Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution Journal Article
| Authors: | Vierstra, J.; Rynes, E.; Sandstrom, R.; Zhang, M.; Canfield, T.; Scott Hansen, R.; Stehling-Sun, S.; Sabo, P. J.; Byron, R.; Humbert, R.; Thurman, R. E.; Johnson, A. K.; Vong, S.; Lee, K.; Bates, D.; Neri, F.; Diegel, M.; Giste, E.; Haugen, E.; Dunn, D.; Wilken, M. S.; Josefowicz, S.; Samstein, R.; Chang, K. H.; Eichler, E. E.; De Bruijn, M.; Reh, T. A.; Skoultchi, A.; Rudensky, A.; Orkin, S. H.; Papayannopoulou, T.; Treuting, P. M.; Selleri, L.; Kaul, R.; Groudine, M.; Bender, M. A.; Stamatoyannopoulos, J. A. |
| Article Title: | Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution |
| Abstract: | To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes. |
| Keywords: | adult; unclassified drug; human cell; promoter region; exon; nonhuman; animal cell; mouse; animal tissue; embryo; embryonic stem cell; genetic association; transcription factor; cell fate; evolution; evolutionary biology; dna; molecular recognition; genome; rodent; mapping; cells and cell components; human; article; regulatory dna |
| Journal Title: | Science |
| Volume: | 346 |
| Issue: | 6212 |
| ISSN: | 0036-8075 |
| Publisher: | American Association for the Advancement of Science |
| Date Published: | 2014-11-21 |
| Start Page: | 1007 |
| End Page: | 1012 |
| Language: | English |
| DOI: | 10.1126/science.1246426 |
| PROVIDER: | scopus |
| PUBMED: | 25411453 |
| PMCID: | PMC4337786 |
| DOI/URL: | |
| Notes: | Export Date: 2 January 2015 -- Source: Scopus |
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