Expanded encyclopaedias of DNA elements in the human and mouse genomes

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. Nostrand, Peter Freese, David U. Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A. Williams, Ali Mortazavi, Cheryl A. Keller, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Diane E. Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B. Chhetri, Jialing Zhang, Alec Victorsen, Kevin P. White, Axel Visel, Gene W. Yeo, Christopher B. Burge, Eric Lécuyer, David M. Gilbert, Job Dekker, John Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert J. Klein, William S. Noble, Anshul Kundaje, Roderic Guigó, Peggy J. Farnham, 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 () and Zhiping Weng ()
Additional contact information
Jill E. Moore: University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology
Michael J. Purcaro: University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology
Henry E. Pratt: University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology
Charles B. Epstein: The Broad Institute of Harvard and MIT
Noam Shoresh: The Broad Institute of Harvard and MIT
Jessika Adrian: Stanford University
Trupti Kawli: Stanford University
Carrie A. Davis: Functional Genomics
Alexander Dobin: Functional Genomics
Rajinder Kaul: Altius Institute for Biomedical Sciences
Jessica Halow: Altius Institute for Biomedical Sciences
Eric L. Nostrand: University of California, San Diego
Peter Freese: Massachusetts Institute of Technology
David U. Gorkin: University of California, San Diego
Yin Shen: University of California, San Diego
Yupeng He: The Salk Institute for Biological Studies
Mark Mackiewicz: HudsonAlpha Institute for Biotechnology
Florencia Pauli-Behn: HudsonAlpha Institute for Biotechnology
Brian A. Williams: California Institute of Technology
Ali Mortazavi: University of California Irvine
Cheryl A. Keller: The Pennsylvania State University
Xiao-Ou Zhang: University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology
Shaimae I. Elhajjajy: University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology
Jack Huey: University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology
Diane E. Dickel: Lawrence Berkeley National Laboratory
Valentina Snetkova: Lawrence Berkeley National Laboratory
Xintao Wei: Institute for Systems Genomics, UConn Health
Xiaofeng Wang: Université de Montréal, Montréal
Juan Carlos Rivera-Mulia: Florida State University
Joel Rozowsky: Yale University
Jing Zhang: Yale University
Surya B. Chhetri: HudsonAlpha Institute for Biotechnology
Jialing Zhang: Yale University
Alec Victorsen: The University of Chicago
Kevin P. White: Tempus Labs
Axel Visel: Lawrence Berkeley National Laboratory
Gene W. Yeo: University of California, San Diego
Christopher B. Burge: Massachusetts Institute of Technology
Eric Lécuyer: Université de Montréal, Montréal
David M. Gilbert: Florida State University
Job Dekker: University of Massachusetts Medical School
John Rinn: University of Colorado Boulder
Eric M. Mendenhall: HudsonAlpha Institute for Biotechnology
Joseph R. Ecker: The Salk Institute for Biological Studies
Manolis Kellis: The Broad Institute of Harvard and MIT
Robert J. Klein: Icahn School of Medicine at Mount Sinai
William S. Noble: University of Washington School of Medicine
Anshul Kundaje: Stanford University
Roderic Guigó: The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra
Peggy J. Farnham: University of Southern California
J. Michael Cherry: Stanford University
Richard M. Myers: HudsonAlpha Institute for Biotechnology
Bing Ren: University of California, San Diego
Brenton R. Graveley: Institute for Systems Genomics, UConn Health
Mark B. Gerstein: Yale University
Len A. Pennacchio: Lawrence Berkeley National Laboratory
Michael P. Snyder: Stanford University
Bradley E. Bernstein: Massachusetts General Hospital and Harvard Medical School
Barbara Wold: California Institute of Technology
Ross C. Hardison: The Pennsylvania State University
Thomas R. Gingeras: Functional Genomics
John A. Stamatoyannopoulos: Altius Institute for Biomedical Sciences
Zhiping Weng: University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology

Nature, 2020, vol. 583, issue 7818, 699-710

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41586-020-2493-4

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