An integrated encyclopedia of DNA elements in the human genome

• Published in: Nature (London) Vol. 489; no. 7414; pp. 57 - 74
• Main Authors: Kundaje, Anshul, Collins, Patrick J, Davis, Carrie A, Khatun, Jainab, Lajoie, Bryan R, Landt, Stephen G, Safi, Alexias, Altshuler, Robert C, Cheng, Chao, Greven, Melissa, Hoffman, Michael M, Lassmann, Timo, Thurman, Robert E, Wu, Weisheng, Xi, Hualin S, Zhuang, Jiali, Gunter, Chris, Dekker, Job, Elnitski, Laura, Giddings, Morgan C, Margulies, Elliott H, Stamatoyannopoulos, John A, Wold, Barbara, Kuiper, Heather C, Dobin, Alex, Tanzer, Andrea, Xue, Chenghai, Zaleski, Chris, Roder, Maik, Baer, Michael T, Bell, Kimberly, Gordon, Assaf, Howald, Cedric, Johnson, Rory, Kingswood, Colin, Li, Guoliang, Luo, Oscar J, Robyr, Daniel, Ruan, Xiaoan, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Wang, Huaien, Hayashizaki, Yoshihide, Hannon, Gregory J, Malladi, Venkat S, Dreszer, Timothy R, Showers, Kimberly A, London, Darin, Zhang, Zhancheng, Keefe, Damian, Zheng, Meizhen, Vielmetter, Jost, Jain, Preti, Pusey, Barbara, Meadows, Sarah K, Absher, Devin M, Pennachio, Len A, Abyzov, Alexej, Barrell, Daniel, Bignell, Alexandra, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Hunt, Toby, Jungreis, Irwin, Loveland, Jane, Manthravadi, Deepa, Pei, Baikang, Snow, Catherine, Zhang, Zhengdong, Alexander, Roger P, Balasubramanian, Suganthi, Bettinger, Keith, Cayting, Philip, Habegger, Lukas, Lamarre-Vincent, Nathan, Lindahl-Allen, Marianne, Monahan, Hannah, Patacsil, Dorrelyn, Struhl, Kevin, Ma, Lijia, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Bates, Daniel L, Canfield, Theresa K, Boatman, Lisa, Neph, Shane J, Roach, Vaughn, Sanchez, Minerva E, Shafer, Anthony O, Vernot, Benjamin, Weaver, Molly A, Akey, Joshua M, Bender, Michael, Navas, Patrick, Hussami, Nadine, Schaub, Marc A
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.09.2012; Nature Publishing Group
• Subjects: 631/208/191; 631/208/205/2138; 631/208/726/649; 631/337; Alleles; Animals; Binding Sites - genetics; Biological and medical sciences; Chromatin - genetics; Chromatin - metabolism; Chromatin Immunoprecipitation; Chromosomes, Human - genetics; Chromosomes, Human - metabolism; Classical genetics, quantitative genetics, hybrids; Deoxyribonuclease I - metabolism; Deoxyribonucleic acid; DNA; DNA - genetics; DNA Footprinting; DNA methylation; DNA Methylation - genetics; DNA-Binding Proteins - metabolism; Encyclopedias as Topic; Exons - genetics; Fundamental and applied biological sciences. Psychology; Genes; Genetic Predisposition to Disease - genetics; Genetic research; Genetic transcription; Genetic Variation - genetics; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genoma humà; Genome, Human - genetics; Genome-Wide Association Study; Genomics; Genètica; Genòmica; Histones - chemistry; Histones - metabolism; Human; Human genome; Humanities and Social Sciences; Humans; Life Sciences; Mammals - genetics; Molecular Sequence Annotation; multidisciplinary; Neoplasms - genetics; Polymorphism, Single Nucleotide - genetics; Promoter Regions, Genetic - genetics; Proteins; Proteins - genetics; Regulatory Sequences, Nucleic Acid - genetics; Science; Sequence Analysis, RNA; Studies; Transcription Factors - metabolism; Transcription, Genetic - genetics; Human; Genome; DNA; chromosome conformation capture; mouse; human cell; in vivo; chromatin; region; map; transcription factor-binding; determinant
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature11247

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research. This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease. ENCODE: the user guide for human DNA The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription-factor association, chromatin structure and histone modification. In this overview, the Consortium guides the readers through the project itself, the data and their integrated analyses. Eighty per cent of the human genome now has at least one biochemical function assigned to it. In addition to expanding our understanding of how gene expression is regulated on a genome-wide scale, the newly identified functional elements should help researchers to interpret the results of genome-wide associated studies because many correspond to sites associated with human disease.