Author
Listed:
- 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
University of Washington School of Medicine)
- 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
University of California, San Diego)
- Yin Shen
(University of California, San Diego
University of California, San Francisco)
- 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
McGill University
Institut de Recherches Cliniques de Montréal (IRCM))
- Juan Carlos Rivera-Mulia
(Florida State University
University of Minnesota Medical School)
- Joel Rozowsky
(Yale University)
- Jing Zhang
(Yale University)
- Surya B. Chhetri
(HudsonAlpha Institute for Biotechnology
University of Alabama in Huntsville)
- Jialing Zhang
(Yale University)
- Alec Victorsen
(The University of Chicago)
- Kevin P. White
(Tempus Labs)
- Axel Visel
(Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
University of California, Merced)
- Gene W. Yeo
(University of California, San Diego)
- Christopher B. Burge
(Massachusetts Institute of Technology)
- Eric Lécuyer
(Université de Montréal, Montréal
McGill University
Institut de Recherches Cliniques de Montréal (IRCM))
- 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
University of Alabama in Huntsville)
- Joseph R. Ecker
(The Salk Institute for Biological Studies
The Salk Institute for Biological Studies)
- Manolis Kellis
(The Broad Institute of Harvard and MIT
Massachusetts Institute of Technology)
- 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
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
Lawrence Berkeley National Laboratory
University of California)
- Michael P. Snyder
(Stanford University
Stanford School of Medicine)
- 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
University of Washington School of Medicine
University of Washington School of Medicine)
- Zhiping Weng
(University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology
Tongji University
Boston University)
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.
Suggested Citation
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. No, 2020.
"Expanded encyclopaedias of DNA elements in the human and mouse genomes,"
Nature, Nature, vol. 583(7818), pages 699-710, July.
Handle:
RePEc:nat:nature:v:583:y:2020:i:7818:d:10.1038_s41586-020-2493-4
DOI: 10.1038/s41586-020-2493-4
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