Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
;
James B Brown;
Madhavan Ganesh;
Sandeep Patel;
Hari Tammana;
Jacqueline Chrast;
Charlotte N Henrichsen;
Chikatoshi Kai;
Jun Kawai;
Ugrappa Nagalakshmi;
Jiaqian Wu;
Zheng Lian;
Jin Lian;
Peter Newburger;
Xueqing Zhang;
Peter Bickel;
John S Mattick;
Piero Carninci;
Yoshihide Hayashizaki;
Sherman Weissman;
Tim Hubbard;
Richard M Myers;
Jane Rogers;
Peter F Stadler;
Todd M Lowe;
Chia-Lin Wei;
Yijun Ruan;
Kevin Struhl;
Mark Gerstein;
Stylianos E Antonarakis;
Yutao Fu;
Eric D Green;
Ulaş Karaöz;
Adam Siepel;
James Taylor;
Laura A Liefer;
Kris A Wetterstrand;
Peter J Good;
Elise A Feingold;
Mark S Guyer;
Gregory M Cooper;
George Asimenos;
Colin N Dewey;
Minmei Hou;
Sergey Nikolaev;
Juan I Montoya-Burgos;
Ari Löytynoja;
Simon Whelan;
Fabio Pardi;
Tim Massingham;
Haiyan Huang;
Nancy R Zhang;
Ian Holmes;
James C Mullikin;
Abel Ureta-Vidal;
Benedict Paten;
Michael Seringhaus;
Deanna Church;
Kate Rosenbloom;
W James Kent;
Eric A Stone;
NISC Comparative Sequencing Program;
Baylor College of Medicine Human Genome Sequencing Center;
Washington University Genome Sequencing Center;
Broad Institute;
Children's Hospital Oakland Research Institute;
Serafim Batzoglou;
Nick Goldman;
Ross C Hardison;
David Haussler;
Webb Miller;
Arend Sidow;
Nathan D Trinklein;
Zhengdong D Zhang;
Leah Barrera;
Rhona Stuart;
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Stefan Enroth;
Mark C Bieda;
Jonghwan Kim;
Akshay A Bhinge;
Nan Jiang;
Jun Liu;
Fei Yao;
Vinsensius B Vega;
Charlie WH Lee;
Patrick Ng;
Atif Shahab;
Annie Yang;
Zarmik Moqtaderi;
Zhou Zhu;
Xiaoqin Xu;
Sharon Squazzo;
Matthew J Oberley;
David Inman;
Michael A Singer;
Todd A Richmond;
Kyle J Munn;
Alvaro Rada-Iglesias;
Ola Wallerman;
Jan Komorowski;
Joanna C Fowler;
Phillippe Couttet;
Alexander W Bruce;
Oliver M Dovey;
Peter D Ellis;
Cordelia F Langford;
David A Nix;
Ghia Euskirchen;
Stephen Hartman;
Alexander E Urban;
Peter Kraus;
Sara Van Calcar;
Nate Heintzman;
Tae Hoon Kim;
Kun Wang;
Chunxu Qu;
Gary Hon;
Rosa Luna;
Christopher K Glass;
M Geoff Rosenfeld;
Shelley Force Aldred;
Sara J Cooper;
Anason Halees;
Jane M Lin;
Hennady P Shulha;
Xiaoling Zhang;
Mousheng Xu;
Jaafar NS Haidar;
Yong Yu;
Yijun Ruan;
Vishwanath R Iyer;
Roland D 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 Smith;
Archana Thakkapallayil;
Galt Barber;
Robert M Kuhn;
Donna Karolchik;
Lluis Armengol;
Christine P Bird;
Paul IW de Bakker;
Andrew D Kern;
Nuria Lopez-Bigas;
Joel D Martin;
Barbara E Stranger;
Abigail Woodroffe;
Eugene Davydov;
Antigone Dimas;
Eduardo Eyras;
Ingileif B Hallgrímsdóttir;
Julian Huppert;
Michael C Zody;
Gonçalo R Abecasis;
Xavier Estivill;
Gerard G Bouffard;
Xiaobin Guan;
Nancy F Hansen;
Jacquelyn R Idol;
Valerie VB Maduro;
Baishali Maskeri;
Jennifer C McDowell;
Morgan Park;
Pamela J Thomas;
Alice C 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 Fulton;
Elaine R Mardis;
Richard K Wilson;
Michele Clamp;
James Cuff;
Sante Gnerre;
David B Jaffe;
Jean L Chang;
Kerstin Lindblad-Toh;
Eric S Lander;
Maxim Koriabine;
Mikhail Nefedov;
Kazutoyo Osoegawa;
Yuko Yoshinaga;
Baoli Zhu;
Pieter J de Jong;
(2007)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature, 447 (7146).
pp. 799-816.
ISSN 0028-0836
DOI: 10.1038/nature05874
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.