Abstract
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 799-816 |
| Number of pages | 18 |
| Journal | Nature |
| Volume | 447 |
| Issue number | 7146 |
| DOIs | |
| State | Published - Jun 14 2007 |
| Externally published | Yes |
ASJC Scopus subject areas
- General
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In: Nature, Vol. 447, No. 7146, 14.06.2007, p. 799-816.
Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
AU - Birney, Ewan
AU - Stamatoyannopoulos, John A.
AU - Dutta, Anindya
AU - Guigó, Roderic
AU - Gingeras, Thomas R.
AU - Margulies, Elliott H.
AU - Weng, Zhiping
AU - Snyder, Michael
AU - Dermitzakis, Emmanouil T.
AU - Thurman, Robert E.
AU - Kuehn, Michael S.
AU - Taylor, Christopher M.
AU - Neph, Shane
AU - Koch, Christoph M.
AU - Asthana, Saurabh
AU - Malhotra, Ankit
AU - Adzhubei, Ivan
AU - Greenbaum, Jason A.
AU - Andrews, Robert M.
AU - Flicek, Paul
AU - Boyle, Patrick J.
AU - Cao, Hua
AU - Carter, Nigel P.
AU - Clelland, Gayle K.
AU - Davis, Sean
AU - Day, Nathan
AU - Dhami, Pawandeep
AU - Dillon, Shane C.
AU - Dorschner, Michael O.
AU - Fiegler, Heike
AU - Giresi, Paul G.
AU - Goldy, Jeff
AU - Hawrylycz, Michael
AU - Haydock, Andrew
AU - Humbert, Richard
AU - James, Keith D.
AU - Johnson, Brett E.
AU - Johnson, Ericka M.
AU - Frum, Tristan T.
AU - Rosenzweig, Elizabeth R.
AU - Karnani, Neerja
AU - Lee, Kirsten
AU - Lefebvre, Gregory C.
AU - Navas, Patrick A.
AU - Neri, Fidencio
AU - Parker, Stephen C.J.
AU - Sabo, Peter J.
AU - Sandstrom, Richard
AU - Shafer, Anthony
AU - Vetrie, David
AU - Weaver, Molly
AU - Wilcox, Sarah
AU - Yu, Man
AU - Collins, Francis S.
AU - Dekker, Job
AU - Lieb, Jason D.
AU - Tullius, Thomas D.
AU - Crawford, Gregory E.
AU - Sunyaev, Shamil
AU - Noble, William S.
AU - Dunham, Ian
AU - Denoeud, France
AU - Reymond, Alexandre
AU - Kapranov, Philipp
AU - Rozowsky, Joel
AU - Zheng, Deyou
AU - Castelo, Robert
AU - Frankish, Adam
AU - Harrow, Jennifer
AU - Ghosh, Srinka
AU - Sandelin, Albin
AU - Hofacker, Ivo L.
AU - Baertsch, Robert
AU - Keefe, Damian
AU - Dike, Sujit
AU - Cheng, Jill
AU - Hirsch, Heather A.
AU - Sekinger, Edward A.
AU - Lagarde, Julien
AU - Abril, Josep F.
AU - Shahab, Atif
AU - Flamm, Christoph
AU - Fried, Claudia
AU - Hackermüller, Jörg
AU - Hertel, Jana
AU - Lindemeyer, Manja
AU - Missal, Kristin
AU - Tanzer, Andrea
AU - Washietl, Stefan
AU - Korbel, Jan
AU - Emanuelsson, Olof
AU - Pedersen, Jakob S.
AU - Holroyd, Nancy
AU - Taylor, Ruth
AU - Swarbreck, David
AU - Matthews, Nicholas
AU - Dickson, Mark C.
AU - Thomas, Daryl J.
AU - Weirauch, Matthew T.
AU - Gilbert, James
AU - Drenkow, Jorg
AU - Bell, Ian
AU - Zhao, Xiaodong
AU - Srinivasan, K. G.
AU - Sung, Wing Kin
AU - Ooi, Hong Sain
AU - Chiu, Kuo Ping
AU - Foissac, Sylvain
AU - Alioto, Tyler
AU - Brent, Michael
AU - Pachter, Lior
AU - Tress, Michael L.
AU - Valencia, Alfonso
AU - Choo, Siew Woh
AU - Choo, Chiou Yu
AU - Ucla, Catherine
AU - Manzano, Caroline
AU - Wyss, Carine
AU - Cheung, Evelyn
AU - Clark, Taane G.
AU - Brown, James B.
AU - Ganesh, Madhavan
AU - Patel, Sandeep
AU - Tammana, Hari
AU - Chrast, Jacqueline
AU - Henrichsen, Charlotte N.
AU - Kai, Chikatoshi
AU - Kawai, Jun
AU - Nagalakshmi, Ugrappa
AU - Wu, Jiaqian
AU - Lian, Zheng
AU - Lian, Jin
AU - Newburger, Peter
AU - Zhang, Xueqing
AU - Bickel, Peter
AU - Mattick, John S.
AU - Carninci, Piero
AU - Hayashizaki, Yoshihide
AU - Weissman, Sherman
AU - Hubbard, Tim
AU - Myers, Richard M.
AU - Rogers, Jane
AU - Stadler, Peter F.
AU - Lowe, Todd M.
AU - Wei, Chia Lin
AU - Ruan, Yijun
AU - Struhl, Kevin
AU - Gerstein, Mark
AU - Antonarakis, Stylianos E.
AU - Fu, Yutao
AU - Green, Eric D.
AU - Karaöz, Ulaş
AU - Siepel, Adam
AU - Taylor, James
AU - Liefer, Laura A.
AU - Wetterstrand, Kris A.
AU - Good, Peter J.
AU - Feingold, Elise A.
AU - Guyer, Mark S.
AU - Cooper, Gregory M.
AU - Asimenos, George
AU - Dewey, Colin N.
AU - Hou, Minmei
AU - Nikolaev, Sergey
AU - Montoya-Burgos, Juan I.
AU - Löytynoja, Ari
AU - Whelan, Simon
AU - Pardi, Fabio
AU - Massingham, Tim
AU - Huang, Haiyan
AU - Zhang, Nancy R.
AU - Holmes, Ian
AU - Mullikin, James C.
AU - Ureta-Vidal, Abel
AU - Paten, Benedict
AU - Seringhaus, Michael
AU - Church, Deanna
AU - Rosenbloom, Kate
AU - Kent, W. James
AU - Stone, Eric A.
AU - Batzoglou, Serafim
AU - Goldman, Nick
AU - Hardison, Ross C.
AU - Haussler, David
AU - Miller, Webb
AU - Sidow, Arend
AU - Trinklein, Nathan D.
AU - Zhang, Zhengdong D.
AU - Barrera, Leah
AU - Stuart, Rhona
AU - King, David C.
AU - Ameur, Adam
AU - Enroth, Stefan
AU - Bieda, Mark C.
AU - Kim, Jonghwan
AU - Bhinge, Akshay A.
AU - Jiang, Nan
AU - Liu, Jun
AU - Yao, Fei
AU - Vega, Vinsensius B.
AU - Lee, Charlie W.H.
AU - Ng, Patrick
AU - Yang, Annie
AU - Moqtaderi, Zarmik
AU - Zhu, Zhou
AU - Xu, Xiaoqin
AU - Squazzo, Sharon
AU - Oberley, Matthew J.
AU - Inman, David
AU - Singer, Michael A.
AU - Richmond, Todd A.
AU - Munn, Kyle J.
AU - Rada-Iglesias, Alvaro
AU - Wallerman, Ola
AU - Komorowski, Jan
AU - Fowler, Joanna C.
AU - Couttet, Phillippe
AU - Bruce, Alexander W.
AU - Dovey, Oliver M.
AU - Ellis, Peter D.
AU - Langford, Cordelia F.
AU - Nix, David A.
AU - Euskirchen, Ghia
AU - Hartman, Stephen
AU - Urban, Alexander E.
AU - Kraus, Peter
AU - Van Calcar, Sara
AU - Heintzman, Nate
AU - Hoon Kim, Tae
AU - Wang, Kun
AU - Qu, Chunxu
AU - Hon, Gary
AU - Luna, Rosa
AU - Glass, Christopher K.
AU - Rosenfeld, M. Geoff
AU - Aldred, Shelley Force
AU - Cooper, Sara J.
AU - Halees, Anason
AU - Lin, Jane M.
AU - Shulha, Hennady P.
AU - Zhang, Xiaoling
AU - Xu, Mousheng
AU - Haidar, Jaafar N.S.
AU - Yu, Yong
AU - Iyer, Vishwanath R.
AU - Green, Roland D.
AU - Wadelius, Claes
AU - Farnham, Peggy J.
AU - Ren, Bing
AU - Harte, Rachel A.
AU - Hinrichs, Angie S.
AU - Trumbower, Heather
AU - Clawson, Hiram
AU - Hillman-Jackson, Jennifer
AU - Zweig, Ann S.
AU - Smith, Kayla
AU - Thakkapallayil, Archana
AU - Barber, Galt
AU - Kuhn, Robert M.
AU - Karolchik, Donna
AU - Armengol, Lluis
AU - Bird, Christine P.
AU - De Bakker, Paul I.W.
AU - Kern, Andrew D.
AU - Lopez-Bigas, Nuria
AU - Martin, Joel D.
AU - Stranger, Barbara E.
AU - Woodroffe, Abigail
AU - Davydov, Eugene
AU - Dimas, Antigone
AU - Eyras, Eduardo
AU - Hallgrímsdóttir, Ingileif B.
AU - Huppert, Julian
AU - Zody, Michael C.
AU - Abecasis, Gonçalo R.
AU - Estivill, Xavier
AU - Bouffard, Gerard G.
AU - Guan, Xiaobin
AU - Hansen, Nancy F.
AU - Idol, Jacquelyn R.
AU - Maduro, Valerie V.B.
AU - Maskeri, Baishali
AU - McDowell, Jennifer C.
AU - Park, Morgan
AU - Thomas, Pamela J.
AU - Young, Alice C.
AU - Blakesley, Robert W.
AU - Muzny, Donna M.
AU - Sodergren, Erica
AU - Wheeler, David A.
AU - Worley, Kim C.
AU - Jiang, Huaiyang
AU - Weinstock, George M.
AU - Gibbs, Richard A.
AU - Graves, Tina
AU - Fulton, Robert
AU - Mardis, Elaine R.
AU - Wilson, Richard K.
AU - Clamp, Michele
AU - Cuff, James
AU - Gnerre, Sante
AU - Jaffe, David B.
AU - Chang, Jean L.
AU - Lindblad-Toh, Kerstin
AU - Lander, Eric S.
AU - Koriabine, Maxim
AU - Nefedov, Mikhail
AU - Osoegawa, Kazutoyo
AU - Yoshinaga, Yuko
AU - Zhu, Baoli
AU - De Jong, Pieter J.
N1 - Funding Information: Acknowledgements We thank D. Leja for providing graphical expertise and support. Funding support is acknowledged from the following sources: National Institutes of Health, The European Union BioSapiens NoE, Affymetrix, Swiss National Science Foundation, the Spanish Ministerio de Educación y Ciencia, Spanish Ministry of Education and Science, CIBERESP, Genome Spain and Generalitat de Catalunya, Ministry of Education, Culture, Sports, Science and Technology of Japan, the NCCR Frontiers in Genetics, the Jérôme Lejeune Foundation, the Childcare Foundation, the Novartis Foundations, the Danish Research Council, the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the Wellcome Trust, the Howard Hughes Medical Institute, the Bio-X Institute, the RIKEN Institute, the US Army, National Science Foundation, the Deutsche Forschungsgemeinschaft, the Austrian Gen-AU program, the BBSRC and The European Molecular Biology Laboratory. We thank the Barcelona SuperComputing Center and the NIH Biowulf cluster for computer facilities. The Consortium thanks the ENCODE Scientific Advisory Panel for their advice on the project: G. Weinstock, M. Cherry, G. Churchill, M. Eisen, S. Elgin, J. Lis, J. Rine, M. Vidal and P. Zamore.
PY - 2007/6/14
Y1 - 2007/6/14
N2 - We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
AB - We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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UR - http://www.scopus.com/inward/citedby.url?scp=34250305146&partnerID=8YFLogxK
U2 - 10.1038/nature05874
DO - 10.1038/nature05874
M3 - Article
C2 - 17571346
AN - SCOPUS:34250305146
SN - 0028-0836
VL - 447
SP - 799
EP - 816
JO - Nature
JF - Nature
IS - 7146
ER -