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Nature DOI:10.1038/s41586-020-2493-4

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Publication TypeJournal Article
Year of Publication2020
AuthorsMoore, 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 AuthorsENCODE Project Consortium
JournalNature
Volume583
Issue7818
Pages699-710
Date Published2020 07
ISSN1476-4687
KeywordsAnimals, 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.

DOI10.1038/s41586-020-2493-4
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/32728249?dopt=Abstract

Alternate JournalNature
PubMed ID32728249
PubMed Central IDPMC7410828
Grant ListU24 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