Home LiteratureArticle Details
PMID: 17571346 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nature ·Vol. 447 ·No. 7146 ·2007-06-14 ·Pages 799-816

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó 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 SC, 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 X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, 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 CL, 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, Kent WJ, Stone EA, 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, 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 CW, 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 TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, 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 PI, Kern AD, Lopez-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 VV, 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

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.

MeSH Terms
Chromatin/genetics,metabolism Chromatin Immunoprecipitation Conserved Sequence/genetics DNA Replication Evolution, Molecular Exons/genetics Genetic Variation/genetics Genome, Human/genetics Genomics Heterozygote Histones/metabolism Humans Pilot Projects Protein Binding RNA, Messenger/genetics RNA, Untranslated/genetics Regulatory Sequences, Nucleic Acid/genetics Transcription Factors/metabolism Transcription Initiation Site Transcription, Genetic/genetics
Chemicals
Chromatin Histones RNA, Messenger RNA, Untranslated Transcription Factors
Authors & Affiliations
319 authors, click to expand affiliations / ORCID
ENCODE Project Consortium
Birney Ewan
Stamatoyannopoulos John A
Dutta Anindya
Guigó Roderic
Gingeras Thomas R
Margulies Elliott H
Weng Zhiping
Snyder Michael
Dermitzakis Emmanouil T
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
Yu Man
Collins Francis S
Dekker Job
Lieb Jason D
Tullius Thomas D
Crawford Gregory E
Sunyaev Shamil
Noble William S
Dunham Ian
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
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
Hubbard Tim
Myers Richard M
Rogers Jane
Stadler Peter F
Lowe Todd M
Wei Chia-Lin
Ruan Yijun
Struhl Kevin
Gerstein Mark
Antonarakis Stylianos E
Fu Yutao
Green Eric D
Karaöz Ulaş
Siepel Adam
Taylor James
Liefer Laura A
Wetterstrand Kris A
Good Peter J
Feingold Elise A
Guyer Mark S
Cooper Gregory M
Asimenos George
Dewey Colin N
Hou Minmei
Nikolaev Sergey
Montoya-Burgos Juan I
Löytynoja Ari
Whelan Simon
Pardi Fabio
Massingham Tim
Huang Haiyan
Zhang Nancy R
Holmes Ian
Mullikin James C
Ureta-Vidal Abel
Paten Benedict
Seringhaus Michael
Church Deanna
Rosenbloom Kate
Kent W James
Stone Eric A
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
Batzoglou Serafim
Goldman Nick
Hardison Ross C
Haussler David
Miller Webb
Sidow Arend
Trinklein Nathan D
Zhang Zhengdong D
Barrera Leah
Stuart Rhona
King David C
Ameur Adam
Enroth Stefan
Bieda Mark C
Kim Jonghwan
Bhinge Akshay A
Jiang Nan
Liu Jun
Yao Fei
Vega Vinsensius B
Lee Charlie W H
Ng Patrick
Shahab Atif
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
Fowler Joanna C
Couttet Phillippe
Bruce Alexander W
Dovey Oliver M
Ellis Peter D
Langford Cordelia F
Nix David A
Euskirchen Ghia
Hartman Stephen
Urban Alexander E
Kraus Peter
Van Calcar Sara
Heintzman Nate
Kim Tae Hoon
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
Ruan Yijun
Iyer Vishwanath R
Green Roland D
Wadelius Claes
Farnham Peggy J
Ren Bing
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
Armengol Lluis
Bird Christine P
de Bakker Paul I W
Kern Andrew D
Lopez-Bigas Nuria
Martin Joel D
Stranger Barbara E
Woodroffe Abigail
Davydov Eugene
Dimas Antigone
Eyras Eduardo
Hallgrímsdóttir Ingileif B
Huppert Julian
Zody Michael C
Abecasis Gonçalo R
Estivill Xavier
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
References (126)
126 references, click to expand
  1. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
    Nature. 2004 Dec 9;432(7018):695-716 PMID: 15592404
  2. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.
    Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17771-6 PMID: 15591350
  3. Global identification of human transcribed sequences with genome tiling arrays.
    Science. 2004 Dec 24;306(5705):2242-6 PMID: 15539566
  4. Highly conserved non-coding sequences are associated with vertebrate development.
    PLoS Biol. 2005 Jan;3(1):e7 PMID: 15630479
  5. A model of the statistical power of comparative genome sequence analysis.
    PLoS Biol. 2005 Jan;3(1):e10 PMID: 15660152
  6. Reading signals on the nucleosome with a new nomenclature for modified histones.
    Nat Struct Mol Biol. 2005 Feb;12(2):110-2 PMID: 15702071
  7. Conserved non-genic sequences - an unexpected feature of mammalian genomes.
    Nat Rev Genet. 2005 Feb;6(2):151-7 PMID: 15716910
  8. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome.
    Genome Res. 2006 Jan;16(1):1-10 PMID: 16344566
  9. A global map of p53 transcription-factor binding sites in the human genome.
    Cell. 2006 Jan 13;124(1):207-19 PMID: 16413492
  10. Structural variation in the human genome.
    Nat Rev Genet. 2006 Feb;7(2):85-97 PMID: 16418744
  11. Conserved noncoding sequences are selectively constrained and not mutation cold spots.
    Nat Genet. 2006 Feb;38(2):223-7 PMID: 16380714
  12. Gene regulation and large-scale chromatin organization in the nucleus.
    Chromosome Res. 2006;14(1):117-26 PMID: 16506101
  13. A question of timing: emerging links between transcription and replication.
    Curr Opin Genet Dev. 2006 Apr;16(2):177-83 PMID: 16503127
  14. Control of developmental regulators by Polycomb in human embryonic stem cells.
    Cell. 2006 Apr 21;125(2):301-13 PMID: 16630818
  15. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.
    Nature. 2004 Oct 21;431(7011):946-57 PMID: 15496914
  16. The ENCODE (ENCyclopedia Of DNA Elements) Project.
    Science. 2004 Oct 22;306(5696):636-40 PMID: 15499007
  17. A test of neutral molecular evolution based on nucleotide data.
    Genetics. 1987 May;116(1):153-9 PMID: 3110004
  18. Structural details of an adenine tract that does not cause DNA to bend.
    Nature. 1988 Feb 4;331(6155):455-7 PMID: 3340190
  19. Replication program of active and inactive multigene families in mammalian cells.
    Mol Cell Biol. 1988 May;8(5):2149-58 PMID: 3386634
  20. Adaptive protein evolution at the Adh locus in Drosophila.
    Nature. 1991 Jun 20;351(6328):652-4 PMID: 1904993
  21. How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequences.
    Biochemistry. 1993 Jan 12;32(1):127-36 PMID: 8380329
  22. A high-resolution map of active promoters in the human genome.
    Nature. 2005 Aug 11;436(7052):876-80 PMID: 15988478
  23. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.
    Annu Rev Genomics Hum Genet. 2005;6:143-64 PMID: 16124857
  24. Initial sequence of the chimpanzee genome and comparison with the human genome.
    Nature. 2005 Sep 1;437(7055):69-87 PMID: 16136131
  25. A genome-wide comparison of recent chimpanzee and human segmental duplications.
    Nature. 2005 Sep 1;437(7055):88-93 PMID: 16136132
  26. The transcriptional landscape of the mammalian genome.
    Science. 2005 Sep 2;309(5740):1559-63 PMID: 16141072
  27. Antisense transcription in the mammalian transcriptome.
    Science. 2005 Sep 2;309(5740):1564-6 PMID: 16141073
  28. Genome-scale profiling of histone H3.3 replacement patterns.
    Nat Genet. 2005 Oct;37(10):1090-7 PMID: 16155569
  29. Adaptive evolution of non-coding DNA in Drosophila.
    Nature. 2005 Oct 20;437(7062):1149-52 PMID: 16237443
  30. Epigenetic deregulation of imprinting in congenital diseases of aberrant growth.
    Bioessays. 2006 May;28(5):453-9 PMID: 16615080
  31. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions.
    Genes Dev. 2006 May 1;20(9):1123-36 PMID: 16618801
  32. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome.
    Genome Res. 2006 May;16(5):595-605 PMID: 16606705
  33. Genome-wide analysis of mammalian promoter architecture and evolution.
    Nat Genet. 2006 Jun;38(6):626-35 PMID: 16645617
  34. Genome-wide associations of gene expression variation in humans.
    PLoS Genet. 2005 Dec;1(6):e78 PMID: 16362079
  35. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.
    Nat Methods. 2006 Jul;3(7):503-9 PMID: 16791207
  36. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.
    Nat Methods. 2006 Jul;3(7):511-8 PMID: 16791208
  37. TUF love for "junk" DNA.
    Cell. 2006 Jun 30;125(7):1215-20 PMID: 16814704
  38. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res. 2003 Apr;13(4):721-31 PMID: 12654723
  39. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.
    Genome Res. 2003 May;13(5):813-20 PMID: 12727901
  40. Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network.
    Genes Dev. 2003 May 1;17(9):1101-14 PMID: 12695332
  41. Genomic targets of the human c-Myc protein.
    Genes Dev. 2003 May 1;17(9):1115-29 PMID: 12695333
  42. Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication.
    Nat Cell Biol. 2003 Jul;5(7):668-74 PMID: 12833066
  43. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells.
    Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8164-9 PMID: 12808131
  44. Spatial organization of gene expression: the active chromatin hub.
    Chromosome Res. 2003;11(5):447-59 PMID: 12971721
  45. The RNA polymerase II core promoter.
    Annu Rev Biochem. 2003;72:449-79 PMID: 12651739
  46. Scanning human gene deserts for long-range enhancers.
    Science. 2003 Oct 17;302(5644):413 PMID: 14563999
  47. Pseudogenes: are they "junk" or functional DNA?
    Annu Rev Genet. 2003;37:123-51 PMID: 14616058
  48. Identification and characterization of multi-species conserved sequences.
    Genome Res. 2003 Dec;13(12):2507-18 PMID: 14656959
  49. A haplotype map of the human genome.
    Nature. 2005 Oct 27;437(7063):1299-320 PMID: 16255080
  50. Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays.
    Hum Mol Genet. 2005 Nov 15;14(22):3435-47 PMID: 16221759
  51. Genome sequence, comparative analysis and haplotype structure of the domestic dog.
    Nature. 2005 Dec 8;438(7069):803-19 PMID: 16341006
  52. Tandem chimerism as a means to increase protein complexity in the human genome.
    Genome Res. 2006 Jan;16(1):37-44 PMID: 16344564
  53. Vertebrate pseudogenes.
    FEBS Lett. 2000 Feb 25;468(2-3):109-14 PMID: 10692568
  54. Genome-wide location and function of DNA binding proteins.
    Science. 2000 Dec 22;290(5500):2306-9 PMID: 11125145
  55. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.
    Nature. 2001 Jan 25;409(6819):533-8 PMID: 11206552
  56. The sequence of the human genome.
    Science. 2001 Feb 16;291(5507):1304-51 PMID: 11181995
  57. Initial sequencing and analysis of the human genome.
    Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
  58. The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A.
    Hum Mol Genet. 2001 Nov 1;10(23):2687-700 PMID: 11726556
  59. GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.
    Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2924-9 PMID: 11867748
  60. Large-scale transcriptional activity in chromosomes 21 and 22.
    Science. 2002 May 3;296(5569):916-9 PMID: 11988577
  61. Replication timing and transcriptional control: beyond cause and effect.
    Curr Opin Cell Biol. 2002 Jun;14(3):377-83 PMID: 12067662
  62. Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover.
    Mol Biol Evol. 2002 Jul;19(7):1114-21 PMID: 12082130
  63. Parallel construction of orthologous sequence-ready clone contig maps in multiple species.
    Genome Res. 2002 Aug;12(8):1277-85 PMID: 12176935
  64. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.
    Science. 2002 Aug 23;297(5585):1301-10 PMID: 12142439
  65. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing.
    Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4795-800 PMID: 15778292
  66. Functional evolution of a cis-regulatory module.
    PLoS Biol. 2005 Apr;3(4):e93 PMID: 15757364
  67. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
    Nucleic Acids Res. 2005;33(8):2374-83 PMID: 15860774
  68. High-throughput localization of functional elements by quantitative chromatin profiling.
    Nat Methods. 2004 Dec;1(3):219-25 PMID: 15782197
  69. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.
    Nat Methods. 2005 Feb;2(2):105-11 PMID: 15782207
  70. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.
    Nat Methods. 2005 Jan;2(1):47-53 PMID: 15782160
  71. Temporal profile of replication of human chromosomes.
    Proc Natl Acad Sci U S A. 2005 May 3;102(18):6419-24 PMID: 15845769
  72. Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
    J Mol Biol. 2005 May 27;349(1):27-45 PMID: 15876366
  73. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.
    Science. 2005 May 20;308(5725):1149-54 PMID: 15790807
  74. Direct isolation and identification of promoters in the human genome.
    Genome Res. 2005 Jun;15(6):830-9 PMID: 15899964
  75. Subtree power analysis and species selection for comparative genomics.
    Proc Natl Acad Sci U S A. 2005 May 31;102(22):7900-5 PMID: 15911755
  76. Distribution and intensity of constraint in mammalian genomic sequence.
    Genome Res. 2005 Jul;15(7):901-13 PMID: 15965027
  77. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays.
    Genome Res. 2005 Jul;15(7):987-97 PMID: 15998911
  78. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res. 2005 Aug;15(8):1034-50 PMID: 16024819
  79. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex.
    Cell. 2002 Oct 18;111(2):197-208 PMID: 12408864
  80. Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing.
    Nat Genet. 2002 Nov;32(3):438-42 PMID: 12355067
  81. Role of histone H3 lysine 27 methylation in Polycomb-group silencing.
    Science. 2002 Nov 1;298(5595):1039-43 PMID: 12351676
  82. Initial sequencing and comparative analysis of the mouse genome.
    Nature. 2002 Dec 5;420(6915):520-62 PMID: 12466850
  83. Identification and functional analysis of human transcriptional promoters.
    Genome Res. 2003 Feb;13(2):308-12 PMID: 12566409
  84. Widespread occurrence of antisense transcription in the human genome.
    Nat Biotechnol. 2003 Apr;21(4):379-86 PMID: 12640466
  85. Replication timing of the human genome.
    Hum Mol Genet. 2004 Jan 15;13(2):191-202 PMID: 14645202
  86. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species.
    Mol Cell. 2004 Jan 30;13(2):291-8 PMID: 14759373
  87. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.
    Cell. 2004 Feb 20;116(4):499-509 PMID: 14980218
  88. Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
    Nature. 2004 Apr 1;428(6982):493-521 PMID: 15057822
  89. Characterization of evolutionary rates and constraints in three Mammalian genomes.
    Genome Res. 2004 Apr;14(4):539-48 PMID: 15059994
  90. MAVID: constrained ancestral alignment of multiple sequences.
    Genome Res. 2004 Apr;14(4):693-9 PMID: 15060012
  91. Aligning multiple genomic sequences with the threaded blockset aligner.
    Genome Res. 2004 Apr;14(4):708-15 PMID: 15060014
  92. Ultraconserved elements in the human genome.
    Science. 2004 May 28;304(5675):1321-5 PMID: 15131266
  93. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export.
    EMBO J. 2006 Aug 9;25(15):3565-75 PMID: 16874305
  94. A computational approach for identifying pseudogenes in the ENCODE regions.
    Genome Biol. 2006;7 Suppl 1:S13.1-10 PMID: 16925835
  95. EGASP: the human ENCODE Genome Annotation Assessment Project.
    Genome Biol. 2006;7 Suppl 1:S2.1-31 PMID: 16925836
  96. Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
    Genome Biol. 2006;7 Suppl 1:S3.1-13 PMID: 16925837
  97. GENCODE: producing a reference annotation for ENCODE.
    Genome Biol. 2006;7 Suppl 1:S4.1-9 PMID: 16925838
  98. Transcriptional regulatory elements in the human genome.
    Annu Rev Genomics Hum Genet. 2006;7:29-59 PMID: 16719718
  99. Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters.
    PLoS Genet. 2006 Sep 22;2(9):e158 PMID: 17002501
  100. Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts.
    BMC Genomics. 2006;7:301 PMID: 17134498
  101. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
    Nat Genet. 2007 Mar;39(3):311-8 PMID: 17277777
  102. The implications of alternative splicing in the ENCODE protein complement.
    Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500 PMID: 17372197
  103. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
    Genome Res. 2007 Jun;17(6):886-97 PMID: 17119069
  104. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.
    Genome Res. 2007 Jun;17(6):877-85 PMID: 17179217
  105. The landscape of histone modifications across 1% of the human genome in five human cell lines.
    Genome Res. 2007 Jun;17(6):691-707 PMID: 17567990
  106. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.
    Genome Res. 2007 Jun;17(6):720-31 PMID: 17567992
  107. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
    Genome Res. 2007 Jun;17(6):732-45 PMID: 17567993
  108. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
    Genome Res. 2007 Jun;17(6):746-59 PMID: 17567994
  109. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.
    Genome Res. 2007 Jun;17(6):787-97 PMID: 17567997
  110. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
    Genome Res. 2007 Jun;17(6):839-51 PMID: 17568002
  111. Structured RNAs in the ENCODE selected regions of the human genome.
    Genome Res. 2007 Jun;17(6):852-64 PMID: 17568003
  112. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas.
    Genome Res. 2007 Jun;17(6):865-76 PMID: 17568004
  113. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.
    Genome Res. 2007 Jun;17(6):898-909 PMID: 17568005
  114. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).
    Genome Res. 2007 Jun;17(6):910-6 PMID: 17568006
  115. Identification of higher-order functional domains in the human ENCODE regions.
    Genome Res. 2007 Jun;17(6):917-27 PMID: 17568007
  116. Detection of DNA structural motifs in functional genomic elements.
    Genome Res. 2007 Jun;17(6):940-6 PMID: 17568009
  117. Functional constraint and small insertions and deletions in the ENCODE regions of the human genome.
    Genome Biol. 2007;8(9):R180 PMID: 17784950
  118. PromoSer: improvements to the algorithm, visualization and accessibility.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W191-4 PMID: 15215378
  119. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27.
    Genes Dev. 2004 Jul 1;18(13):1592-605 PMID: 15231737
  120. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers.
    Cell. 2004 Sep 3;118(5):555-66 PMID: 15339661
  121. Finishing the euchromatic sequence of the human genome.
    Nature. 2004 Oct 21;431(7011):931-45 PMID: 15496913
  122. Cloning and expression of human TAFII250: a TBP-associated factor implicated in cell-cycle regulation.
    Nature. 1993 Mar 11;362(6416):175-9 PMID: 7680771
  123. Evolutionary dynamics of the enhancer region of even-skipped in Drosophila.
    Mol Biol Evol. 1995 Nov;12(6):1002-11 PMID: 8524036
  124. The timing of XIST replication: dominance of the domain.
    Hum Mol Genet. 1999 Jun;8(6):1085-9 PMID: 10332041
  125. An intermediate grade of finished genomic sequence suitable for comparative analyses.
    Genome Res. 2004 Nov;14(11):2235-44 PMID: 15479945
  126. Coordination of replication and transcription along a Drosophila chromosome.
    Genes Dev. 2004 Dec 15;18(24):3094-105 PMID: 15601823
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
DOI
10.1038/nature05874
Published
2007-06-14
Pages
799-816
Language
English
Region
England
NLM ID
0410462
PMCID
PMC2212820
Subset
IM
Grants
NHGRI NIH HHS · R01 HG003541 · United States
NHGRI NIH HHS · U54 HG003067-01 · United States
NHGRI NIH HHS · P41 HG002371-03S1 · United States
NHGRI NIH HHS · U01 HG003157-03 · United States
NHGRI NIH HHS · U01 HG003147 · United States
NHGRI NIH HHS · U01 HG003162-03 · United States
NHGRI NIH HHS · U01 HG002523-01 · United States
NHGRI NIH HHS · U01 HG003168-02 · United States
NHGRI NIH HHS · U54 HG003067 · United States
NHGRI NIH HHS · U54 HG003079-01 · United States
NHGRI NIH HHS · R01 HG003110-03 · United States
NHGRI NIH HHS · U01 HG003156-03 · United States
NHGRI NIH HHS · R01 HG003521-01 · United States
NHGRI NIH HHS · R01 HG003143 · United States
NHGRI NIH HHS · R01 HG003143-04 · United States
NHGRI NIH HHS · U01 HG003150-03 · United States
NHGRI NIH HHS · P41 HG002371 · United States
NHGRI NIH HHS · U01 HG003147-02 · United States
NHGRI NIH HHS · R01 HG003532-01 · United States
NHGRI NIH HHS · R01 HG003521 · United States
NHGRI NIH HHS · U54 HG003273 · United States
NHGRI NIH HHS · U01 HG003161-03 · United States
NHGRI NIH HHS · U01 HG003156 · United States
NHGRI NIH HHS · R01 HG003532 · United States
NHGRI NIH HHS · R01 HG002238-15 · United States
NHGRI NIH HHS · U01 HG003162 · United States
NHGRI NIH HHS · K22 HG003169 · United States
NHGRI NIH HHS · R01 HG003541-03 · United States
NHGRI NIH HHS · K22 HG003169-01A1 · United States
NCI NIH HHS · F32 CA108313 · United States
Wellcome Trust · 077198 · United Kingdom
NHGRI NIH HHS · U54 HG003079 · United States
NHGRI NIH HHS · U54 HG003273-01 · United States
NHGRI NIH HHS · U01 HG003151 · United States
NHGRI NIH HHS · U01 HG003157 · United States
Wellcome Trust · 062023 · United Kingdom
NHGRI NIH HHS · R01 HG003110 · United States
NHGRI NIH HHS · U01 HG003151-03 · United States
NHGRI NIH HHS · U01 HG002523 · United States
NHGRI NIH HHS · U01 HG003161 · United States
NHGRI NIH HHS · R01 HG003129-03 · United States
NHGRI NIH HHS · U01 HG003150 · United States
NHGRI NIH HHS · R01 HG002238 · United States
Corrections
CommentIn
PMID: 17568710
CommentIn
PMID: 17568731
External Links
PubMed source DOI: 10.1038/nature05874 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2