Conservation of trans-acting circuitry during mammalian regulatory evolution
作者： Andrew B. Stergachis , Shane Neph , Richard Sandstrom , Eric Haugen , Alex P. Reynolds
DOI: 10.1038/NATURE13972
关键词: Computational biology 、 Genome 、 Genetics 、 Body plan 、 Transcription factor 、 Human genome 、 DNase-I Footprinting 、 ENCODE 、 Trans-acting 、 Gene 、 Biology
摘要: The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject evolutionary constraint. To quantify cis- versus trans-acting contributions regulatory we performed genomic DNase I footprinting mouse across 25 cell tissue types, collectively defining ∼8.6 million transcription factor (TF) occupancy sites at nucleotide resolution. Here show that TF footprints conjointly encode lexicon is ∼95% similar with derived from footprints. However, ∼20% orthologues. Despite substantial turnover cis-regulatory landscape, nearly half all pairwise interactions connecting genes maintained in orthologous types through innovation recognition sequences. Furthermore, higher-level organization TF-to-TF connections into cellular network architectures identical human. Our results indicate selection on gene regulation targeted chiefly level trans-regulatory circuitry, enabling potentiating plasticity.
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sci-hub.se 参考文章(41)
J.A. Stamatoyannopoulos, A. Goodwin, T. Joyce, C.H. Lowrey, NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region. The EMBO Journal. ,vol. 14, pp. 106- 116 ,(1995) , 10.1002/J.1460-2075.1995.TB06980.X
Rudolf A. Raff, The Shape of Life: Genes, Development, and the Evolution of Animal Form ,(1996)
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot, Kavita Garg, Sam John, Richard Sandstrom, Daniel Bates, Lisa Boatman, Theresa K Canfield, Morgan Diegel, Douglas Dunn, Abigail K Ebersol, Tristan Frum, Erika Giste, Audra K Johnson, Ericka M Johnson, Tanya Kutyavin, Bryan Lajoie, Bum-Kyu Lee, Kristen Lee, Darin London, Dimitra Lotakis, Shane Neph, Fidencio Neri, Eric D Nguyen, Hongzhu Qu, Alex P Reynolds, Vaughn Roach, Alexias Safi, Minerva E Sanchez, Amartya Sanyal, Anthony Shafer, Jeremy M Simon, Lingyun Song, Shinny Vong, Molly Weaver, Yongqi Yan, Zhancheng Zhang, Zhuzhu Zhang, Boris Lenhard, Muneesh Tewari, Michael O Dorschner, R Scott Hansen, Patrick A Navas, George Stamatoyannopoulos, Vishwanath R Iyer, Jason D Lieb, Shamil R Sunyaev, Joshua M Akey, Peter J Sabo, Rajinder Kaul, Terrence S Furey, Job Dekker, Gregory E Crawford, John A Stamatoyannopoulos, None, The accessible chromatin landscape of the human genome Nature. ,vol. 489, pp. 75- 82 ,(2012) , 10.1038/NATURE11232
Shannon Fisher, Elizabeth A Grice, Ryan M Vinton, Seneca L Bessling, Andrew S McCallion, Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science. ,vol. 312, pp. 276- 279 ,(2006) , 10.1126/SCIENCE.1124070
Myong-Hee Sung, Michael J. Guertin, Songjoon Baek, Gordon L. Hager, DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence Molecular Cell. ,vol. 56, pp. 275- 285 ,(2014) , 10.1016/J.MOLCEL.2014.08.016
Robert M Samstein, Aaron Arvey, Steven Z Josefowicz, Xiao Peng, Alex Reynolds, Richard Sandstrom, Shane Neph, Peter Sabo, Jeong M Kim, Will Liao, Ming O Li, Christina Leslie, John A Stamatoyannopoulos, Alexander Y Rudensky, None, Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification Cell. ,vol. 151, pp. 153- 166 ,(2012) , 10.1016/J.CELL.2012.06.053
R. Drmanac, A. B. Sparks, M. J. Callow, A. L. Halpern, N. L. Burns, B. G. Kermani, P. Carnevali, I. Nazarenko, G. B. Nilsen, G. Yeung, F. Dahl, A. Fernandez, B. Staker, K. P. Pant, J. Baccash, A. P. Borcherding, A. Brownley, R. Cedeno, L. Chen, D. Chernikoff, A. Cheung, R. Chirita, B. Curson, J. C. Ebert, C. R. Hacker, R. Hartlage, B. Hauser, S. Huang, Y. Jiang, V. Karpinchyk, M. Koenig, C. Kong, T. Landers, C. Le, J. Liu, C. E. McBride, M. Morenzoni, R. E. Morey, K. Mutch, H. Perazich, K. Perry, B. A. Peters, J. Peterson, C. L. Pethiyagoda, K. Pothuraju, C. Richter, A. M. Rosenbaum, S. Roy, J. Shafto, U. Sharanhovich, K. W. Shannon, C. G. Sheppy, M. Sun, J. V. Thakuria, A. Tran, D. Vu, A. W. Zaranek, X. Wu, S. Drmanac, A. R. Oliphant, W. C. Banyai, B. Martin, D. G. Ballinger, G. M. Church, C. A. Reid, Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays Science. ,vol. 327, pp. 78- 81 ,(2010) , 10.1126/SCIENCE.1181498
Camilla Looman, Magnus Åbrink, Charlotta Mark, Lars Hellman, KRAB Zinc Finger Proteins: An Analysis of the Molecular Mechanisms Governing Their Increase in Numbers and Complexity During Evolution Molecular Biology and Evolution. ,vol. 19, pp. 2118- 2130 ,(2002) , 10.1093/OXFORDJOURNALS.MOLBEV.A004037
A. Lazarovici, T. Zhou, A. Shafer, A. C. Dantas Machado, T. R. Riley, R. Sandstrom, P. J. Sabo, Y. Lu, R. Rohs, J. A. Stamatoyannopoulos, H. J. Bussemaker, Probing DNA shape and methylation state on a genomic scale with DNase I Proceedings of the National Academy of Sciences of the United States of America. ,vol. 110, pp. 6376- 6381 ,(2013) , 10.1073/PNAS.1216822110
Edgar Wingender, Peter Dietze, Holger Karas, Rainer Knüppel, TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research. ,vol. 24, pp. 238- 241 ,(1996) , 10.1093/NAR/24.1.238