DOI: 10.1038/nature05874
OpenAccess: Bronze
This work has “Bronze” OA status. This means it is free to read on the publisher landing page, but without any identifiable license.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Ewan Birney,John A. Stamatoyannopoulos,Anindya Dutta,Roderic Guigó,Thomas R. Gingeras,Elliott H. Margulies,Zhiping Weng,Xin Li,Emmanouil T. Dermitzakis,Robert E. Thurman,Michael R. Kuehn,Christopher J. Taylor,Shane Neph,Christoph Koch,Saurabh Asthana,Ankit Malhotra,Ivan Adzhubei,Jason A. Greenbaum,Robert K. Andrews,Paul Flicek,Patrick M. Boyle,Hua Cao,Nigel P. Carter,Gayle K. Clelland,Sean M. Davis,Nathan Day,Pawandeep Dhami,Shane C. Dillon,Michael O. Dorschner,Heike Fiegler,Paul G. Giresi,Jeff Goldy,Michael Hawrylycz,Andrew Haydock,Richard Humbert,Keith James,Brett C. Johnson,Ericka Johnson,Tristan Frum,Elizabeth Rosenzweig,Neerja Karnani,Kirsten M Lee,Gregory Lefebvre,Patrick A. Navas,Fidencio Neri,Stephen C. Parker,Peter J. Sabo,Richard Sandstrom,Anthony Shafer,David Vetrie,Molly Weaver,Sarah Wilcox,Man Yu,Francis S. Collins,Job Dekker,Jason D. Lieb,Thomas D. Tullius,Gregory P. Crawford,Shamil R. Sunyaev,William Stafford Noble,Ian Dunham,Alexandre Reymond,Philipp Kapranov,Joel Rozowsky,Deyou Zheng,Robert Castelo,Adam Frankish,Jennifer Harrow,Srinka Ghosh,Albin Sandelin,Ivo L. Hofacker,Robert Baertsch,Damian Keefe,Sujit Dike,Jill Cheng,Heather A. Hirsch,Edward A. Sekinger,Julien Lagarde,Josep F. Abril,Atif Shahab,Christoph Flamm,Claudia Fried,Jörg Hackermüller,Jana Hertel,Manja Lindemeyer,Kristin Missal,Stefan Washietl,Jan O. Korbel,Olof Emanuelsson,Jakob Skou Pedersen,Nancy Holroyd,Ruth Taylor,David Swarbreck,Nicholas L. Matthews,Mark A. Dickson,Daryl J. Thomas,Matthew T. Weirauch,James Gilbert,Jorg Drenkow,Ian H. Bell,Xiaodong Zhao,Kannupal Srinivasan,Wing-Kin Sung,Hong-Kean Ooi,Kuo Ping Chiu,Sylvain Foissac,Tyler Alioto,Michael H. Brent,Lior Pachter,Michael L. Tress,Alfonso Valencia,Siew Woh Choo,Chiou Yu Choo,Catherine Ucla,Caroline Manzano,Carine Wyss,Evelyn J. Cheung,Taane G. Clark,James H. Brown,Madhavan Ganesh,Sandeep Patel,Hari Tammana,Jacqueline Chrast,Charlotte N. Henrichsen,Chikatoshi Kai,Jun Kawai,Ugrappa Nagalakshmi,Jia Qian Wu,Zheng Lian,Jin Lian,Peter E. Newburger,Xuan Zhang,Peter J. Bickel,John S. Mattick,Didier Samuel,Yoshihide Hayashizaki,Sherman M. Weissman,Tim Hubbard,Richard M. Myers,Jane Rogers,Peter F. Stadler,Todd M. Lowe,Chia-Chien Wei,Dariusz Plewczynski,Kevin Struhl,Mark Gerstein,Stylianos E. Antonarakis,Yutao Fu,Eric D. Green,Ulas Karaoz,Adam Siepel,James Taylor,Laura A. Liefer,Kris A. Wetterstrand,Peter Good,Elise A. Feingold,Mark S. Guyer,Gregory S. Cooper,George Asimenos,Colin N. Dewey,Minmei Hou,Sergey Nikolaev,Juan I. Montoya-Burgos,Ari Löytynoja,Simon Whelan,Fabio Pardi,Tim Massingham,Haiyan Huang,Nan Zhang,Ian Holmes,James C. Mullikin,Abel Ureta-Vidal,Benedict Paten,Michael Seringhaus,Deanna M. Church,Kate R. Rosenbloom,W. James Kent,Eric A. Stone,Serafim Batzoglou,Nick Goldman,Ross C. Hardison,David Haussler,Webb Miller,Arend Sidow,Nathan D. Trinklein,Zhengdong Zhang,Leah O. Barrera,Rhona K. Stuart,David A. King,Adam Ameur,Stefan Enroth,Mark Bieda,Jong-Hwan Kim,Akshay Bhinge,Nan Jiang,Jun Liu,Fei Yao,Vinsensius B. Vega,Charlie W.H. Lee,Patrick Ng,Annie Yang,Zarmik Moqtaderi,Zhou Zhu,Xiaoqin Xu,Sharon L. Squazzo,Matthew J. Oberley,David R. Inman,Michael Bliss Singer,Todd Richmond,Kyle J. Munn,Alvaro Rada-Iglesias,Ola Wallerman,Jan Komorowski,Joanna S. Fowler,Phillippe Couttet,Alexander W. Bruce,Oliver M. Dovey,Peter M. Ellis,Cordelia Langford,David E. Nix,Ghia Euskirchen,Stephen Hartman,Alexander E. Urban,Peter M. Kraus,Sara Van Calcar,Nate Heintzman,Tae Yong Kim,Kun Wang,Chunxu Qu,Gary C. Hon,Rosa Luna,Christopher K. Glass,Michael G. Rosenfeld,Shelley Force Aldred,Anason S. Halees,Jun-Song Lin,Hennady P. Shulha,Xiaoling Zhang,Mousheng Xu,Jaafar N. Haidar,Yong Yu,Vishwanath R. Iyer,Roland Green,Claes Wadelius,Peggy J. Farnham,Bing Ren,Rachel A. Harte,Angie S. Hinrichs,Heather Trumbower,Hiram Clawson,Jennifer Hillman-Jackson,Ann S. Zweig,Kayla E. Smith,Archana Thakkapallayil,Galt P. Barber,Robert J. Kuhn,Donna Karolchik,Lluís Armengol,Christine P. Bird,Paul I.W. de Bakker,Andrew D. Kern,Nuria Lopez-Bigas,Joel W. Martin,Barbara E. Stranger,Abigail Woodroffe,Eugene Davydov,Antigone S. Dimas,Eduardo Eyras,Ingileif Hallgrimsdottir,Julian L. Huppert,Michael C. Zody,Gonçalo R. Abecasis,Xavier Estivill,Gerard G. Bouffard,Xiaobin Guan,Nancy F. Hansen,Jacquelyn R. Idol,Valerie Maduro,Baishali Maskeri,Jennifer E. McDowell,Morgan Park,Pam A. Thomas,Alice M. Young,Robert W. Blakesley,Donna M. Muzny,Erica Sodergren,David A. Wheeler,Kim C. Worley,Huaiyang Jiang,George M. Weinstock,Richard A. Gibbs,Tina Graves,Robert S. Fulton,Elaine R. Mardis,Richard K. Wilson,Michele Clamp,James Cuff,Sante Gnerre,David M. Jaffe,Jean Chang,Kerstin Lindblad-Toh,Eric S. Lander,Maxim Koriabine,Mikhail Nefedov,Kazutoyo Osoegawa,Yuko Yoshinaga,Baoli Zhu,Pieter J. de Jong

ENCODE
Genome
Computational biology
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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