TY - JOUR
T1 - Expanded encyclopaedias of DNA elements in the human and mouse genomes
AU - ENCODE Project Consortium
AU - Moore, Jill E
AU - Purcaro, Michael J
AU - Pratt, Henry E
AU - Epstein, Charles B
AU - Shoresh, Noam
AU - Adrian, Jessika
AU - Kawli, Trupti
AU - Davis, Carrie A
AU - Dobin, Alexander
AU - Kaul, Rajinder
AU - Halow, Jessica
AU - Van Nostrand, Eric L
AU - Freese, Peter
AU - Gorkin, David U
AU - Shen, Yin
AU - He, Yupeng
AU - Mackiewicz, Mark
AU - Pauli-Behn, Florencia
AU - Williams, Brian A
AU - Mortazavi, Ali
AU - Keller, Cheryl A
AU - Zhang, Xiao-Ou
AU - Elhajjajy, Shaimae I
AU - Huey, Jack
AU - Dickel, Diane E
AU - Snetkova, Valentina
AU - Wei, Xintao
AU - Wang, Xiaofeng
AU - Rivera-Mulia, Juan Carlos
AU - Rozowsky, Joel
AU - Zhang, Jing
AU - Chhetri, Surya B
AU - Zhang, Jialing
AU - Victorsen, Alec
AU - White, Kevin P
AU - Visel, Axel
AU - Yeo, Gene W
AU - Burge, Christopher B
AU - Lécuyer, Eric
AU - Gilbert, David M
AU - Dekker, Job
AU - Rinn, John
AU - Mendenhall, Eric M
AU - Ecker, Joseph R
AU - Kellis, Manolis
AU - Klein, Robert J
AU - Noble, William S
AU - Kundaje, Anshul
AU - Guigó, Roderic
AU - Farnham, Peggy J
N1 - Funding Information:
Acknowledgements 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.
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/7/30
Y1 - 2020/7/30
N2 - 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.
AB - 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.
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U2 - 10.1038/s41586-020-2493-4
DO - 10.1038/s41586-020-2493-4
M3 - Article
C2 - 32728249
SN - 0028-0836
VL - 583
SP - 699
EP - 710
JO - Nature
JF - Nature
IS - 7818
ER -