An integrated encyclopedia of DNA elements in the human genome

Ian Correction Dunham, Anshul Kundaje, Shelley F. Aldred, Patrick J. Collins, Carrie A. Davis, Francis Doyle, Charles B. Epstein, Seth Frietze, Jennifer Harrow, Rajinder Kaul, Jainab Khatun, Bryan R. Lajoie, Stephen G. Landt, Bum Kyu Lee, Florencia Pauli, Kate R. Rosenbloom, Peter Sabo, Alexias Safi, Amartya Sanyal, Noam ShoreshJeremy M. Simon, Lingyun Song, Nathan D. Trinklein, Robert C. Altshuler, Ewan Birney, James B. Brown, Chao Cheng, Sarah Djebali, Xianjun Dong, Jason Ernst, Terrence S. Furey, Mark Gerstein, Belinda Giardine, Melissa Greven, Ross C. Hardison, Robert S. Harris, Javier Herrero, Michael M. Hoffman, Sowmya Iyer, Manolis Kellis, Pouya Kheradpour, Timo Lassmann, Qunhua Li, Xinying Lin, Georgi K. Marinov, Angelika Merkel, Ali Mortazavi, Stephen C J Parker, Timothy E. Reddy, Joel Rozowsky, Felix Schlesinger, Robert E. Thurman, Jie Wang, Lucas D. Ward, Troy W. Whitfield, Steven P. Wilder, Weisheng Wu, Hualin S. Xi, Kevin Y. Yip, Jiali Zhuang, Bradley E. Bernstein, Eric D. Green, Chris Gunter, Michael Snyder, Michael J. Pazin, Rebecca F. Lowdon, Laura A L Dillon, Leslie B. Adams, Caroline J. Kelly, Julia Zhang, Judith R. Wexler, Peter J. Good, Elise A. Feingold, Gregory E. Crawford, Job Dekker, Laura Elnitski, Peggy J. Farnham, Morgan C. Giddings, Thomas R. Gingeras, Roderic Guigó, Timothy J. Hubbard, W. James Kent, Jason D. Lieb, Elliott H. Margulies, Richard M. Myers, John A. Stamatoyannopoulos, Scott A. Tenenbaum, Zhiping Weng, Kevin P. White, Barbara Wold, Yanbao Yu, John Wrobel, Brian A. Risk, Harsha P. Gunawardena, Heather C. Kuiper, Christopher W. Maier, Ling Xie, Xian Chen, Tarjei S. Mikkelsen, Shawn Gillespie, Alon Goren, Oren Ram, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael J. Coyne, Timothy Durham, Manching Ku, Thanh Truong, Matthew L. Eaton, Alex Dobin, Andrea Tanzer, Julien Lagarde, Wei Lin, Chenghai Xue, Brian A. Williams, Chris Zaleski, Maik Röder, Felix Kokocinski, Rehab F. Abdelhamid, Tyler Alioto, Igor Antoshechkin, Michael T. Baer, Philippe Batut, Ian Bell, Kimberly Bell, Sudipto Chakrabortty, Jacqueline Chrast, Joao Curado, Thomas Derrien, Jorg Drenkow, Erica Dumais, Jackie Dumais, Radha Duttagupta, Megan Fastuca, Kata Fejes-Toth, Pedro Ferreira, Sylvain Foissac, Melissa J. Fullwood, Hui Gao, David Gonzalez, Assaf Gordon, Cédric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Guoliang Li, Oscar J. Luo, Eddie Park, Jonathan B. Preall, Kimberly Presaud, Paolo Ribeca, Daniel Robyr, Xiaoan Ruan, Michael Sammeth, Kuljeet Singh Sandhu, Lorain Schaeffer, Lei Hoon See, Atif Shahab, Jorgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, Yoshihide Hayashizaki, Alexandre Reymond, Stylianos E. Antonarakis, Gregory J. Hannon, Yijun Ruan, Piero Carninci, Cricket A. Sloan, Katrina Learned, Venkat S. Malladi, Matthew C. Wong, Galt P. Barber, Melissa S. Cline, Timothy R. Dreszer, Steven G. Heitner, Donna Karolchik, Vanessa M. Kirkup, Laurence R. Meyer, Jeffrey C. Long, Morgan Maddren, Brian J. Raney, Linda L. Grasfeder, Paul G. Giresi, Anna Battenhouse, Nathan C. Sheffield, Kimberly A. Showers, Darin London, Akshay A. Bhinge, Christopher Shestak, Matthew R. Schaner, Seul Ki Kim, Zhuzhu Z. Zhang, Piotr A. Mieczkowski, Joanna O. Mieczkowska, Zheng Liu, Ryan M. McDaniell, Yunyun Ni, Naim U. Rashid, Min Jae Kim, Sheera Adar, Zhancheng Zhang, Tianyuan Wang, Deborah Winter, Damian Keefe, Vishwanath R. Iyer, Meizhen Zheng, Ping Wang, Jason Gertz, Jost Vielmetter, E. Christopher Partridge, Katherine E. Varley, Clarke Gasper, Anita Bansal, Shirley Pepke, Preti Jain, Henry Amrhein, Kevin M. Bowling, Michael Anaya, Marie K. Cross, Michael A. Muratet, Kimberly M. Newberry, Kenneth McCue, Amy S. Nesmith, Katherine I. Fisher-Aylor, Barbara Pusey, Gilberto DeSalvo, Stephanie L. Parker, Sreeram Balasubramanian, Nicholas S. Davis, Sarah K. Meadows, Tracy Eggleston, J. Scott Newberry, Shawn E. Levy, Devin M. Absher, Wing H. Wong, Matthew J. Blow, Axel Visel, Len A. Pennachio, Hanna M. Petrykowska, Alexej Abyzov, Bronwen Aken, Daniel Barrell, Gemma Barson, Andrew Berry, Alexandra Bignell, Veronika Boychenko, Giovanni Bussotti, Claire Davidson, Gloria Despacio-Reyes, Mark Diekhans, Iakes Ezkurdia, Adam Frankish, James Gilbert, Jose Manuel Gonzalez, Ed Griffiths, Rachel Harte, David A. Hendrix, Toby Hunt, Irwin Jungreis, Mike Kay, Ekta Khurana, Jing Leng, Michael F. Lin, Jane Loveland, Zhi Lu, Deepa Manthravadi, Marco Mariotti, Jonathan Mudge, Gaurab Mukherjee, Cedric Notredame, Baikang Pei, Jose Manuel Rodriguez, Gary Saunders, Andrea Sboner, Stephen Searle, Cristina Sisu, Catherine Snow, Charlie Steward, Electra Tapanari, Michael L. Tress, Marijke J. Van Baren, Stefan Washietl, Laurens Wilming, Amonida Zadissa, Zhengdong Zhang, Michael Brent, David Haussler, Alfonso Valencia, Nick Addleman, Roger P. Alexander, Raymond K. Auerbach, Suganthi Balasubramanian, Keith Bettinger, Nitin Bhardwaj, Alan P. Boyle, Alina R. Cao, Philip Cayting, Alexandra Charos, Yong Cheng, Catharine Eastman, Ghia Euskirchen, Joseph D. Fleming, Fabian Grubert, Lukas Habegger, Manoj Hariharan, Arif Harmanci, Sushma Iyengar, Victor X. Jin, Konrad J. Karczewski, Maya Kasowski, Phil Lacroute, Hugo Lam, Nathan Lamarre-Vincent, Jin Lian, Marianne Lindahl-Allen, Renqiang Min, Benoit Miotto, Hannah Monahan, Zarmik Moqtaderi, Xinmeng J. Mu, Henriette O'Geen, Zhengqing Ouyang, Dorrelyn Patacsil, Debasish Raha, Lucia Ramirez, Brian Reed, Minyi Shi, Teri Slifer, Heather Witt, Linfeng Wu, Xiaoqin Xu, Koon Kiu Yan, Xinqiong Yang, Kevin Struhl, Sherman M. Weissman, Luiz O. Penalva, Subhradip Karmakar, Raj R. Bhanvadia, Alina Choudhury, Marc Domanus, Lijia Ma, Jennifer Moran, Alec Victorsen, Thomas Auer, Lazaro Centanin, Michael Eichenlaub, Franziska Gruhl, Stephan Heermann, Burkhard Hoeckendorf, Daigo Inoue, Tanja Kellner, Stephan Kirchmaier, Claudia Mueller, Robert Reinhardt, Lea Schertel, Stephanie Schneider, Rebecca Sinn, Beate Wittbrodt, Jochen Wittbrodt, Gaurav Jain, Gayathri Balasundaram, Daniel L. Bates, Rachel Byron, Theresa K. Canfield, Morgan J. Diegel, Douglas Dunn, Abigail K. Ebersol, Tristan Frum, Kavita Garg, Erica Gist, R. Scott Hansen, Lisa Boatman, Eric Haugen, Richard Humbert, Audra K. Johnson, Ericka M. Johnson, Tattyana V. Kutyavin, Kristen Lee, Dimitra Lotakis, Matthew T. Maurano, Shane J. Neph, Fiedencio V. Neri, Eric D. Nguyen, Hongzhu Qu, Alex P. Reynolds, Vaughn Roach, Eric Rynes, Minerva E. Sanchez, Richard S. Sandstrom, Anthony O. Shafer, Andrew B. Stergachis, Sean Thomas, Benjamin Vernot, Jeff Vierstra, Shinny Vong, Hao Wang, Molly A. Weaver, Yongqi Yan, Miaohua Zhang, Joshua M. Akey, Michael Bender, Michael O. Dorschner, Mark Groudine, Michael J. MacCoss, Patrick Navas, George Stamatoyannopoulos, Kathryn Beal, Alvis Brazma, Paul Flicek, Nathan Johnson, Margus Lukk, Nicholas M. Luscombe, Daniel Sobral, Juan M. Vaquerizas, Serafim Batzoglou, Arend Sidow, Nadine Hussami, Sofia Kyriazopoulou-Panagiotopoulou, Max W. Libbrecht, Marc A. Schaub, Webb Miller, Peter J. Bickel, Balazs Banfai, Nathan P. Boley, Haiyan Huang, Jingyi Jessica Li, William Stafford Noble, Jeffrey A. Bilmes, Orion J. Buske, Avinash D. Sahu, Peter V. Kharchenko, Peter J. Park, Dannon Baker, James Taylor, Lucas Lochovsky

Research output: Contribution to journalArticle

8191 Scopus citations

Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Original languageEnglish (US)
Pages (from-to)57-74
Number of pages18
JournalNature
Volume489
Issue number7414
DOIs
StatePublished - Sep 6 2012
Externally publishedYes

ASJC Scopus subject areas

  • General

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    Correction Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C. A., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., Sanyal, A., ... Lochovsky, L. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74. https://doi.org/10.1038/nature11247