Abstract
The ENCyclopedia Of DNA Elements (ENCODE) project is a public research consortium that aims to identify all functional elements of the human genome sequence. The project comprised 1640 data sets, from 147 different cell type and the findings were released in a coordinated set of 34 publications across several journals. The ENCODE publications report that 80.4% of the human genome displays some functionality. These data have important implications for interpreting results from large-scale genetics studies. We reviewed some of the key findings from the ENCODE publications and discuss how they can influence or inform further investigations into the genetic factors contributing to neuropsychiatric disorders.
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References
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447: 799–816.
Ni Y, Weber Hall A, Battenhouse A, Iyer VR . Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genet 2012; 13: 46.
Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H et al. Systematic localization of common disease-associated variation in regulatory DNA. Science (New York, NY) 2012; 337: 1190–1195.
Ward LD, Kellis M . Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science 2012; 337: 1675–1678.
Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA . Circuitry and dynamics of human transcription factor regulatory networks. Cell 2012; 150: 1274–1286.
Felsenfeld G, Boyes J, Chung J, Clark D, Studitsky V . Chromatin structure and gene expression. Proc Natl Acad Sci USA 1996; 93 (18): 9384–9388.
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E et al. The accessible chromatin landscape of the human genome. Nature 2012; 489: 75–82.
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol 2012; 13: R53.
Dekker J . Gene regulation in the third dimension. Science (New York, NY) 2008; 319: 1793–1794.
Sanyal A, Lajoie BR, Jain G, Dekker J . The long-range interaction landscape of gene promoters. Nature, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 2012; 489: 109–113.
Maston GA, Evans SK, Green MR . Transcriptional regulatory elements in the human genome. Annu Rev Genomics Human Genet 2006; 7: 29–59.
Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A et al. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol 2012; 13: R48.
Whiteld TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND et al. Functional analysis of transcription factor binding sites in human promoters. Genome Biol 2012; 13: R50.
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan K-K, Cheng C et al. Architecture of the human regulatory network derived from ENCODE data. Nature 2012; 489: 91–100.
Dorus S, Vallender EJ, Evans PD, Anderson JR, Gilbert SL, Mahowald M et al. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 2004; 119: 1027–1040.
Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 2006; 443: 167–172.
Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012; 489: 83–90.
Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE et al. Personal and population genomics of human regulatory variation. Genome Res 2012; 22: 1689–1697.
Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 2012; 22: 1790–1797.
Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M . Linking disease associations with regulatory information in the human genome. Genome Res 2012; 22: 1748–1759.
Acknowledgements
Our work is supported by an MRC Centre Grant (G0801418) and an MRC Programme Grant (G0800509).
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Kavanagh, D., Dwyer, S., O'Donovan, M. et al. The ENCODE project: implications for psychiatric genetics. Mol Psychiatry 18, 540–542 (2013). https://doi.org/10.1038/mp.2013.13
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DOI: https://doi.org/10.1038/mp.2013.13
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