssa; Nutt, Stephen L. Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.00383	journal	April 2017
Implications of Epigenetic Variability within a Cell Population for “Cell Type” Classification Tabansky, Inna; Stern, Joel N. H.; Pfaff, Donald W. Frontiers in Behavioral Neuroscience, Vol. 9 https://doi.org/10.3389/fnbeh.2015.00342	journal	December 2015
Genetic and epigenetic variation in the lineage specification of regulatory T cells Arvey, Aaron; van der Veeken, Joris; Plitas, George eLife, Vol. 4 https://doi.org/10.7554/elife.07571	journal	October 2015
Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity Khoueiry, Pierre; Girardot, Charles; Ciglar, Lucia eLife, Vol. 6 https://doi.org/10.7554/elife.28440	journal	August 2017

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