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Expanded encyclopaedias of DNA elements in the human and mouse genomes

Moore, Jill E. and Purcaro, Michael J. and Pratt, Henry E. and Epstein, Charles B. and Shoresh, Noam and Adrian, Jessika and Kawli, Trupti and Davis, Carrie A. and Dobin, Alexander and Kaul, Rajinder and Halow, Jessica and Van Nostrand, Eric L. and Freese, Peter and Gorkin, David U. and Shen, Yin and He, Yupeng and Mackiewicz, Mark and Pauli-Behn, Florencia and Williams, Brian A. and Mortazavi, Ali and Keller, Cheryl A. and Zhang, Xiao-Ou and Elhajjajy, Shaimae I. and Huey, Jack and Dickel, Diane E. and Snetkova, Valentina and Wei, Xintao and Wang, Xiaofeng and Rivera-Mulia, Juan Carlos and Rozowsky, Joel and Zhang, Jing and Chhetri, Surya B. and Zhang, Jialing and Victorsen, Alec and White, Kevin P. and Visel, Axel and Yeo, Gene W. and Burge, Christopher B. and Lécuyer, Eric and Gilbert, David M. and Dekker, Job and Rinn, John and Mendenhall, Eric M. and Ecker, Joseph R. and Kellis, Manolis and Klein, Robert J. and Noble, William S. and Kundaje, Anshul and Guigó, Roderic and Farnham, Peggy J. and Cherry, J. Michael and Myers, Richard M. and Ren, Bing and Graveley, Brenton R. and Gerstein, Mark B. and Pennacchio, Len A. and Snyder, Michael P. and Bernstein, Bradley E. and Wold, Barbara and Hardison, Ross C. and Gingeras, Thomas R. and Stamatoyannopoulos, John A. and Weng, Zhiping (2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 583 (7818). pp. 699-710. ISSN 0028-0836. https://resolver.caltech.edu/CaltechAUTHORS:20200729-134110926

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41586-020-2493-4DOIArticle
https://rdcu.be/b5WwWPublisherFree ReadCube access
https://github.com/weng-lab/ENCODE-cCREsRelated ItemCode
https://github.com/weng-lab/SCREENRelated ItemCode
ORCID:
AuthorORCID
Moore, Jill E.0000-0002-3023-0806
Purcaro, Michael J.0000-0002-4735-4215
Epstein, Charles B.0000-0001-8358-8345
Kaul, Rajinder0000-0002-7895-9284
Gorkin, David U.0000-0003-4944-4107
Shen, Yin0000-0001-9901-5613
Mackiewicz, Mark0000-0002-7088-1902
Mortazavi, Ali0000-0002-4259-6362
Keller, Cheryl A.0000-0001-6594-0245
Dickel, Diane E.0000-0001-5497-6824
Rivera-Mulia, Juan Carlos0000-0002-7566-3875
Rozowsky, Joel0000-0002-3565-0762
Visel, Axel0000-0002-4130-7784
Yeo, Gene W.0000-0002-0799-6037
Burge, Christopher B.0000-0001-9047-5648
Gilbert, David M.0000-0001-8087-9737
Dekker, Job0000-0001-5631-0698
Rinn, John0000-0002-7231-7539
Mendenhall, Eric M.0000-0002-7395-6295
Ecker, Joseph R.0000-0001-5799-5895
Kellis, Manolis0000-0001-7113-9630
Klein, Robert J.0000-0003-3539-5391
Kundaje, Anshul0000-0003-3084-2287
Farnham, Peggy J.0000-0003-4469-7914
Cherry, J. Michael0000-0001-9163-5180
Ren, Bing0000-0002-5435-1127
Pennacchio, Len A.0000-0002-8748-3732
Snyder, Michael P.0000-0003-0784-7987
Bernstein, Bradley E.0000-0002-5726-6278
Hardison, Ross C.0000-0003-4084-7516
Weng, Zhiping0000-0002-3032-7966
Additional Information:© 2020 Springer Nature Limited. Received 26 August 2017; Accepted 27 May 2020; Published 29 July 2020. Data availability: All data are available on the ENCODE data portal: www.encodeproject.org. Code availability: All code is available on GitHub from the links provided in the methods section. Code related to the Registry of cCREs can be found at https://github.com/weng-lab/ENCODE-cCREs. Code related to SCREEN can be found at https://github.com/weng-lab/SCREEN. We thank additional members of our laboratories and institutions who contributed to the experimental and analytical components of this project. We also thank the external advisors of the ENCODE Project for providing valuable input. This work was supported by grants from the NIH under U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442. These authors contributed equally: Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A. Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L. Van Nostrand, Peter Freese, David U. Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn These authors jointly supervised this work: J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos & Zhiping Weng Author Contributions: See the consortium author list in the Supplementary Information for full details of author contributions. Data analysis coordination (data analysis): J.E.M., M.J.P., H.E.P., B.W., R.C.H., T.R.G., J.A.S., Z.W. Data production coordination (data production): C.B.E., N.S., J.A., T.K., C.A.D., A.D., R.K., J.H., E.L.V.N., P.F., D.U.G., Y.S., Y.H., M.M., F.P.-B., R.M.M., B.R., B.R.G., L.A.P., M.P.S., B.E.B., B.W., R.C.H., T.R.G., J.A.S. Data analysis leads (data analysis): J.E.M., M.J.P., H.E.P., X.-O.Z., S.I.E., J.H., J.R., J.Z., M.K., R.J.K., W.S.N., A.K., R.G., M.B.G., B.W., R.C.H., Z.W. Data production leads (data production): C.B.E., N.S., J.A., T.K., C.A.D., A.D., R.K., J.H., E.L.V.N., P.F., D.U.G., Y.S., Y.H., M.M., F.P.-B., B.A.W., A.M., C.A.K., S.B.C., J.Z., A.V., K.P.W., A.V., G.W.Y., C.B.B., E.L., D.M.G., J.D., J.R., E.M.M., J.R.E., P.J.F., R.M.M., B.R., B.R.G., L.A.P., M.P.S., B.E.B., B.W., R.C.H., T.R.G., J.A.S. Writing group: R.M.M., B.R., B.R.G., L.A.P., M.P.S., B.E.B., B.W., R.C.H., T.R.G., J.A.S., Z.W. Principal investigators (steering committee): J.M.C., R.M.M., B.R., B.R.G., M.P.S., B.E.B., T.R.G., J.A.S., Z.W. Competing interests: B.E.B. declares outside interests in Fulcrum Therapeutics, 1CellBio, HiFiBio, Arsenal Biosciences, Cell Signaling Technologies, BioMillenia, and Nohla Therapeutics. P. Flicek is a member of the Scientific Advisory Boards of Fabric Genomics, Inc. and Eagle Genomics, Ltd. M.P.S. is cofounder of Personalis, SensOmics, Mirvie, Qbio, January, Filtircine, and Genome Heart. He serves on the scientific advisory board of these companies and Genapsys and Jupiter. Z. Weng is a cofounder of Rgenta Therapeutics and she serves on its scientific advisory board. G.W.Y. is co-founder, member of the Board of Directors, on the SAB, equity holder, and paid consultant for Locana and Eclipse BioInnovations, and a visiting professor at the National University of Singapore. G.W.Y.’s interests have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. E.L.V.N. is co-founder, member of the Board of Directors, on the SAB, equity holder, and paid consultant for Eclipse BioInnovations. E.L.V.N.’s interests have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. B.R. is a co-founder and member of SAB of Arima Genomics, Inc. The authors declare no other competing financial interests.
Funders:
Funding AgencyGrant Number
NIHU01HG007019
NIHU01HG007033
NIHU01HG007036
NIHU01HG007037
NIHU41HG006992
NIHU41HG006993
NIHU41HG006994
NIHU41HG006995
NIHU41HG006996
NIHU41HG006997
NIHU41HG006998
NIHU41HG006999
NIHU41HG007000
NIHU41HG007001
NIHU41HG007002
NIHU41HG007003
NIHU54HG006991
NIHU54HG006997
NIHU54HG006998
NIHU54HG007004
NIHU54HG007005
NIHU54HG007010
NIHUM1HG009442
Subject Keywords:Data integration; Epigenomics; Functional genomics
Issue or Number:7818
Record Number:CaltechAUTHORS:20200729-134110926
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200729-134110926
Official Citation:Abascal, F., Acosta, R., Addleman, N.J. et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583, 699–710 (2020). https://doi.org/10.1038/s41586-020-2493-4
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:104642
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:29 Jul 2020 22:00
Last Modified:29 Jul 2020 22:00

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