Perspectives on ENCODE

ENCODE Project Consortium; Juan Carlos Rivera-Mulia

doi:10.1038/s41586-020-2449-8

Perspectives on ENCODE

ENCODE Project Consortium, Juan Carlos Rivera-Mulia

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Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Original language	English (US)
Pages (from-to)	693-698
Number of pages	6
Journal	Nature
Volume	583
Issue number	7818
DOIs	https://doi.org/10.1038/s41586-020-2449-8
State	Published - Jul 30 2020

Bibliographical note

Funding Information:
Acknowledgements We thank S. Moore, E. Cahill, M. Kellis and J. Li for their assistance, and B. Wold for helpful comments. This work was supported by grants from the NIH: U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U41HG007234, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442.

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© 2020, The Author(s).

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title = "Perspectives on ENCODE",

abstract = "The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.",

author = "{ENCODE Project Consortium} and Snyder, {Michael P} and Gingeras, {Thomas R} and Moore, {Jill E} and Zhiping Weng and Gerstein, {Mark B} and Bing Ren and Hardison, {Ross C} and Stamatoyannopoulos, {John A} and Graveley, {Brenton R} and Feingold, {Elise A} and Pazin, {Michael J} and Michael Pagan and Gilchrist, {Daniel A} and Hitz, {Benjamin C} and Cherry, {J Michael} and Bernstein, {Bradley E} and Mendenhall, {Eric M} and Zerbino, {Daniel R} and Adam Frankish and Paul Flicek and Myers, {Richard M} and Rivera-Mulia, {Juan Carlos}",

note = "Funding Information: Acknowledgements We thank S. Moore, E. Cahill, M. Kellis and J. Li for their assistance, and B. Wold for helpful comments. This work was supported by grants from the NIH: U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U41HG007234, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

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doi = "10.1038/s41586-020-2449-8",

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AU - Snyder, Michael P

AU - Gingeras, Thomas R

AU - Moore, Jill E

AU - Weng, Zhiping

AU - Gerstein, Mark B

AU - Ren, Bing

AU - Hardison, Ross C

AU - Stamatoyannopoulos, John A

AU - Graveley, Brenton R

AU - Feingold, Elise A

AU - Pazin, Michael J

AU - Pagan, Michael

AU - Gilchrist, Daniel A

AU - Hitz, Benjamin C

AU - Cherry, J Michael

AU - Bernstein, Bradley E

AU - Mendenhall, Eric M

AU - Zerbino, Daniel R

AU - Frankish, Adam

AU - Flicek, Paul

AU - Myers, Richard M

AU - Rivera-Mulia, Juan Carlos

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ER -

Perspectives on ENCODE

Abstract

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