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

ENCODE Project Consortium; Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean 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 D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen CJ 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 E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; 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; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; 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; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie WH Lee; Patrick Ng; 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; 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

doi:10.1038/nature05874

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

Article de revue

Avec comité de lecture

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

ENCODE Project Consortium, Ewan Birney, John A Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R Gingeras, Elliott H Margulies, Zhiping Weng, Michael Snyder, Emmanouil T Dermitzakis, …

Nature, Vol.447(7146), pp.799-816

2007

DOI: https://doi.org/10.1038/nature05874

Résumé

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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Titre: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Créateurs - sans rôle: ENCODE Project Consortium
Ewan Birney
John A Stamatoyannopoulos
Anindya Dutta
Roderic Guigó
Thomas R Gingeras
Elliott H Margulies
Zhiping Weng
Michael Snyder
Emmanouil T Dermitzakis
Robert E Thurman
Michael S Kuehn
Christopher M Taylor
Shane Neph
Christoph M Koch
Saurabh Asthana
Ankit Malhotra
Ivan Adzhubei
Jason A Greenbaum
Robert M Andrews
Paul Flicek
Patrick J Boyle
Hua Cao
Nigel P Carter
Gayle K Clelland
Sean 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 D James
Brett E Johnson
Ericka M Johnson
Tristan T Frum
Elizabeth R Rosenzweig
Neerja Karnani
Kirsten Lee
Gregory C Lefebvre
Patrick A Navas
Fidencio Neri
Stephen CJ 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 E Crawford
Shamil Sunyaev
William S Noble
Ian Dunham
France Denoeud
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
Andrea Tanzer
Stefan Washietl
Jan Korbel
Olof Emanuelsson
Jakob S Pedersen
Nancy Holroyd
Ruth Taylor
David Swarbreck
Nicholas Matthews
Mark C Dickson
Daryl J Thomas
Matthew T Weirauch
James Gilbert
Jorg Drenkow
Ian Bell
XiaoDong Zhao
K G Srinivasan
Wing-Kin Sung
Hong Sain Ooi
Kuo Ping Chiu
Sylvain Foissac
Tyler Alioto
Michael Brent
Lior Pachter
Michael L Tress
Alfonso Valencia
Siew Woh Choo
Chiou Yu Choo
Catherine Ucla
Caroline Manzano
Carine Wyss
Evelyn Cheung
Taane G Clark
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
David C King
Adam Ameur
Stefan Enroth
Mark C Bieda
Jonghwan Kim
Akshay A Bhinge
Nan Jiang
Jun Liu
Fei Yao
Vinsensius B Vega
Charlie WH Lee
Patrick Ng
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
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
Détails de publication: Nature, Vol.447(7146), pp.799-816
Éditeur: Nature Research
Identifiants: 99157131809311
Unité académique: Laboratoire d'Informatique de Robotique et de Microélectronique de Mtp - LIRMM
Langue: English
Type de ressource: Journal article