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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-07

AUTHORS

Ewan Birney, John A. Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R. Gingeras, Elliott H. Margulies, Zhiping Weng, Michael Snyder, Emmanouil T. Dermitzakis, John A. Stamatoyannopoulos, 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 C. J. 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, Anindya Dutta, Roderic Guigó, 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, Paul Flicek, 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, Emmanouil T. Dermitzakis, Elliott H. Margulies, Tim Hubbard, Richard M. Myers, Jane Rogers, Peter F. Stadler, Todd M. Lowe, Chia-Lin Wei, Yijun Ruan, Michael Snyder, Ewan Birney, Kevin Struhl, Mark Gerstein, Stylianos E. Antonarakis, Thomas R. Gingeras, James B. Brown, Paul Flicek, Yutao Fu, Damian Keefe, Ewan Birney, France Denoeud, Mark Gerstein, Eric D. Green, Philipp Kapranov, Ulaş Karaöz, Richard M. Myers, William S. Noble, Alexandre Reymond, Joel Rozowsky, Kevin Struhl, Adam Siepel, John A. Stamatoyannopoulos, Christopher M. Taylor, James Taylor, Robert E. Thurman, Thomas D. Tullius, Stefan Washietl, Deyou Zheng, Laura A. Liefer, Kris A. Wetterstrand, Peter J. Good, Elise A. Feingold, Mark S. Guyer, Francis S. Collins, Elliott H. Margulies, Gregory M. Cooper, George Asimenos, Daryl J. Thomas, Colin N. Dewey, Adam Siepel, Ewan Birney, Damian Keefe, Minmei Hou, James Taylor, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Löytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, James B. Brown, Haiyan Huang, Nancy R. Zhang, Peter Bickel, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Michael Seringhaus, Deanna Church, Kate Rosenbloom, W. James Kent, Eric A. Stone, Mark Gerstein, Stylianos E. Antonarakis, Serafim Batzoglou, Nick Goldman, Ross C. Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D. Green, Arend Sidow, Zhiping Weng, Nathan D. Trinklein, Yutao Fu, Zhengdong D. Zhang, Ulaş Karaöz, Leah Barrera, Rhona Stuart, Deyou Zheng, Srinka Ghosh, Paul Flicek, David C. King, James Taylor, Adam Ameur, Stefan Enroth, Mark C. Bieda, Christoph M. Koch, Heather A. Hirsch, Chia-Lin Wei, Jill Cheng, Jonghwan Kim, Akshay A. Bhinge, Paul G. Giresi, Nan Jiang, Jun Liu, Fei Yao, Wing-Kin Sung, Kuo Ping Chiu, Vinsensius B. Vega, Charlie W.H. Lee, Patrick Ng, Atif Shahab, Edward A. Sekinger, 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, Gayle K. Clelland, Sarah Wilcox, Shane C. Dillon, Robert M. Andrews, Joanna C. Fowler, Phillippe Couttet, Keith D. James, Gregory C. Lefebvre, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Pawandeep Dhami, Cordelia F. Langford, Nigel P. Carter, David Vetrie, Philipp Kapranov, David A. Nix, Ian Bell, Sandeep Patel, Joel Rozowsky, Ghia Euskirchen, Stephen Hartman, Jin Lian, Jiaqian Wu, 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 N. S. Haidar, Yong Yu, Ewan Birney*, Sherman Weissman, Yijun Ruan, Jason D. Lieb, Vishwanath R. Iyer, Roland D. Green, Thomas R. Gingeras, Claes Wadelius, Ian Dunham, Kevin Struhl, Ross C. Hardison, Mark Gerstein, Peggy J. Farnham, Richard M. Myers, Bing Ren, Michael Snyder, Daryl J. Thomas, Kate Rosenbloom, 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, David Haussler, W. James Kent, Emmanouil T. Dermitzakis, Lluis Armengol, Christine P. Bird, Taane G. Clark, Gregory M. Cooper, Paul I. W. de Bakker, Andrew D. Kern, Nuria Lopez-Bigas, Joel D. Martin, Barbara E. Stranger, Daryl J. Thomas, Abigail Woodroffe, Serafim Batzoglou, Eugene Davydov, Antigone Dimas, Eduardo Eyras, Ingileif B. Hallgrímsdóttir, Ross C. Hardison, Julian Huppert, Arend Sidow, James Taylor, Heather Trumbower, Michael C. Zody, Roderic Guigó, James C. Mullikin, Gonçalo R. Abecasis, Xavier Estivill, Ewan Birney, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V.B. 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

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. More... »

PAGES

799

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  • Journal

    TITLE

    Nature

    ISSUE

    7146

    VOLUME

    447

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature05874

    DOI

    http://dx.doi.org/10.1038/nature05874

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1005913886

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/17571346


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