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

Birney, Ewan; Stamatoyannopoulos, John A.; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R.; Margulies, Elliott H.; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T.; Stamatoyannopoulos, John A.; Thurman, Robert E.; Kuehn, Michael S.; Taylor, Christopher M.; Neph, Shane; Koch, Christoph M.; Asthana, Saurabh; Malhotra, Ankit; Adzhubei, Ivan; Greenbaum, Jason A.; Andrews, Robert M.; Flicek, Paul; Boyle, Patrick J.; Cao, Hua; Carter, Nigel P.; Clelland, Gayle K.; Davis, Sean; Day, Nathan; Dhami, Pawandeep; Dillon, Shane C.; Dorschner, Michael O.; Fiegler, Heike; Giresi, Paul G.; Goldy, Jeff; Hawrylycz, Michael; Haydock, Andrew; Humbert, Richard; James, Keith D.; Johnson, Brett E.; Johnson, Ericka M.; Frum, Tristan T.; Rosenzweig, Elizabeth R.; Karnani, Neerja; Lee, Kirsten; Lefebvre, Gregory C.; Navas, Patrick A.; Neri, Fidencio; Parker, Stephen C. J.; Sabo, Peter J.; Sandstrom, Richard; Shafer, Anthony; Vetrie, David; Weaver, Molly; Wilcox, Sarah; Yu1, Man; Collins, Francis S.; Dekker, Job; Lieb, Jason D.; Tullius, Thomas D.; Crawford, Gregory E.; Sunyaev, Shamil; Noble, William S.; Dunham, Ian; Dutta, Anindya; Guigó, Roderic; Denoeud, France; Reymond, Alexandre; Kapranov, Philipp; Rozowsky, Joel; Zheng, Deyou; Castelo, Robert; Frankish, Adam; Harrow, Jennifer; Ghosh, Srinka; Sandelin, Albin; Hofacker, Ivo L.; Baertsch, Robert; Keefe, Damian; Flicek, Paul; Dike, Sujit; Cheng, Jill; Hirsch, Heather A.; Sekinger, Edward A.; Lagarde, Julien; Abril, Josep F.; Shahab, Atif; Flamm, Christoph; Fried, Claudia; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Missal, Kristin; Tanzer, Andrea; Washietl, Stefan; Korbel, Jan; Emanuelsson, Olof; Pedersen, Jakob S.; Holroyd, Nancy; Taylor, Ruth; Swarbreck, David; Matthews, Nicholas; Dickson, Mark C.; Thomas, Daryl J.; Weirauch, Matthew T.; Gilbert, James; Drenkow, Jorg; Bell, Ian; Zhao, XiaoDong; Srinivasan, K.G.; Sung, Wing-Kin; Ooi, Hong Sain; Chiu, Kuo Ping; Foissac, Sylvain; Alioto, Tyler; Brent, Michael; Pachter, Lior; Tress, Michael L.; Valencia, Alfonso; Choo, Siew Woh; Choo, Chiou Yu; Ucla, Catherine; Manzano, Caroline; Wyss, Carine; Cheung, Evelyn; Clark, Taane G.; Brown, James B.; Ganesh, Madhavan; Patel, Sandeep; Tammana, Hari; Chrast, Jacqueline; Henrichsen, Charlotte N.; Kai, Chikatoshi; Kawai, Jun; Nagalakshmi, Ugrappa; Wu, Jiaqian; Lian, Zheng; Lian, Jin; Newburger, Peter; Zhang, Xueqing; Bickel, Peter; Mattick, John S.; Carninci, Piero; Hayashizaki, Yoshihide; Weissman, Sherman; Dermitzakis, Emmanouil T.; Margulies, Elliott H.; Hubbard, Tim; Myers, Richard M.; Rogers, Jane; Stadler, Peter F.; Lowe, Todd M.; Wei, Chia-Lin; Ruan, Yijun; Snyder, Michael; Birney, Ewan; Struhl, Kevin; Gerstein, Mark; Antonarakis, Stylianos E.; Gingeras, Thomas R.; Brown, James B.; Flicek, Paul; Fu, Yutao; Keefe, Damian; Birney, Ewan; Denoeud, France; Gerstein, Mark; Green, Eric D.; Kapranov, Philipp; Karaöz, UlaÅ ; Myers, Richard M.; Noble, William S.; Reymond, Alexandre; Rozowsky, Joel; Struhl, Kevin; Siepel, Adam; Stamatoyannopoulos, John A.; Taylor, Christopher M.; Taylor, James; Thurman, Robert E.; Tullius, Thomas D.; Washietl, Stefan; Zheng, Deyou; Liefer, Laura A.; Wetterstrand, Kris A.; Good, Peter J.; Feingold, Elise A.; Guyer, Mark S.; Collins, Francis S.; Margulies, Elliott H.; Cooper, Gregory M.; Asimenos, George; Thomas, Daryl J.; Dewey, Colin N.; Siepel, Adam; Birney, Ewan; Keefe, Damian; Hou, Minmei; Taylor, James; Nikolaev, Sergey; Montoya-Burgos, Juan I.; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Brown, James B.; Huang, Haiyan; Zhang, Nancy R.; Bickel, Peter; Holmes, Ian; Mullikin, James C.; Ureta-Vidal, Abel; Paten, Benedict; Seringhaus, Michael; Church, Deanna; Rosenbloom, Kate; Kent, W. James; Stone, Eric A.; Gerstein, Mark; Antonarakis, Stylianos E.; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross C.; Haussler, David; Miller, Webb; Pachter, Lior; Green, Eric D.; Sidow, Arend; Weng, Zhiping; Trinklein, Nathan D.; Fu, Yutao; Zhang, Zhengdong D.; Karaöz, UlaÅ ; Barrera, Leah; Stuart, Rhona; Zheng, Deyou; Ghosh, Srinka; Flicek, Paul; King, David C.; Taylor, James; Ameur, Adam; Enroth, Stefan; Bieda, Mark C.; Koch, Christoph M.; Hirsch, Heather A.; Wei, Chia-Lin; Cheng, Jill; Kim, Jonghwan; Bhinge, Akshay A.; Giresi, Paul G.; Jiang, Nan; Liu, Jun; Yao, Fei; Sung, Wing-Kin; Chiu, Kuo Ping; Vega, Vinsensius B.; Lee, Charlie W.H.; Ng, Patrick; Shahab, Atif; Sekinger, Edward A.; Yang, Annie; Moqtaderi, Zarmik; Zhu, Zhou; Xu, Xiaoqin; Squazzo, Sharon; Oberley, Matthew J.; Inman, David; Singer, Michael A.; Richmond, Todd A.; Munn, Kyle J.; Rada-Iglesias, Alvaro; Wallerman, Ola; Komorowski, Jan; Clelland, Gayle K.; Wilcox, Sarah; Dillon, Shane C.; Andrews, Robert M.; Fowler, Joanna C.; Couttet, Phillippe; James, Keith D.; Lefebvre, Gregory C.; Bruce, Alexander W.; Dovey, Oliver M.; Ellis, Peter D.; Dhami, Pawandeep; Langford, Cordelia F.; Carter, Nigel P.; Vetrie, David; Kapranov, Philipp; Nix, David A.; Bell, Ian; Patel, Sandeep; Rozowsky, Joel; Euskirchen, Ghia; Hartman, Stephen; Lian, Jin; Wu, Jiaqian; Urban, Alexander E.; Kraus, Peter; Van Calcar, Sara; Heintzman, Nate; Hoon Kim, Tae; Wang, Kun; Qu, Chunxu; Hon, Gary; Luna, Rosa; Glass, Christopher K.; Rosenfeld, M. Geoff; Aldred, Shelley Force; Cooper, Sara J.; Halees, Anason; Lin, Jane M.; Shulha, Hennady P.; Zhang, Xiaoling; Xu, Mousheng; Haidar, Jaafar N. S.; Yu, Yong; Birney*, Ewan; Weissman, Sherman; Ruan, Yijun; Lieb, Jason D.; Iyer, Vishwanath R.; Green, Roland D.; Gingeras, Thomas R.; Wadelius, Claes; Dunham, Ian; Struhl, Kevin; Hardison, Ross C.; Gerstein, Mark; Farnham, Peggy J.; Myers, Richard M.; Ren, Bing; Snyder, Michael; Thomas, Daryl J.; Rosenbloom, Kate; Harte, Rachel A.; Hinrichs, Angie S.; Trumbower, Heather; Clawson, Hiram; Hillman-Jackson, Jennifer; Zweig, Ann S.; Smith, Kayla; Thakkapallayil, Archana; Barber, Galt; Kuhn, Robert M.; Karolchik, Donna; Haussler, David; Kent, W. James; Dermitzakis, Emmanouil T.; Armengol, Lluis; Bird, Christine P.; Clark, Taane G.; Cooper, Gregory M.; de Bakker, Paul I. W.; Kern, Andrew D.; Lopez-Bigas, Nuria; Martin, Joel D.; Stranger, Barbara E.; Thomas, Daryl J.; Woodroffe, Abigail; Batzoglou, Serafim; Davydov, Eugene; Dimas, Antigone; Eyras, Eduardo; Hallgrímsdóttir, Ingileif B.; Hardison, Ross C.; Huppert, Julian; Sidow, Arend; Taylor, James; Trumbower, Heather; Zody, Michael C.; Guigó, Roderic; Mullikin, James C.; Abecasis, Gonçalo R.; Estivill, Xavier; Birney, Ewan; Bouffard, Gerard G.; Guan, Xiaobin; Hansen, Nancy F.; Idol, Jacquelyn R.; Maduro, Valerie V.B.; Maskeri, Baishali; McDowell, Jennifer C.; Park, Morgan; Thomas, Pamela J.; Young, Alice C.; Blakesley, Robert W.; Muzny, Donna M.; Sodergren, Erica; Wheeler, David A.; Worley, Kim C.; Jiang, Huaiyang; Weinstock, George M.; Gibbs, Richard A.; Graves, Tina; Fulton, Robert; Mardis, Elaine R.; Wilson, Richard K.; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B.; Chang, Jean L.; Lindblad-Toh, Kerstin; Lander, Eric S.; Koriabine, Maxim; Nefedov, Mikhail; Osoegawa, Kazutoyo; Yoshinaga, Yuko; Zhu, Baoli; de Jong, Pieter J.; The ENCODE Project Consortium; Analysis Coordination; Chromatin and Replication; Genes and Transcripts; Integrated Analysis and Manuscript Preparation; Management Group; Multi-species Sequence Analysis; NISC Comparative Sequencing Program*; Baylor College of Medicine Human Genome Sequencing Center*; Washington University Genome Sequencing Center*; Broad Institute*; Childrenâ s Hospital Oakland Research Institute*; Transcriptional Regulatory Elements; UCSC Genome Browser; Variation; NISC Comparative Sequencing Program; Baylor College of Medicine, Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Childrenâ s Hospital Oakland Research Institute; Stadler, Peter F.; ;; Gerstein, Mark; ;; Gerstein, Mark; ;; Siepel, Adam; ;; Siepel, Adam; ;; Gerstein, Mark; ;; Haussler, David; ;; Miller, Webb; ;; Gerstein, Mark; ;; Haussler, David; ;
Журнал: Nature
Дата: 2007

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Аннотация:

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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