An integrated encyclopedia of DNA elements in the human genome

An integrated encyclopedia of DNA elements in the human genome 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nature Springer Journals

An integrated encyclopedia of DNA elements in the human genome

Dunham, Ian; Kundaje, Anshul; Aldred, Shelley F.; Collins, Patrick J.; Davis, Carrie A.; Doyle, Francis; Epstein, Charles B.; Frietze, Seth; Harrow, Jennifer; Kaul, Rajinder; Khatun, Jainab; Lajoie, Bryan R.; Landt, Stephen G.; Lee, Bum-Kyu; Pauli, Florencia; Rosenbloom, Kate R.; Sabo, Peter; Safi, Alexias; Sanyal, Amartya; Shoresh, Noam; Simon, Jeremy M.; Song, Lingyun; Trinklein, Nathan D.; Altshuler, Robert C.; Brown, James B.; Cheng, Chao; Djebali, Sarah; Dong, Xianjun; Dunham, Ian; Ernst, Jason; Furey, Terrence S.; Gerstein, Mark; Giardine, Belinda; Greven, Melissa; Hardison, Ross C.; Harris, Robert S.; Herrero, Javier; Hoffman, Michael M.; Iyer, Sowmya; Kellis, Manolis; Khatun, Jainab; Kheradpour, Pouya; Kundaje, Anshul; Lassmann, Timo; Li, Qunhua; Lin, Xinying; Marinov, Georgi K.; Merkel, Angelika; Mortazavi, Ali; Parker, Stephen C. 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James; Lieb, Jason D.; Margulies, Elliott H.; Myers, Richard M.; Snyder, Michael; Stamatoyannopoulos, John A.; Tenenbaum, Scott A.; Weng, Zhiping; White, Kevin P.; Wold, Barbara; Khatun, Jainab; Yu, Yanbao; Wrobel, John; Risk, Brian A.; Gunawardena, Harsha P.; Kuiper, Heather C.; Maier, Christopher W.; Xie, Ling; Chen, Xian; Giddings, Morgan C.; Bernstein, Bradley E.; Epstein, Charles B.; Shoresh, Noam; Ernst, Jason; Kheradpour, Pouya; Mikkelsen, Tarjei S.; Gillespie, Shawn; Goren, Alon; Ram, Oren; Zhang, Xiaolan; Wang, Li; Issner, Robbyn; Coyne, Michael J.; Durham, Timothy; Ku, Manching; Truong, Thanh; Ward, Lucas D.; Altshuler, Robert C.; Eaton, Matthew L.; Kellis, Manolis; Djebali, Sarah; Davis, Carrie A.; Merkel, Angelika; Dobin, Alex; Lassmann, Timo; Mortazavi, Ali; Tanzer, Andrea; Lagarde, Julien; Lin, Wei; Schlesinger, Felix; Xue, Chenghai; Marinov, Georgi K.; Khatun, Jainab; Williams, Brian A.; Zaleski, Chris; Rozowsky, Joel; Röder, Maik; Kokocinski, Felix; Abdelhamid, Rehab F.; Alioto, Tyler; Antoshechkin, Igor; Baer, Michael T.; Batut, Philippe; Bell, Ian; Bell, Kimberly; Chakrabortty, Sudipto; Chen, Xian; Chrast, Jacqueline; Curado, Joao; Derrien, Thomas; Drenkow, Jorg; Dumais, Erica; Dumais, Jackie; Duttagupta, Radha; Fastuca, Megan; Fejes-Toth, Kata; Ferreira, Pedro; Foissac, Sylvain; Fullwood, Melissa J.; Gao, Hui; Gonzalez, David; Gordon, Assaf; Gunawardena, Harsha P.; Howald, Cédric; Jha, Sonali; Johnson, Rory; Kapranov, Philipp; King, Brandon; Kingswood, Colin; Li, Guoliang; Luo, Oscar J.; Park, Eddie; Preall, Jonathan B.; Presaud, Kimberly; Ribeca, Paolo; Risk, Brian A.; Robyr, Daniel; Ruan, Xiaoan; Sammeth, Michael; Sandhu, Kuljeet Singh; Schaeffer, Lorain; See, Lei-Hoon; Shahab, Atif; Skancke, Jorgen; Suzuki, Ana Maria; Takahashi, Hazuki; Tilgner, Hagen; Trout, Diane; Walters, Nathalie; Wang, Huaien; Wrobel, John; Yu, Yanbao; Hayashizaki, Yoshihide; Harrow, Jennifer; Gerstein, Mark; Hubbard, Timothy J.; Reymond, Alexandre; Antonarakis, Stylianos E.; Hannon, Gregory J.; Giddings, Morgan C.; Ruan, Yijun; Wold, Barbara; Carninci, Piero; Guigó Roderic; Gingeras, Thomas R.; Rosenbloom, Kate R.; Sloan, Cricket A.; Learned, Katrina; Malladi, Venkat S.; Wong, Matthew C.; Barber, Galt P.; Cline, Melissa S.; Dreszer, Timothy R.; Heitner, Steven G.; Karolchik, Donna; Kent, W. 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Scott; Levy, Shawn E.; Absher, Devin M.; Mortazavi, Ali; Wong, Wing H.; Wold, Barbara; Blow, Matthew J.; Visel, Axel; Pennachio, Len A.; Elnitski, Laura; Margulies, Elliott H.; Parker, Stephen C. J.; Petrykowska, Hanna M.; Abyzov, Alexej; Aken, Bronwen; Barrell, Daniel; Barson, Gemma; Berry, Andrew; Bignell, Alexandra; Boychenko, Veronika; Bussotti, Giovanni; Chrast, Jacqueline; Davidson, Claire; Derrien, Thomas; Despacio-Reyes, Gloria; Diekhans, Mark; Ezkurdia, Iakes; Frankish, Adam; Gilbert, James; Gonzalez, Jose Manuel; Griffiths, Ed; Harte, Rachel; Hendrix, David A.; Howald, Cédric; Hunt, Toby; Jungreis, Irwin; Kay, Mike; Khurana, Ekta; Kokocinski, Felix; Leng, Jing; Lin, Michael F.; Loveland, Jane; Lu, Zhi; Manthravadi, Deepa; Mariotti, Marco; Mudge, Jonathan; Mukherjee, Gaurab; Notredame, Cedric; Pei, Baikang; Rodriguez, Jose Manuel; Saunders, Gary; Sboner, Andrea; Searle, Stephen; Sisu, Cristina; Snow, Catherine; Steward, Charlie; Tanzer, Andrea; Tapanari, Electra; Tress, Michael L.; van Baren, Marijke J.; Walters, Nathalie; Washietl, Stefan; Wilming, Laurens; Zadissa, Amonida; Zhang, Zhengdong; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Gerstein, Mark; Reymond, Alexandre; Guigó Roderic; Harrow, Jennifer; Hubbard, Timothy J.; Landt, Stephen G.; Frietze, Seth; Abyzov, Alexej; Addleman, Nick; Alexander, Roger P.; Auerbach, Raymond K.; Balasubramanian, Suganthi; Bettinger, Keith; Bhardwaj, Nitin; Boyle, Alan P.; Cao, Alina R.; Cayting, Philip; Charos, Alexandra; Cheng, Yong; Cheng, Chao; Eastman, Catharine; Euskirchen, Ghia; Fleming, Joseph D.; Grubert, Fabian; Habegger, Lukas; Hariharan, Manoj; Harmanci, Arif; Iyengar, Sushma; Jin, Victor X.; Karczewski, Konrad J.; Kasowski, Maya; Lacroute, Phil; Lam, Hugo; Lamarre-Vincent, Nathan; Leng, Jing; Lian, Jin; Lindahl-Allen, Marianne; Min, Renqiang; Miotto, Benoit; Monahan, Hannah; Moqtaderi, Zarmik; Mu, Xinmeng J.; O’Geen, Henriette; Ouyang, Zhengqing; Patacsil, Dorrelyn; Pei, Baikang; Raha, Debasish; Ramirez, Lucia; Reed, Brian; Rozowsky, Joel; Sboner, Andrea; Shi, Minyi; Sisu, Cristina; Slifer, Teri; Witt, Heather; Wu, Linfeng; Xu, Xiaoqin; Yan, Koon-Kiu; Yang, Xinqiong; Yip, Kevin Y.; Zhang, Zhengdong; Struhl, Kevin; Weissman, Sherman M.; Gerstein, Mark; Farnham, Peggy J.; Snyder, Michael; Tenenbaum, Scott A.; Penalva, Luiz O.; Doyle, Francis; Karmakar, Subhradip; Landt, Stephen G.; Bhanvadia, Raj R.; Choudhury, Alina; Domanus, Marc; Ma, Lijia; Moran, Jennifer; Patacsil, Dorrelyn; Slifer, Teri; Victorsen, Alec; Yang, Xinqiong; Snyder, Michael; White, Kevin P.; Auer, Thomas; Centanin, Lazaro; Eichenlaub, Michael; Gruhl, Franziska; Heermann, Stephan; Hoeckendorf, Burkhard; Inoue, Daigo; Kellner, Tanja; Kirchmaier, Stephan; Mueller, Claudia; Reinhardt, Robert; Schertel, Lea; Schneider, Stephanie; Sinn, Rebecca; Wittbrodt, Beate; Wittbrodt, Jochen; Weng, Zhiping; Whitfield, Troy W.; Wang, Jie; Collins, Patrick J.; Aldred, Shelley F.; Trinklein, Nathan D.; Partridge, E. 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Scott; Boatman, Lisa; Haugen, Eric; Humbert, Richard; Jain, Gaurav; Johnson, Audra K.; Johnson, Ericka M.; Kutyavin, Tattyana V.; Lajoie, Bryan R.; Lee, Kristen; Lotakis, Dimitra; Maurano, Matthew T.; Neph, Shane J.; Neri, Fiedencio V.; Nguyen, Eric D.; Qu, Hongzhu; Reynolds, Alex P.; Roach, Vaughn; Rynes, Eric; Sabo, Peter; Sanchez, Minerva E.; Sandstrom, Richard S.; Sanyal, Amartya; Shafer, Anthony O.; Stergachis, Andrew B.; Thomas, Sean; Thurman, Robert E.; Vernot, Benjamin; Vierstra, Jeff; Vong, Shinny; Wang, Hao; Weaver, Molly A.; Yan, Yongqi; Zhang, Miaohua; Akey, Joshua M.; Bender, Michael; Dorschner, Michael O.; Groudine, Mark; MacCoss, Michael J.; Navas, Patrick; Stamatoyannopoulos, George; Kaul, Rajinder; Dekker, Job; Stamatoyannopoulos, John A.; Dunham, Ian; Beal, Kathryn; Brazma, Alvis; Flicek, Paul; Herrero, Javier; Johnson, Nathan; Keefe, Damian; Lukk, Margus; Luscombe, Nicholas M.; Sobral, Daniel; Vaquerizas, Juan M.; Wilder, Steven P.; Batzoglou, Serafim; Sidow, Arend; Hussami, Nadine; Kyriazopoulou-Panagiotopoulou, Sofia; Libbrecht, Max W.; Schaub, Marc A.; Kundaje, Anshul; Hardison, Ross C.; Miller, Webb; Giardine, Belinda; Harris, Robert S.; Wu, Weisheng; Bickel, Peter J.; Banfai, Balazs; Boley, Nathan P.; Brown, James B.; Huang, Haiyan; Li, Qunhua; Li, Jingyi Jessica; Noble, William Stafford; Bilmes, Jeffrey A.; Buske, Orion J.; Hoffman, Michael M.; Sahu, Avinash D.; Kharchenko, Peter V.; Park, Peter J.; Baker, Dannon; Taylor, James; Weng, Zhiping; Iyer, Sowmya; Dong, Xianjun; Greven, Melissa; Lin, Xinying; Wang, Jie; Xi, Hualin S.; Zhuang, Jiali; Gerstein, Mark; Alexander, Roger P.; Balasubramanian, Suganthi; Cheng, Chao; Harmanci, Arif; Lochovsky, Lucas; Min, Renqiang; Mu, Xinmeng J.; Rozowsky, Joel; Yan, Koon-Kiu; Yip, Kevin Y.; Birney, Ewan; Birney, Ewan; Birney, Ewan; Birney, Ewan; Birney, Ewan
Nature, Volume 489 (7414) – Sep 5, 2012

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Publisher
Springer Journals
Copyright
Copyright © 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
ISSN
0028-0836
eISSN
1476-4687
DOI
10.1038/nature11247
Publisher site
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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.

Journal

NatureSpringer Journals

Published: Sep 5, 2012

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