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

Authors
Ewan Birney,J Stamatoyannopoulos
Anindya Dutta,Roderic Guigó,Thomas Gingeras,Elliott Margulies,Zhiping Weng,M Snyder,Emmanouil Dermitzakis,Robert Thurman,Michael Kuehn,Christopher Taylor,Shane Neph,Christof Koch,Saurabh Asthana,Ankit Malhotra,Ivan Adzhubei,Jason Greenbaum,Robert Andrews,Paul Flicek,Patrick Boyle,Hua Cao,Huanming Yang,Gayle Clelland,Sean Davis,Nathan Day,Pawandeep Dhami,Shane Dillon,Michael Konstan,Heike Fiegler,Paul Giresi,Jeff Goldy,Michael Hawrylycz,Andrew Haydock,Richard Humbert,Keith James,Brett Johnson,Ericka Johnson,Tristan Frum,Elizabeth Rosenzweig,Neerja Karnani,Kirsten Lee,Grégory Lefebvre,Patrick Navas,Fidencio Neri,Stephen Parker,Peter Sabo,Richard Sandstrom,Anthony Shafer,David Vetrie,Molly Weaver,Sarah Wilcox,Man Yu,Francis Collins,Raúl Rabadán,Jason Lieb,Thomas Tullius,Gregory Crawford,Shamil Sunyaev,William Noble,Ian Dunham,Alexandre Reymond,Philipp Kapranov,Joel Rozowsky,Deyou Zheng,Robert Castelo,Adam Frankish,Jennifer Harrow,Srinka Ghosh,Albin Sandelin,Ivo Hofacker,Robert Baertsch,Damian Keefe,Sujit Dike,Jill Cheng,Heather Hirsch,Edward Sekinger,Julien Lagarde,Josep Abril,Atif Shahab,Christoph Flamm,Claudia Fried,Jörg Hackermüller,Jana Hertel,Manja Marz,Kristin Reiche,Andrea Tanzer,Stefan Washietl,Jan Korbel,Olof Emanuelsson,Jakob Pedersen,Nancy Holroyd,Ruth Taylor,David Swarbreck,N Matthews,Mark Dickson,Zhaohui Qin,Matthew Weirauch,James Gilbert,Ian Bell,Xiaodong Zhao,Kandhadayar Srinivasan,Wing‐Kin Sung,Hong Ooi,Kuo Chiu,Sylvain Foissac,Tyler Alioto,Michael Brent,Lior Pachter,Michael Tress,Alfonso Valencia,Siew Choo,Chiou Choo,Catherine Ucla,Caroline Manzano,Carine Wyss,Evelyn Cheung,Taane Clark,James Brown,Madhavan Ganesh,Sandeep Patel,Hari Tammana,Jacqueline Chrast,Charlotte Hor,Chikatoshi Kai,Jun Kawai,Ugrappa Nagalakshmi,Jiaqian Wu,Zheng Lian,Lian Jin,Peter Newburger,Xueqing Zhang,Peter Bickel,John Mattick,Piero Carninci,Yoshihide Hayashizaki,Sherman Weissman,Tim Hubbard,R Myers,Jane Rogers,Peter Stadler,Todd Lowe,Chia‐Lin Wei,Xosé Puente,Kevin Struhl,Mark Gerstein,Stylianos Antonarakis,Yutao Fu,Eric Green,Ulaş Karaöz,Adam Siepel,James Taylor,Laura Liefer,Kris Wetterstrand,Peter Good,Elise Feingold,Mark Guyer,Gregory Cooper,George Asimenos,Colin Dewey,Minmei Hou,Sergey Nikolaev,Juan Montoya‐Burgos,Ari Löytynoja,Simon Whelan,Fabio Pardi,Tim Massingham,Haiyan Huang,Nancy Zhang,Ian Holmes,James Mullikin,Eray Tüzün,David Haussler,Michael Seringhaus,Deanna Church,Kate Rosenbloom,W. Kent,Eric Stone,Laura Clarke,Nick Goldman,Ross Hardison,Laura Elnitski,Arend Sidow,Nathan Trinklein,Zhengdong Zhang,Leah Soriaga,Rhona Stuart,David King,Adam Ameur,Stefan Enroth,Mark Bieda,Jonghwan Kim,Akshay Bhinge,Nan Jiang,Jun Liu,Fei Yao,Vinsensius Vega,Charlie Lee,Patrick Duriez,Annie Yang,Zarmik Moqtaderi,Zhou Zhu,Xiaoqin Xu,Sharon Squazzo,Matthew Oberley,David Inman,Michael Singer,Todd Richmond,Kyle Munn,Álvaro Rada-Iglesias,Ola Wallerman,Jan Komorowski,Joanna Fowler,Philippe Couttet,Alexander Bruce,Oliver Dovey,Peter Ellis,Cordelia Langford,David Nix,Ghia Euskirchen,Stephen Hartman,Alexander Urban,Peter Kraus,Sara Calcar,Nathaniel Heintzman,Tae Kim,Li Wang,Chunxu Qu,Gary Hon,Rosa Luna,Christopher Glass,M Rosenfeld,Shelley Aldred,Sara Cooper,Anason Halees,Jane Lin,Hennady Shulha,Qian Zhang,Mousheng Xu,Jaafar Haidar,Yong Yu,Vishwanath Iyer,Roland Green,Claes Wadelius,Peggy Farnham,Bing Ren,Rachel Harte,Angie Hinrichs,Hiram Clawson,Jennifer Hillman‐Jackson,Ann Zweig,Kayla Smith,A. Thakkapallayil,Galt Barber,Robert Kuhn,Lluı́s Armengol,Christine Bird,Paul Bakker,Andrew Kern,Núria López‐Bigas,Joel Martin,Barbara Stranger,Abigail Woodroffe,Eugene Davydov,Antigone Dimas,Eduardo Eyras,Ingileif Hallgrímsdóttir,J Huppert,Michael Zody,Gonçalo Abecasis,Xavier Estivill,Gerard Bouffard,Xiaobin Guan,Nancy Hansen,Jacquelyn Idol,Valerie Maduro,Baishali Maskeri,Jennifer McDowell,Morgan Park,Pamela Thomas,Alice Young,Robert Blakesley,Donna Muzny,Erica Sodergren,David Wheeler,Kim Worley,Huaiyang Jiang,George Weinstock,Tina Graves,Robert Fulton,Elaine Mardis,Richard Wilson,James Cuff,Sante Gnerre,David Jaffe,Jean Chang,Kerstin Lindblad‐Toh,Eric Lander,Maxim Koriabine,Mikhail Nefedov,Baoli Zhu,Yuko Yoshinaga,Pieter Jong,Raùl Rabadàn,N. Matthews,T Gingeras,N. Carter,Michael Dorschner,Job Dekker,Manja Lindemeyer,Kristin Missal,Nicholas Matthews,Daryl Thomas
+311 authors
,Jörg Drenkow
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Jun 1, 2007
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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. The ENCODE project — standing for ENCyclopedia Of DNA Elements — has set out to identify all the functional elements in the human genome. With the genome sequence now established, the next challenge is to discover how the cell actually uses it as an instruction manual. The ENCODE consortium has completed the 'proof-of-principle' pilot phase of the project, an analysis of functional elements in a targeted 1% of the human genome. The results, published this week, suggest that most bases in the genome are found in primary transcripts, including non-protein-coding transcripts and those that overlap. Examination of transcriptional regulation has yielded new understanding about transcription start sites, and a more sophisticated view about chromatin structure. Integration of these data, in particular with respect to mammalian evolution, reveals new insights about how the information coded in the DNA blueprint is turned into functioning systems in the living cell. The next step after sequencing a genome is to figure out how the cell actually uses it as an instruction manual. A large international consortium has examined 1% of the genome for what part is transcribed, where proteins are bound, what the chromatin structure looks like, and how the sequence compares to that of other organisms.

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