Title |
Principles of regulatory information conservation between mouse and human
|
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Published in |
Nature, November 2014
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DOI | 10.1038/nature13985 |
Pubmed ID | |
Authors |
Yong Cheng, Zhihai Ma, Bong-Hyun Kim, Weisheng Wu, Philip Cayting, Alan P. Boyle, Vasavi Sundaram, Xiaoyun Xing, Nergiz Dogan, Jingjing Li, Ghia Euskirchen, Shin Lin, Yiing Lin, Axel Visel, Trupti Kawli, Xinqiong Yang, Dorrelyn Patacsil, Cheryl A. Keller, Belinda Giardine, The Mouse ENCODE Consortium, Anshul Kundaje, Ting Wang, Len A. Pennacchio, Zhiping Weng, Ross C. Hardison, Michael P. Snyder |
Abstract |
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. Single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 4 | 20% |
Canada | 1 | 5% |
France | 1 | 5% |
Germany | 1 | 5% |
New Zealand | 1 | 5% |
Italy | 1 | 5% |
Unknown | 11 | 55% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 14 | 70% |
Scientists | 4 | 20% |
Science communicators (journalists, bloggers, editors) | 2 | 10% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 16 | 2% |
France | 5 | <1% |
Spain | 5 | <1% |
Germany | 4 | <1% |
United Kingdom | 3 | <1% |
Korea, Republic of | 2 | <1% |
China | 2 | <1% |
Brazil | 1 | <1% |
Sweden | 1 | <1% |
Other | 9 | 1% |
Unknown | 610 | 93% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 178 | 27% |
Student > Ph. D. Student | 165 | 25% |
Student > Bachelor | 51 | 8% |
Student > Master | 46 | 7% |
Professor | 39 | 6% |
Other | 111 | 17% |
Unknown | 68 | 10% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 278 | 42% |
Biochemistry, Genetics and Molecular Biology | 163 | 25% |
Medicine and Dentistry | 39 | 6% |
Computer Science | 24 | 4% |
Neuroscience | 16 | 2% |
Other | 62 | 9% |
Unknown | 76 | 12% |