Expanded encyclopaedias of DNA elements in the human and mouse genomes Journal Article

   

Authors:	The ENCODE Project Consortium; Moore, J. E.; Purcaro, M. J.; Pratt, H. E.; Epstein, C. B.; Shoresh, N.; Adrian, J.; Kawli, T.; Davis, C. A.; Dobin, A.; Kaul, R.; Halow, J.; Van Nostrand, E. L.; Freese, P.; Gorkin, D. U.; Shen, Y.; He, Y.; Mackiewicz, M.; Pauli-Behn, F.; Williams, B. A.; Mortazavi, A.; Keller, C. A.; Zhang, X. O.; Elhajjajy, S. I.; Huey, J.; Dickel, D. E.; Snetkova, V.; Wei, X.; Wang, X.; Rivera-Mulia, J. C.; Rozowsky, J.; Zhang, J.; Chhetri, S. B.; Zhang, J.; Victorsen, A.; White, K. P.; Visel, A.; Yeo, G. W.; Burge, C. B.; Lécuyer, E.; Gilbert, D. M.; Dekker, J.; Rinn, J.; Mendenhall, E. M.; Ecker, J. R.; Kellis, M.; Klein, R. J.; Noble, W. S.; Kundaje, A.; Guigó, R.; Farnham, P. J.; Cherry, J. M.; Myers, R. M.; Ren, B.; Graveley, B. R.; Gerstein, M. B.; Pennacchio, L. A.; Snyder, M. P.; Bernstein, B. E.; Wold, B.; Hardison, R. C.; Gingeras, T. R.; Stamatoyannopoulos, J. A.; Weng, Z.
Contributors:	Gonzalez, A.; Setty, M.; Lu, Y.; Perez, A. R.; Pritykin, Y.; Carty, M.; Leslie, C. S.
Article Title:	Expanded encyclopaedias of DNA elements in the human and mouse genomes
Abstract:	The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes. © 2020, The Author(s).
Keywords:	controlled study; human tissue; human cell; nonhuman; dna replication; genetic analysis; animal cell; animal tissue; genetic association; gene function; dna methylation; rna; genome analysis; dna; epigenetics; chromatin; gene control; genome; dna structure; rodent; dna determination; rna transcription; fetus development; protein rna binding; data set; transposase; genetic organization; deoxyribonuclease i; human; priority journal; article
Journal Title:	Nature
Volume:	583
Issue:	7818
ISSN:	0028-0836
Publisher:	Nature Publishing Group
Date Published:	2020-07-30
Start Page:	699
End Page:	710
Language:	English
DOI:	10.1038/s41586-020-2493-4
PUBMED:	32728249
PROVIDER:	scopus
PMCID:	PMC7410828
DOI/URL:	https://www.scopus.com/inward/record.uri?eid=2-s2.0-85088796075&doi=10.1038%2fs41586-020-2493-4&partnerID=40&md5=3a8401797633300c8a5d03cfc361b0c8
Notes:	Article -- Erratum issued, see DOI: 10.1038/s41586-021-04226-3 -- Source: Scopus

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