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Nature DOI:10.1038/nature05874

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

Publication TypeJournal Article
Year of Publication2007
AuthorsBirney, E, Stamatoyannopoulos, JA, Dutta, A, Guigo, R, Gingeras, TR, Margulies, EH, Weng, Z, Snyder, M, Dermitzakis, ET, Thurman, RE, Kuehn, MS, Taylor, CM, Neph, S, Koch, CM, Asthana, S, Malhotra, A, Adzhubei, I, Greenbaum, JA, Andrews, RM, Flicek, P, Boyle, PJ, Cao, H, Carter, NP, Clelland, GK, Davis, S, Day, N, Dhami, P, Dillon, SC, Dorschner, MO, Fiegler, H, Giresi, PG, Goldy, J, Hawrylycz, M, Haydock, A, Humbert, R, James, KD, Johnson, BE, Johnson, EM, Frum, TT, Rosenzweig, ER, Karnani, N, Lee, K, Lefebvre, GC, Navas, PA, Neri, F, Parker, SCJ, Sabo, PJ, Sandstrom, R, Shafer, A, Vetrie, D, Weaver, M, Wilcox, S, Yu, M, Collins, FS, Dekker, J, Lieb, JD, Tullius, TD, Crawford, GE, Sunyaev, S, Noble, WS, Dunham, I, Denoeud, F, Reymond, A, Kapranov, P, Rozowsky, J, Zheng, D, Castelo, R, Frankish, A, Harrow, J, Ghosh, S, Sandelin, A, Hofacker, IL, Baertsch, R, Keefe, D, Dike, S, Cheng, J, Hirsch, HA, Sekinger, EA, Lagarde, J, Abril, JF, Shahab, A, Flamm, C, Fried, C, Hackermüller, J, Hertel, J, Lindemeyer, M, Missal, K, Tanzer, A, Washietl, S, Korbel, J, Emanuelsson, O, Pedersen, JS, Holroyd, N, Taylor, R, Swarbreck, D, Matthews, N, Dickson, MC, Thomas, DJ, Weirauch, MT, Gilbert, J, Drenkow, J, Bell, I, Zhao, XD, Srinivasan, KG, Sung, W-K, Ooi, HSain, Chiu, KPing, Foissac, S, Alioto, T, Brent, M, Pachter, L, Tress, ML, Valencia, A, Choo, SWoh, Choo, CYu, Ucla, C, Manzano, C, Wyss, C, Cheung, E, Clark, TG, Brown, JB, Ganesh, M, Patel, S, Tammana, H, Chrast, J, Henrichsen, CN, Kai, C, Kawai, J, Nagalakshmi, U, Wu, J, Lian, Z, Lian, J, Newburger, P, Zhang, X, Bickel, P, Mattick, JS, Carninci, P, Hayashizaki, Y, Weissman, S, Hubbard, T, Myers, RM, Rogers, J, Stadler, PF, Lowe, TM, Wei, C-L, Ruan, Y, Struhl, K, Gerstein, M, Antonarakis, SE, Fu, Y, Green, ED, Karaöz, U, Siepel, A, Taylor, J, Liefer, LA, Wetterstrand, KA, Good, PJ, Feingold, EA, Guyer, MS, Cooper, GM, Asimenos, G, Dewey, CN, Hou, M, Nikolaev, S, Montoya-Burgos, JI, Löytynoja, A, Whelan, S, Pardi, F, Massingham, T, Huang, H, Zhang, NR, Holmes, I, Mullikin, JC, Ureta-Vidal, A, Paten, B, Seringhaus, M, Church, D, Rosenbloom, K, W Kent, J, Stone, EA, Batzoglou, S, Goldman, N, Hardison, RC, Haussler, D, Miller, W, Sidow, A, Trinklein, ND, Zhang, ZD, Barrera, L, Stuart, R, King, DC, Ameur, A, Enroth, S, Bieda, MC, Kim, J, Bhinge, AA, Jiang, N, Liu, J, Yao, F, Vega, VB, Lee, CWH, Ng, P, Shahab, A, Yang, A, Moqtaderi, Z, Zhu, Z, Xu, X, Squazzo, S, Oberley, MJ, Inman, D, Singer, MA, Richmond, TA, Munn, KJ, Rada-Iglesias, A, Wallerman, O, Komorowski, J, Fowler, JC, Couttet, P, Bruce, AW, Dovey, OM, Ellis, PD, Langford, CF, Nix, DA, Euskirchen, G, Hartman, S, Urban, AE, Kraus, P, Van Calcar, S, Heintzman, N, Kim, THoon, Wang, K, Qu, C, Hon, G, Luna, R, Glass, CK, M Rosenfeld, G, Aldred, SForce, Cooper, SJ, Halees, A, Lin, JM, Shulha, HP, Zhang, X, Xu, M, Haidar, JNS, Yu, Y, Ruan, Y, Iyer, VR, Green, RD, Wadelius, C, Farnham, PJ, Ren, B, Harte, RA, Hinrichs, AS, Trumbower, H, Clawson, H, Hillman-Jackson, J, Zweig, AS, Smith, K, Thakkapallayil, A, Barber, G, Kuhn, RM, Karolchik, D, Armengol, L, Bird, CP, de Bakker, PIW, Kern, AD, López-Bigas, N, Martin, JD, Stranger, BE, Woodroffe, A, Davydov, E, Dimas, A, Eyras, E, Hallgrímsdóttir, IB, Huppert, J, Zody, MC, Abecasis, GR, Estivill, X, Bouffard, GG, Guan, X, Hansen, NF, Idol, JR, Maduro, VVB, Maskeri, B, McDowell, JC, Park, M, Thomas, PJ, Young, AC, Blakesley, RW, Muzny, DM, Sodergren, E, Wheeler, DA, Worley, KC, Jiang, H, Weinstock, GM, Gibbs, RA, Graves, T, Fulton, R, Mardis, ER, Wilson, RK, Clamp, M, Cuff, J, Gnerre, S, Jaffe, DB, Chang, JL, Lindblad-Toh, K, Lander, ES, Koriabine, M, Nefedov, M, Osoegawa, K, Yoshinaga, Y, Zhu, B, de Jong, PJ
Corporate AuthorsENCODE Project Consortium, 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
JournalNature
Volume447
Issue7146
Pages799-816
Date Published2007 Jun 14
ISSN1476-4687
KeywordsChromatin, Chromatin Immunoprecipitation, Conserved Sequence, DNA Replication, Evolution, Molecular, Exons, Genetic Variation, Genome, Human, Genomics, Heterozygote, Histones, Humans, Pilot Projects, Protein Binding, Regulatory Sequences, Nucleic Acid, RNA, Messenger, RNA, Untranslated, Transcription Factors, Transcription Initiation Site, Transcription, Genetic
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.

URLhttp://dx.doi.org/10.1038/nature05874
DOI10.1038/nature05874
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/17571346?dopt=Abstract

Alternate JournalNature
PubMed ID17571346
PubMed Central IDPMC2212820
Grant ListR01 HG003541 / HG / NHGRI NIH HHS / United States
U54 HG003067-01 / HG / NHGRI NIH HHS / United States
P41 HG002371-03S1 / HG / NHGRI NIH HHS / United States
U01 HG003157-03 / HG / NHGRI NIH HHS / United States
U01 HG003147 / HG / NHGRI NIH HHS / United States
U01 HG003162-03 / HG / NHGRI NIH HHS / United States
U01 HG002523-01 / HG / NHGRI NIH HHS / United States
U01 HG003168-02 / HG / NHGRI NIH HHS / United States
U54 HG003067 / HG / NHGRI NIH HHS / United States
U54 HG003079-01 / HG / NHGRI NIH HHS / United States
R01 HG003110-03 / HG / NHGRI NIH HHS / United States
U01 HG003156-03 / HG / NHGRI NIH HHS / United States
R01 HG003521-01 / HG / NHGRI NIH HHS / United States
R01 HG003143 / HG / NHGRI NIH HHS / United States
R01 HG003143-04 / HG / NHGRI NIH HHS / United States
U01 HG003150-03 / HG / NHGRI NIH HHS / United States
P41 HG002371 / HG / NHGRI NIH HHS / United States
U01 HG003147-02 / HG / NHGRI NIH HHS / United States
R01 HG003532-01 / HG / NHGRI NIH HHS / United States
R01 HG003521 / HG / NHGRI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
U01 HG003161-03 / HG / NHGRI NIH HHS / United States
U01 HG003156 / HG / NHGRI NIH HHS / United States
R01 HG003532 / HG / NHGRI NIH HHS / United States
R01 HG002238-15 / HG / NHGRI NIH HHS / United States
U01 HG003162 / HG / NHGRI NIH HHS / United States
K22 HG003169 / HG / NHGRI NIH HHS / United States
R01 HG003541-03 / HG / NHGRI NIH HHS / United States
K22 HG003169-01A1 / HG / NHGRI NIH HHS / United States
F32 CA108313 / CA / NCI NIH HHS / United States
077198 / / Wellcome Trust / United Kingdom
U54 HG003079 / HG / NHGRI NIH HHS / United States
U54 HG003273-01 / HG / NHGRI NIH HHS / United States
U01 HG003151 / HG / NHGRI NIH HHS / United States
U01 HG003157 / HG / NHGRI NIH HHS / United States
062023 / / Wellcome Trust / United Kingdom
R01 HG003110 / HG / NHGRI NIH HHS / United States
U01 HG003151-03 / HG / NHGRI NIH HHS / United States
U01 HG002523 / HG / NHGRI NIH HHS / United States
/ / Wellcome Trust / United Kingdom
U01 HG003161 / HG / NHGRI NIH HHS / United States
R01 HG003129-03 / HG / NHGRI NIH HHS / United States
U01 HG003150 / HG / NHGRI NIH HHS / United States
R01 HG002238 / HG / NHGRI NIH HHS / United States