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A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

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The ENCODE Project Consortium·2011·PLoS Biology
DOI 10.1371/journal.pbio.1001046
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Abstract

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

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Show all 26 references

Research works printed but not linked: 95

  1. 2004, The ENCODE (ENCyclopedia Of DNA Elements) Project., Science, 306, 636, 10.1126/science.1105136 · DOI · Paper page
  2. F Chiaromonte, 2003, The share of human genomic DNA under selection estimated from human-mouse genomic alignments., Cold Spring Harb Symp Quant Biol, 68, 245, 10.1101/sqb.2003.68.245 · DOI · Paper page
  3. E. A Stone, 2005, Trade-offs in detecting evolutionarily constrained sequence by comparative genomics., Annu Rev Genomics Hum Genet, 6, 143, 10.1146/annurev.genom.6.080604.162146 · DOI
  4. S. C Parker, 2009, Local DNA topography correlates with functional noncoding regions of the human genome., Science, 324, 389, 10.1126/science.1169050 · DOI
  5. S Asthana, 2007, Widely distributed noncoding purifying selection in the human genome., Proc Natl Acad Sci U S A, 104, 12410, 10.1073/pnas.0705140104 · DOI
  6. B Wold, 2008, Sequence census methods for functional genomics., Nature Meth, 5, 19, 10.1038/nmeth1157 · DOI · Paper page
  7. K. R Rosenbloom, 2010, ENCODE whole-genome data in the UCSC Genome Browser., Nucleic Acids Res, 38, D620, 10.1093/nar/gkp961 · DOI · Paper page
  8. B Rhead, 2010, The UCSC Genome Browser database: update 2010., Nucleic Acids Res, 38, D613, 10.1093/nar/gkp939 · DOI · Paper page
  9. C. B Lozzio, 1975, Human chronic myelogenous leukemia cell-line with positive Philadelphia chromosome., Blood, 45, 321, 10.1182/blood.V45.3.321.321 · DOI · Paper page
  10. J. A Thomson, 1998, Embryonic stem cell lines derived from human blastocysts., Science, 282, 1145, 10.1126/science.282.5391.1145 · DOI · Paper page
  11. G. O Gey, 1952, Tissue culture studies of the proliferative capacity of cervical carcinoma and normal epithelium., Cancer Res, 12, 264
  12. B. B Knowles, 1980, Human hepatocellular carcinoma cell lines secrete the major plasma proteins and hepatitis B surface antigen., Science, 209, 497, 10.1126/science.6248960 · DOI · Paper page
  13. E. A Jaffe, 1973, Culture of human endothelial cells derived from umbilical veins: Identification by morphologic and immunologic criteria., J Clin Invest, 52, 2745, 10.1172/JCI107470 · DOI · Paper page
  14. 2004, Finishing the euchromatic sequence of the human genome., Nature, 431, 931, 10.1038/nature03001 · DOI · Paper page
  15. R Guigó, 2006, EGASP: the human ENCODE Genome Annotation Assessment Project., Genome Biol, 7, S2 1, 10.1186/gb-2006-7-s1-s2 · DOI
  16. J Harrow, 2006, GENCODE: producing a reference annotation for ENCODE., Genome Biol, 7, S4 1, 10.1186/gb-2006-7-s1-s4 · DOI · Paper page
  17. Z Zhang, 2006, PseudoPipe: an automated pseudogene identification pipeline., Bioinformatics, 22, 1437, 10.1093/bioinformatics/btl116 · DOI
  18. P Flicek, 2010, Ensembl's 10th year., Nucleic Acids Res, 38, D557, 10.1093/nar/gkp972 · DOI · Paper page
  19. D Kampa, 2004, Novel RNAs identified from a comprehensive analysis of the transcriptome of human chromosomes 21 and 22., Genome Res, 14, 331, 10.1101/gr.2094104 · DOI · Paper page
  20. M Schmid, 2010, Nuclear quality control of RNA polymerase II transcripts., J Wiley Interdisciplinary Review
  21. J. P Bachellerie, 2002, The expanding snoRNA world., Biochimie, 84, 775, 10.1016/S0300-9084(02)01402-5 · DOI · Paper page
  22. P Kapranov, 2007, Genome-wide transcription and the implications for genomic organization., Nat Rev Genet, 8, 413, 10.1038/nrg2083 · DOI · Paper page
  23. M. J Fullwood, 2009, Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses., Genome Res, 19, 521, 10.1101/gr.074906.107 · DOI · Paper page
  24. T Shiraki, 2003, Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage., Proc Natl Acad Sci U S A, 100, 15776, 10.1073/pnas.2136655100 · DOI · Paper page
  25. E Valen, 2009, Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE., Genome Res, 19, 255, 10.1101/gr.084541.108 · DOI
  26. M. A Frohman, 1988, Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer., Proc Natl Acad Sci U S A, 85, 8998, 10.1073/pnas.85.23.8998 · DOI · Paper page
  27. M. C Giddings, 2003, Genome-based peptide fingerprint scanning., Proc Natl Acad Sci U S A, 100, 20, 10.1073/pnas.0136893100 · DOI
  28. G. E Merrihew, 2008, Use of shotgun proteomics for the identification, confirmation, and correction of C elegans gene annotations., Genome Res, 18, 1660, 10.1101/gr.077644.108 · DOI
  29. C Wu, 1980, The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I., Nature, 286, 854, 10.1038/286854a0 · DOI · Paper page
  30. M. A Keene, 1981, DNase I hypersensitive sites in Drosophila chromatin occur at the 5′ ends of regions of transcription., Proc Natl Acad Sci U S A, 78, 143, 10.1073/pnas.78.1.143 · DOI
  31. J. D McGhee, 1981, A 200 base pair region at the 5′ end of the chicken adult beta-globin gene is accessible to nuclease digestion., Cell, 27, 45, 10.1016/0092-8674(81)90359-7 · DOI · Paper page
  32. D. S Gross, 1988, Nuclease hypersensitive sites in chromatin., Annu Rev Biochem, 57, 159, 10.1146/annurev.bi.57.070188.001111 · DOI · Paper page
  33. P. G Giresi, 2007, FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin., Genome Res, 17, 877, 10.1101/gr.5533506 · DOI · Paper page
  34. R. K Auerbach, 2009, Mapping accessible chromatin regions using Sono-Seq., Proc Natl Acad Sci U S A, 106, 14926, 10.1073/pnas.0905443106 · DOI
  35. G Liang, 2004, Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome., Proc Natl Acad Sci U S A, 11, 7357, 10.1073/pnas.0401866101 · DOI · Paper page
  36. R Schneider, 2004, Histone H3 lysine 4 methylation patterns in higher eukaryotic genes., Nat Cell Biol, 6, 73, 10.1038/ncb1076 · DOI · Paper page
  37. B. E Bernstein, 2005, Genomic maps and comparative analysis of histone modifications in human and mouse., Cell, 28, 169, 10.1016/j.cell.2005.01.001 · DOI · Paper page
  38. L. A Boyer, 2006, Polycomb complexes repress developmental regulators in murine embryonic stem cells., Nature, 18, 349, 10.1038/nature04733 · DOI · Paper page
  39. T. I Lee, 2006, Control of developmental regulators by Polycomb in human embryonic stem cells., Cell, 21, 301, 10.1016/j.cell.2006.02.043 · DOI · Paper page
  40. B. D Strahl, 2000, The language of covalent histone modifications., Nature, 6, 41, 10.1038/47412 · DOI · Paper page
  41. P. J Sabo, 2004, Discovery of functional noncoding elements by digital analysis of chromatin structure., Proc Natl Acad Sci U S A, 101, 16837, 10.1073/pnas.0407387101 · DOI
  42. A. P Boyle, 2008, High-resolution mapping and characterization of open chromatin across the genome., Cell, 25, 311, 10.1016/j.cell.2007.12.014 · DOI · Paper page
  43. P. J Sabo, 2006, Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays., Nat Methods, 3, 511, 10.1038/nmeth890 · DOI · Paper page
  44. M Sekimata, 2009, CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus., Immunity, 31, 551, 10.1016/j.immuni.2009.08.021 · DOI
  45. P. G Giresi, 2009, Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)., Methods, 48, 233, 10.1016/j.ymeth.2009.03.003 · DOI
  46. K. J Gaulton, 2010, A map of open chromatin in human pancreatic islets., Nat Genet, 42, 255, 10.1038/ng.530 · DOI · Paper page
  47. D. S Johnson, 2007, Genome-wide mapping of in vivo protein-DNA interactions., Science, 316, 1497, 10.1126/science.1141319 · DOI · Paper page
  48. I Poser, 2008, BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals., Nat Methods, 5, 409, 10.1038/nmeth.1199 · DOI · Paper page
  49. S Hua, 2009, Genomic antagonism between retinoic acid and estrogen signaling in breast cancer., Cell, 137, 1259, 10.1016/j.cell.2009.04.043 · DOI · Paper page
  50. D Raha, 2010, ChIP-seq: a method for global identification of regulatory elements in the genome., Curr Protoc Mol Biol Chapter, 21, Unit 2119 1, 10.1002/0471142727.mb2119s91 · DOI
  51. T. H Kim, 2007, Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome., Cell, 128, 1231, 10.1016/j.cell.2006.12.048 · DOI · Paper page
  52. R Jaenisch, 1997, DNA methylation and imprinting: Why bother?, Trends Genet, 13, 323, 10.1016/S0168-9525(97)01180-3 · DOI · Paper page
  53. H Noushmehr, 2010, Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma., Cancer Cell, 17, 510, 10.1016/j.ccr.2010.03.017 · DOI · Paper page
  54. A. E Teschendorff, 2010, Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer., Genome Res, 20, 440, 10.1101/gr.103606.109 · DOI · Paper page
  55. L Laurent, 2010, Dynamic changes in the human methylome during differentiation., Genome Res, 20, 320, 10.1101/gr.101907.109 · DOI · Paper page
  56. V. K Rakyan, 2010, Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains., Genome Res, 20, 434, 10.1101/gr.103101.109 · DOI · Paper page
  57. A. L Brunner, 2009, Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver., Genome Res, 19, 1044, 10.1101/gr.088773.108 · DOI · Paper page
  58. D. J Galas, 1978, DNAse footprinting: a simple method for the detection of protein-DNA binding specificity., Nucleic Acids Res, 5, 3157, 10.1093/nar/5.9.3157 · DOI · Paper page
  59. E. C Strauss, 1992, In vivo protein-DNA interactions at hypersensitive site 3 of the human beta-globin locus control region., Proc Natl Acad Sci U S A, 89, 5809, 10.1073/pnas.89.13.5809 · DOI
  60. A. P Boyle, 2011, High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells., Genome Res
  61. Y Lu, 2010, Common genetic variants near the Brittle Cornea Syndrome locus ZNF469 influence the blinding disease risk factor central corneal thickness., PLoS Genet, 6, e1000947, 10.1371/journal.pgen.1000947 · DOI
  62. R McDaniell, 2010, Heritable individual-specific and allele-specific chromatin signatures in humans., Science, 328, 235, 10.1126/science.1184655 · DOI · Paper page
  63. M Kasowski, 2010, Variation in transcription factor binding among humans., Science, 328, 232, 10.1126/science.1183621 · DOI · Paper page
  64. R Redon, 2006, Global variation in copy number in the human genome., Nature, 444, 444, 10.1038/nature05329 · DOI · Paper page
  65. J. O Korbel, 2007, Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome., Proc Natl Acad Sci U S A, 104, 10110, 10.1073/pnas.0703834104 · DOI
  66. D. F Conrad, 2010, Mutation spectrum revealed by breakpoint sequencing of human germline CNVs., Nat Genet, 42, 385, 10.1038/ng.564 · DOI · Paper page
  67. A Miele, 2008, Long-range chromosomal interactions and gene regulation., Mol Biosyst, 4, 1046, 10.1039/b803580f · DOI
  68. J Dostie, 2006, Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements., Genome Res, 16, 1299, 10.1101/gr.5571506 · DOI · Paper page
  69. B. R Lajoie, 2009, My5C: web tools for chromosome conformation capture studies., Nat Methods, 6, 690, 10.1038/nmeth1009-690 · DOI
  70. T. E Baroni, 2008, Advances in RIP-chip analysis: RNA-binding protein immunoprecipitation-microarray profiling., Methods Mol Biol, 419, 93, 10.1007/978-1-59745-033-1_6 · DOI
  71. J. D Keene, 2006, RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts., Nat Protoc, 1, 302, 10.1038/nprot.2006.47 · DOI · Paper page
  72. S. A Tenenbaum, 2000, Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays., Proc Natl Acad Sci U S A, 97, 14085, 10.1073/pnas.97.26.14085 · DOI · Paper page
  73. S. A Tenenbaum, 2002, Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays., Methods, 26, 191, 10.1016/S1046-2023(02)00022-1 · DOI · Paper page
  74. N. D Trinklein, 2007, Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome., Genome Res, 17, 720, 10.1101/gr.5716607 · DOI
  75. J. M Lin, 2007, Transcription factor binding and histone modifications in human bidirectional promoters., Genome Res, 17, 818, 10.1101/gr.5623407 · DOI
  76. P. J Collins, 2007, The ets-related transcription factor GABP directs bidirectional transcription., PLoS Genet, 3, e208, 10.1371/journal.pgen.0030208 · DOI
  77. H. M Petrykowska, 2008, Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus., Genome Research, 18, 1238, 10.1101/gr.073817.107 · DOI
  78. J. M Landolin, 2010, Sequence features that drive human promoter function and tissue specificity., Genome Res, 20, 890, 10.1101/gr.100370.109 · DOI
  79. J Khatun, 2008, Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification., Bioinformatics, 24, 674, 10.1093/bioinformatics/btn011 · doi:10.1093/bioinformatics/btn011
  80. B Paten, 2008, Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs., Genome Res, 8, 1814, 10.1101/gr.076554.108 · DOI · Paper page
  81. B Paten, 2008, Genome-wide nucleotide-level mammalian ancestor reconstruction., Genome Res, 18, 1829, 10.1101/gr.076521.108 · DOI
  82. G. M Cooper, 2005, Distribution and intensity of constraint in mammalian genomic sequence., Genome Res, 15, 901, 10.1101/gr.3577405 · DOI · Paper page
  83. S Asthana, 2007, Analysis of sequence conservation at nucleotide resolution., PLoS Comput Biol, 3, e254, 10.1371/journal.pcbi.0030254 · DOI
  84. K. S Pollard, 2010, Detection of nonneutral substitution rates on mammalian phylogenies., Genome Res, 20, 110, 10.1101/gr.097857.109 · DOI · Paper page
  85. J Rozowsky, 2009, PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls., Nat Biotechnol, 27, 66, 10.1038/nbt.1518 · DOI · Paper page
  86. E Birney, 2009, Prepublication data sharing., Nature, 461, 168, 10.1038/461168a · DOI · Paper page
  87. D Wokolorczyk, 2008, A range of cancers is associated with the rs6983267 marker on chromosome 8., Cancer Res, 68, 9982, 10.1158/0008-5472.CAN-08-1838 · DOI
  88. K Curtin, 2009, Meta association of colorectal cancer confirms risk alleles at 8q24 and 18q21., Cancer Epidemiol Biomarkers Prev, 18, 616, 10.1158/1055-9965.EPI-08-0690 · DOI
  89. A. A Al Olama, 2009, Multiple loci on 8q24 associated with prostate cancer susceptibility., Nat Genet, 41, 1058, 10.1038/ng.452 · DOI · Paper page
  90. L Jia, 2009, Functional enhancers at the gene-poor 8q24 cancer-linked locus., PLoS Gene, 5, e1000597, 10.1371/journal.pgen.1000597 · DOI
  91. S Tuupanen, 2009, The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling., Nat Genet, 41, 885, 10.1038/ng.406 · DOI · Paper page
  92. J. B Wright, 2010, Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells., Mol Cell Biol, 30, 1411, 10.1128/MCB.01384-09 · DOI · Paper page
  93. J. M Kidd, 2010, Characterization of missing human genome sequences and copy-number polymorphic insertions., Nat Methods, 7, 365, 10.1038/nmeth.1451 · DOI
  94. Q Li, 2011, Measuring reproducibility of high-throughput experiments., Annals of Applied Statistics
  95. D Reisman, 1996, A novel transcript encoded within the 10-kb first intron of the human p53 tumor suppressor gene (D17S2179E) is induced during differentiation of myeloid leukemia cells., Genomics, 38, 364, 10.1006/geno.1996.0639 · doi:10.1006/geno.1996.0639

Cited by

Metadata

Authors
The ENCODE Project Consortium
Venue
PLoS Biology
Publisher
Public Library of Science (PLoS)
Published
2011-04-19
Volume
9
Issue
4
Pages
e1001046
ISSN
  • 1544-9173 (ISSN-L)
  • 1545-7885
DOI
10.1371/journal.pbio.1001046
OpenAlex
W1544691147
Cited by
1,506
References
26
FWCI
81.00
Type
journal article
Language
en
Open access
gold
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

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