An integrated encyclopedia of DNA elements in the human genome

Principal investigators (steering committee); Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis); Broad Institute Group (data production and analysis); Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis); Data coordination center at UC Santa Cruz (production data coordination); Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis); Genome Institute of Singapore group (data production and analysis); HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis); Lawrence Berkeley National Laboratory group (targeted experimental validation); NHGRI groups (data production and analysis); Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis); Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis); University of Albany SUNY group (data production and analysis); University of Chicago Stanford group (data production and analysis); University of Heidelberg group (targeted experimental validation); University of Massachusetts Medical School Bioinformatics group (data production and analysis); University of Washington University of Massachusetts Medical Center group (data production and analysis); Data Analysis Center (data analysis); The ENCODE Project Consortium; Data production leads (data production); Lead analysts (data analysis); Writing Group; NHGRI project management (scientific management)

doi:10.1038/nature11247

An integrated encyclopedia of DNA elements in the human genome

Principal investigators (steering committee), Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis), Broad Institute Group (data production and analysis), Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis), Data coordination center at UC Santa Cruz (production data coordination), Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis), Genome Institute of Singapore group (data production and analysis), HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis), Lawrence Berkeley National Laboratory group (targeted experimental validation), NHGRI groups (data production and analysis), Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis), Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis), University of Albany SUNY group (data production and analysis), University of Chicago Stanford group (data production and analysis), University of Heidelberg group (targeted experimental validation), University of Massachusetts Medical School Bioinformatics group (data production and analysis), University of Washington University of Massachusetts Medical Center group (data production and analysis), Data Analysis Center (data analysis), The ENCODE Project Consortium, Data production leads (data production)Lead analysts (data analysis), Writing Group, NHGRI project management (scientific management)

Research output: Contribution to journal › Article › peer-review

12550 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 language	English
Pages (from-to)	57-74
Number of pages	18
Journal	Nature
Volume	489
Issue number	7414
DOIs	https://doi.org/10.1038/nature11247
State	Published - Sep 6 2012

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10.1038/nature11247

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Principal investigators (steering committee), Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis), Broad Institute Group (data production and analysis), Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis), Data coordination center at UC Santa Cruz (production data coordination), Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis), Genome Institute of Singapore group (data production and analysis), HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis), Lawrence Berkeley National Laboratory group (targeted experimental validation), NHGRI groups (data production and analysis), Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis), Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis), University of Albany SUNY group (data production and analysis), University of Chicago Stanford group (data production and analysis), University of Heidelberg group (targeted experimental validation), University of Massachusetts Medical School Bioinformatics group (data production and analysis), University of Washington University of Massachusetts Medical Center group (data production and analysis), Data Analysis Center (data analysis), The ENCODE Project Consortium, ... NHGRI project management (scientific management) (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74. https://doi.org/10.1038/nature11247

@article{6bc70eace61043c7a1f6609929281336,

title = "An integrated encyclopedia of DNA elements in the human genome",

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.",

author = "{Principal investigators (steering committee)} and {Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis)} and {Broad Institute Group (data production and analysis)} and {Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis)} and {Data coordination center at UC Santa Cruz (production data coordination)} and {Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis)} and {Genome Institute of Singapore group (data production and analysis)} and {HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis)} and {Lawrence Berkeley National Laboratory group (targeted experimental validation)} and {NHGRI groups (data production and analysis)} and {Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis)} and {Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis)} and {University of Albany SUNY group (data production and analysis)} and {University of Chicago Stanford group (data production and analysis)} and {University of Heidelberg group (targeted experimental validation)} and {University of Massachusetts Medical School Bioinformatics group (data production and analysis)} and {University of Washington University of Massachusetts Medical Center group (data production and analysis)} and {Data Analysis Center (data analysis)} and {The ENCODE Project Consortium} and {Data production leads (data production)} and {Lead analysts (data analysis)} and {Writing Group} and {NHGRI project management (scientific management)} and Ian Dunham and Anshul Kundaje and Aldred, {Shelley F.} and Collins, {Patrick J.} and Davis, {Carrie A.} and Francis Doyle and Epstein, {Charles B.} and Seth Frietze and Jennifer Harrow and Rajinder Kaul and Jainab Khatun and Lajoie, {Bryan R.} and Landt, {Stephen G.} and Lee, {Bum Kyu} and Florencia Pauli and Rosenbloom, {Kate R.} and Peter Sabo and Alexias Safi and Amartya Sanyal and Noam Shoresh and Simon, {Jeremy M.} and Lingyun Song and Trinklein, {Nathan D.} and Altshuler, {Robert C.} and Ewan Birney and Brown, {James B.} and Chao Cheng and Sarah Djebali and Xianjun Dong and Jason Ernst and Furey, {Terrence S.} and Mark Gerstein and Belinda Giardine and Melissa Greven and Hardison, {Ross C.} and Harris, {Robert S.} and Javier Herrero and Hoffman, {Michael M.} and Sowmya Iyer and Manolis Kellis and Pouya Kheradpour and Timo Lassmann and Qunhua Li and Xinying Lin and Marinov, {Georgi K.} and Angelika Merkel and Ali Mortazavi and Parker, {Stephen C.J.} and Reddy, {Timothy E.} and Joel Rozowsky and Felix Schlesinger and Thurman, {Robert E.} and Jie Wang and Ward, {Lucas D.} and Whitfield, {Troy W.} and Wilder, {Steven P.} and Weisheng Wu and Xi, {Hualin S.} and Yip, {Kevin Y.} and Jiali Zhuang and Bernstein, {Bradley E.} and Green, {Eric D.} and Chris Gunter and Michael Snyder and Pazin, {Michael J.} and Lowdon, {Rebecca F.} and Dillon, {Laura A.L.} and Adams, {Leslie B.} and Kelly, {Caroline J.} and Julia Zhang and Wexler, {Judith R.} and Good, {Peter J.} and Feingold, {Elise A.} and Crawford, {Gregory E.} and Job Dekker and Laura Elnitski and Farnham, {Peggy J.} and Giddings, {Morgan C.} and Gingeras, {Thomas R.} and Roderic Guig{\'o} and Hubbard, {Timothy J.} and Kent, {W. James} and Lieb, {Jason D.} and Margulies, {Elliott H.} and Myers, {Richard M.} and Stamatoyannopoulos, {John A.} and Tenenbaum, {Scott A.} and Zhiping Weng and White, {Kevin P.} and Barbara Wold and Yanbao Yu and John Wrobel and Risk, {Brian A.} and Gunawardena, {Harsha P.} and Kuiper, {Heather C.} and Maier, {Christopher W.} and Ling Xie and Xian Chen and Mikkelsen, {Tarjei S.} and Shawn Gillespie and Alon Goren and Oren Ram and Xiaolan Zhang and Li Wang and Robbyn Issner and Coyne, {Michael J.} and Timothy Durham and Manching Ku and Thanh Truong and Eaton, {Matthew L.} and Alex Dobin and Andrea Tanzer and Julien Lagarde and Wei Lin and Chenghai Xue and Williams, {Brian A.} and Chris Zaleski and Maik R{\"o}der and Felix Kokocinski and Abdelhamid, {Rehab F.} and Tyler Alioto and Igor Antoshechkin and Baer, {Michael T.} and Philippe Batut and Ian Bell and Kimberly Bell and Sudipto Chakrabortty and Jacqueline Chrast and Joao Curado and Thomas Derrien and Jorg Drenkow and Erica Dumais and Jackie Dumais and Radha Duttagupta and Megan Fastuca and Kata Fejes-Toth and Pedro Ferreira and Sylvain Foissac and Fullwood, {Melissa J.} and Hui Gao and David Gonzalez and Assaf Gordon and C{\'e}dric Howald and Sonali Jha and Rory Johnson and Philipp Kapranov and Brandon King and Colin Kingswood and Guoliang Li and Luo, {Oscar J.} and Eddie Park and Preall, {Jonathan B.} and Kimberly Presaud and Paolo Ribeca and Daniel Robyr and Xiaoan Ruan and Michael Sammeth and Sandhu, {Kuljeet Singh} and Lorain Schaeffer and See, {Lei Hoon} and Atif Shahab and Jorgen Skancke and Suzuki, {Ana Maria} and Hazuki Takahashi and Hagen Tilgner and Diane Trout and Nathalie Walters and Huaien Wang and Yoshihide Hayashizaki and Alexandre Reymond and Antonarakis, {Stylianos E.} and Hannon, {Gregory J.} and Yijun Ruan and Piero Carninci and Sloan, {Cricket A.} and Katrina Learned and Malladi, {Venkat S.} and Wong, {Matthew C.} and Barber, {Galt P.} and Cline, {Melissa S.} and Dreszer, {Timothy R.} and Heitner, {Steven G.} and Donna Karolchik and Kirkup, {Vanessa M.} and Meyer, {Laurence R.} and Long, {Jeffrey C.} and Morgan Maddren and Raney, {Brian J.} and Grasfeder, {Linda L.} and Giresi, {Paul G.} and Anna Battenhouse and Sheffield, {Nathan C.} and Showers, {Kimberly A.} and Darin London and Bhinge, {Akshay A.} and Christopher Shestak and Schaner, {Matthew R.} and Kim, {Seul Ki} and Bowling, {Kevin M.} and Michael Brent",

note = "Funding Information: Acknowledgements We thank additional members of our laboratories and institutions who have contributed to the experimental and analytical components of this project. We thank D. Leja for assistance with production of the figures. The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein); U01HG004695 (E. Birney); U54HG004563 (G. E. Crawford); U54HG004557 (T. R. Gingeras); U54HG004555 (T. J. Hubbard); U41HG004568 (W. J. Kent); U54HG004576 (R. M. Myers); U54HG004558 (M. Snyder); U54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker); RC2HG005591 and R01HG003700 (M. C. Giddings); R01HG004456-03 (Y. Ruan); U01HG004571 (S. A. Tenenbaum); U01HG004561 (Z. Weng); RC2HG005679 (K. P. White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541,U01HG004561,RC2HG005679and R01HG003988(L.Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (L. Elnitski, ZIAHG200323; E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.",

year = "2012",

month = sep,

day = "6",

doi = "10.1038/nature11247",

language = "English",

volume = "489",

pages = "57--74",

journal = "Nature",

issn = "0028-0836",

number = "7414",

}

Principal investigators (steering committee), Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis), Broad Institute Group (data production and analysis), Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis), Data coordination center at UC Santa Cruz (production data coordination), Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis), Genome Institute of Singapore group (data production and analysis), HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis), Lawrence Berkeley National Laboratory group (targeted experimental validation), NHGRI groups (data production and analysis), Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis), Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis), University of Albany SUNY group (data production and analysis), University of Chicago Stanford group (data production and analysis), University of Heidelberg group (targeted experimental validation), University of Massachusetts Medical School Bioinformatics group (data production and analysis), University of Washington University of Massachusetts Medical Center group (data production and analysis), Data Analysis Center (data analysis), The ENCODE Project Consortium, Data production leads (data production), Lead analysts (data analysis), Writing Group & NHGRI project management (scientific management) 2012, 'An integrated encyclopedia of DNA elements in the human genome', Nature, vol. 489, no. 7414, pp. 57-74. https://doi.org/10.1038/nature11247

An integrated encyclopedia of DNA elements in the human genome. / Principal investigators (steering committee); Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis); Broad Institute Group (data production and analysis) et al.
In: Nature, Vol. 489, No. 7414, 06.09.2012, p. 57-74.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - An integrated encyclopedia of DNA elements in the human genome

AU - Principal investigators (steering committee)

AU - Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis)

AU - Broad Institute Group (data production and analysis)

AU - Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis)

AU - Data coordination center at UC Santa Cruz (production data coordination)

AU - Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis)

AU - Genome Institute of Singapore group (data production and analysis)

AU - HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis)

AU - Lawrence Berkeley National Laboratory group (targeted experimental validation)

AU - NHGRI groups (data production and analysis)

AU - Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis)

AU - Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis)

AU - University of Albany SUNY group (data production and analysis)

AU - University of Chicago Stanford group (data production and analysis)

AU - University of Heidelberg group (targeted experimental validation)

AU - University of Massachusetts Medical School Bioinformatics group (data production and analysis)

AU - University of Washington University of Massachusetts Medical Center group (data production and analysis)

AU - Data Analysis Center (data analysis)

AU - The ENCODE Project Consortium

AU - Data production leads (data production)

AU - Lead analysts (data analysis)

AU - Writing Group

AU - NHGRI project management (scientific management)

AU - Dunham, Ian

AU - Kundaje, Anshul

AU - Aldred, Shelley F.

AU - Collins, Patrick J.

AU - Davis, Carrie A.

AU - Doyle, Francis

AU - Epstein, Charles B.

AU - Frietze, Seth

AU - Harrow, Jennifer

AU - Kaul, Rajinder

AU - Khatun, Jainab

AU - Lajoie, Bryan R.

AU - Landt, Stephen G.

AU - Lee, Bum Kyu

AU - Pauli, Florencia

AU - Rosenbloom, Kate R.

AU - Sabo, Peter

AU - Safi, Alexias

AU - Sanyal, Amartya

AU - Shoresh, Noam

AU - Simon, Jeremy M.

AU - Song, Lingyun

AU - Trinklein, Nathan D.

AU - Altshuler, Robert C.

AU - Birney, Ewan

AU - Brown, James B.

AU - Cheng, Chao

AU - Djebali, Sarah

AU - Dong, Xianjun

AU - Ernst, Jason

AU - Furey, Terrence S.

AU - Gerstein, Mark

AU - Giardine, Belinda

AU - Greven, Melissa

AU - Hardison, Ross C.

AU - Harris, Robert S.

AU - Herrero, Javier

AU - Hoffman, Michael M.

AU - Iyer, Sowmya

AU - Kellis, Manolis

AU - Kheradpour, Pouya

AU - Lassmann, Timo

AU - Li, Qunhua

AU - Lin, Xinying

AU - Marinov, Georgi K.

AU - Merkel, Angelika

AU - Mortazavi, Ali

AU - Parker, Stephen C.J.

AU - Reddy, Timothy E.

AU - Rozowsky, Joel

AU - Schlesinger, Felix

AU - Thurman, Robert E.

AU - Wang, Jie

AU - Ward, Lucas D.

AU - Whitfield, Troy W.

AU - Wilder, Steven P.

AU - Wu, Weisheng

AU - Xi, Hualin S.

AU - Yip, Kevin Y.

AU - Zhuang, Jiali

AU - Bernstein, Bradley E.

AU - Green, Eric D.

AU - Gunter, Chris

AU - Snyder, Michael

AU - Pazin, Michael J.

AU - Lowdon, Rebecca F.

AU - Dillon, Laura A.L.

AU - Adams, Leslie B.

AU - Kelly, Caroline J.

AU - Zhang, Julia

AU - Wexler, Judith R.

AU - Good, Peter J.

AU - Feingold, Elise A.

AU - Crawford, Gregory E.

AU - Dekker, Job

AU - Elnitski, Laura

AU - Farnham, Peggy J.

AU - Giddings, Morgan C.

AU - Gingeras, Thomas R.

AU - Guigó, Roderic

AU - Hubbard, Timothy J.

AU - Kent, W. James

AU - Lieb, Jason D.

AU - Margulies, Elliott H.

AU - Myers, Richard M.

AU - Stamatoyannopoulos, John A.

AU - Tenenbaum, Scott A.

AU - Weng, Zhiping

AU - White, Kevin P.

AU - Wold, Barbara

AU - Yu, Yanbao

AU - Wrobel, John

AU - Risk, Brian A.

AU - Gunawardena, Harsha P.

AU - Kuiper, Heather C.

AU - Maier, Christopher W.

AU - Xie, Ling

AU - Chen, Xian

AU - Mikkelsen, Tarjei S.

AU - Gillespie, Shawn

AU - Goren, Alon

AU - Ram, Oren

AU - Zhang, Xiaolan

AU - Wang, Li

AU - Issner, Robbyn

AU - Coyne, Michael J.

AU - Durham, Timothy

AU - Ku, Manching

AU - Truong, Thanh

AU - Eaton, Matthew L.

AU - Dobin, Alex

AU - Tanzer, Andrea

AU - Lagarde, Julien

AU - Lin, Wei

AU - Xue, Chenghai

AU - Williams, Brian A.

AU - Zaleski, Chris

AU - Röder, Maik

AU - Kokocinski, Felix

AU - Abdelhamid, Rehab F.

AU - Alioto, Tyler

AU - Antoshechkin, Igor

AU - Baer, Michael T.

AU - Batut, Philippe

AU - Bell, Ian

AU - Bell, Kimberly

AU - Chakrabortty, Sudipto

AU - Chrast, Jacqueline

AU - Curado, Joao

AU - Derrien, Thomas

AU - Drenkow, Jorg

AU - Dumais, Erica

AU - Dumais, Jackie

AU - Duttagupta, Radha

AU - Fastuca, Megan

AU - Fejes-Toth, Kata

AU - Ferreira, Pedro

AU - Foissac, Sylvain

AU - Fullwood, Melissa J.

AU - Gao, Hui

AU - Gonzalez, David

AU - Gordon, Assaf

AU - Howald, Cédric

AU - Jha, Sonali

AU - Johnson, Rory

AU - Kapranov, Philipp

AU - King, Brandon

AU - Kingswood, Colin

AU - Li, Guoliang

AU - Luo, Oscar J.

AU - Park, Eddie

AU - Preall, Jonathan B.

AU - Presaud, Kimberly

AU - Ribeca, Paolo

AU - Robyr, Daniel

AU - Ruan, Xiaoan

AU - Sammeth, Michael

AU - Sandhu, Kuljeet Singh

AU - Schaeffer, Lorain

AU - See, Lei Hoon

AU - Shahab, Atif

AU - Skancke, Jorgen

AU - Suzuki, Ana Maria

AU - Takahashi, Hazuki

AU - Tilgner, Hagen

AU - Trout, Diane

AU - Walters, Nathalie

AU - Wang, Huaien

AU - Hayashizaki, Yoshihide

AU - Reymond, Alexandre

AU - Antonarakis, Stylianos E.

AU - Hannon, Gregory J.

AU - Ruan, Yijun

AU - Carninci, Piero

AU - Sloan, Cricket A.

AU - Learned, Katrina

AU - Malladi, Venkat S.

AU - Wong, Matthew C.

AU - Barber, Galt P.

AU - Cline, Melissa S.

AU - Dreszer, Timothy R.

AU - Heitner, Steven G.

AU - Karolchik, Donna

AU - Kirkup, Vanessa M.

AU - Meyer, Laurence R.

AU - Long, Jeffrey C.

AU - Maddren, Morgan

AU - Raney, Brian J.

AU - Grasfeder, Linda L.

AU - Giresi, Paul G.

AU - Battenhouse, Anna

AU - Sheffield, Nathan C.

AU - Showers, Kimberly A.

AU - London, Darin

AU - Bhinge, Akshay A.

AU - Shestak, Christopher

AU - Schaner, Matthew R.

AU - Kim, Seul Ki

AU - Bowling, Kevin M.

AU - Brent, Michael

N1 - Funding Information: Acknowledgements We thank additional members of our laboratories and institutions who have contributed to the experimental and analytical components of this project. We thank D. Leja for assistance with production of the figures. The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein); U01HG004695 (E. Birney); U54HG004563 (G. E. Crawford); U54HG004557 (T. R. Gingeras); U54HG004555 (T. J. Hubbard); U41HG004568 (W. J. Kent); U54HG004576 (R. M. Myers); U54HG004558 (M. Snyder); U54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker); RC2HG005591 and R01HG003700 (M. C. Giddings); R01HG004456-03 (Y. Ruan); U01HG004571 (S. A. Tenenbaum); U01HG004561 (Z. Weng); RC2HG005679 (K. P. White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541,U01HG004561,RC2HG005679and R01HG003988(L.Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (L. Elnitski, ZIAHG200323; E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.

PY - 2012/9/6

Y1 - 2012/9/6

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84865790047&partnerID=8YFLogxK

U2 - 10.1038/nature11247

DO - 10.1038/nature11247

M3 - Article

C2 - 22955616

AN - SCOPUS:84865790047

SN - 0028-0836

VL - 489

SP - 57

EP - 74

JO - Nature

JF - Nature

IS - 7414

ER -

Principal investigators (steering committee), Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis), Broad Institute Group (data production and analysis), Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis), Data coordination center at UC Santa Cruz (production data coordination), Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis) et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247

An integrated encyclopedia of DNA elements in the human genome

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