Publication Type | Journal Article |
Year of Publication | 2020 |
Authors | Moore, JE, Purcaro, MJ, Pratt, HE, Epstein, CB, Shoresh, N, Adrian, J, Kawli, T, Davis, CA, Dobin, A, Kaul, R, Halow, J, Van Nostrand, EL, Freese, P, Gorkin, DU, Shen, Y, He, Y, Mackiewicz, M, Pauli-Behn, F, Williams, BA, Mortazavi, A, Keller, CA, Zhang, X-O, Elhajjajy, SI, Huey, J, Dickel, DE, Snetkova, V, Wei, X, Wang, X, Rivera-Mulia, JCarlos, Rozowsky, J, Zhang, J, Chhetri, SB, Zhang, J, Victorsen, A, White, KP, Visel, A, Yeo, GW, Burge, CB, Lécuyer, E, Gilbert, DM, Dekker, J, Rinn, J, Mendenhall, EM, Ecker, JR, Kellis, M, Klein, RJ, Noble, WS, Kundaje, A, Guigo, R, Farnham, PJ, J Cherry, M, Myers, RM, Ren, B, Graveley, BR, Gerstein, MB, Pennacchio, LA, Snyder, MP, Bernstein, BE, Wold, B, Hardison, RC, Gingeras, TR, Stamatoyannopoulos, JA, Weng, Z |
Corporate Authors | ENCODE Project Consortium |
Journal | Nature |
Volume | 583 |
Issue | 7818 |
Pages | 699-710 |
Date Published | 2020 07 |
ISSN | 1476-4687 |
Keywords | Animals, Chromatin, Databases, Genetic, Deoxyribonuclease I, DNA, DNA Footprinting, DNA Methylation, DNA Replication Timing, Genome, Genome, Human, Genomics, Histones, Humans, Mice, Mice, Transgenic, Molecular Sequence Annotation, Registries, Regulatory Sequences, Nucleic Acid, RNA-Binding Proteins, Transcription, Genetic, Transposases |
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 ENCODE and Roadmap Epigenomics 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. |
DOI | 10.1038/s41586-020-2493-4 |
Pubmed | |
Alternate Journal | Nature |
PubMed ID | 32728249 |
PubMed Central ID | PMC7410828 |
Grant List | U24 HG009397 / HG / NHGRI NIH HHS / United States U54 HG006991 / HG / NHGRI NIH HHS / United States F32 HG006993 / HG / NHGRI NIH HHS / United States U01 HG007037 / HG / NHGRI NIH HHS / United States U41 HG006992 / HG / NHGRI NIH HHS / United States T32 GM087237 / GM / NIGMS NIH HHS / United States U01 HG007036 / HG / NHGRI NIH HHS / United States UM1 HG009390 / HG / NHGRI NIH HHS / United States U24 HG009446 / HG / NHGRI NIH HHS / United States U54 HG007010 / HG / NHGRI NIH HHS / United States UM1 HG009442 / HG / NHGRI NIH HHS / United States U54 HG006998 / HG / NHGRI NIH HHS / United States P30 CA014195 / CA / NCI NIH HHS / United States U54 HG007004 / HG / NHGRI NIH HHS / United States U01 HG007033 / HG / NHGRI NIH HHS / United States U54 HG006996 / HG / NHGRI NIH HHS / United States U01 HG009431 / HG / NHGRI NIH HHS / United States U54 HG007005 / HG / NHGRI NIH HHS / United States U54 HG007002 / HG / NHGRI NIH HHS / United States R01 DK068634 / DK / NIDDK NIH HHS / United States U01 HG007019 / HG / NHGRI NIH HHS / United States U54 HG006994 / HG / NHGRI NIH HHS / United States U54 HG006997 / HG / NHGRI NIH HHS / United States R01 GM083337 / GM / NIGMS NIH HHS / United States R37 DK050107 / DK / NIDDK NIH HHS / United States U41 HG007000 / HG / NHGRI NIH HHS / United States |
Nature DOI:10.1038/s41586-020-2493-4
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
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