Perspectives on ENCODE

The ENCODE Project Consortium

doi:10.1038/s41586-020-2449-8

Perspectives on ENCODE

The ENCODE Project Consortium

School of Medicine

Research output: Contribution to journal › Review article › peer-review

16 Scopus citations

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

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10.1038/s41586-020-2449-8

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@article{15d6db32e88e455984f085a4d553246e,

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 = "{The ENCODE Project Consortium} and Federico Abascal and Reyes Acosta and Addleman, {Nicholas J.} and Jessika Adrian and Veena Afzal and Bronwen Aken and Akiyama, {Jennifer A.} and Jammal, {Omar Al} and Henry Amrhein and Anderson, {Stacie M.} and Andrews, {Gregory R.} and Igor Antoshechkin and Ardlie, {Kristin G.} and Joel Armstrong and Matthew Astley and Budhaditya Banerjee and Barkal, {Amira A.} and Barnes, {If H.A.} and Iros Barozzi and Daniel Barrell and Gemma Barson and Daniel Bates and Baymuradov, {Ulugbek K.} and Cassandra Bazile and Beer, {Michael A.} and Samantha Beik and Bender, {M. A.} and Ruth Bennett and Bernstein, {Bradley E.} and Anand Bhaskar and Alexandra Bignell and Blue, {Steven M.} and Bodine, {David M.} and Carles Boix and Nathan Boley and Tyler Borrman and Beatrice Borsari and Boyle, {Alan P.} and Brandsmeier, {Laurel A.} and Alessandra Breschi and Brooks, {Jason A.} and Michael Buckley and Burge, {Christopher B.} and Rachel Byron and Eileen Cahill and Lingling Cai and Lulu Cao and Mark Carty and Castanon, {Rosa G.} and Andres Castillo",

note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = jul,

day = "30",

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

language = "English (US)",

volume = "583",

pages = "693--698",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7818",

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T1 - Perspectives on ENCODE

AU - The ENCODE Project Consortium

AU - Abascal, Federico

AU - Acosta, Reyes

AU - Addleman, Nicholas J.

AU - Adrian, Jessika

AU - Afzal, Veena

AU - Aken, Bronwen

AU - Akiyama, Jennifer A.

AU - Jammal, Omar Al

AU - Amrhein, Henry

AU - Anderson, Stacie M.

AU - Andrews, Gregory R.

AU - Antoshechkin, Igor

AU - Ardlie, Kristin G.

AU - Armstrong, Joel

AU - Astley, Matthew

AU - Banerjee, Budhaditya

AU - Barkal, Amira A.

AU - Barnes, If H.A.

AU - Barozzi, Iros

AU - Barrell, Daniel

AU - Barson, Gemma

AU - Bates, Daniel

AU - Baymuradov, Ulugbek K.

AU - Bazile, Cassandra

AU - Beer, Michael A.

AU - Beik, Samantha

AU - Bender, M. A.

AU - Bennett, Ruth

AU - Bernstein, Bradley E.

AU - Bhaskar, Anand

AU - Bignell, Alexandra

AU - Blue, Steven M.

AU - Bodine, David M.

AU - Boix, Carles

AU - Boley, Nathan

AU - Borrman, Tyler

AU - Borsari, Beatrice

AU - Boyle, Alan P.

AU - Brandsmeier, Laurel A.

AU - Breschi, Alessandra

AU - Brooks, Jason A.

AU - Buckley, Michael

AU - Burge, Christopher B.

AU - Byron, Rachel

AU - Cahill, Eileen

AU - Cai, Lingling

AU - Cao, Lulu

AU - Carty, Mark

AU - Castanon, Rosa G.

AU - Castillo, Andres

PY - 2020/7/30

Y1 - 2020/7/30

N2 - 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.

AB - 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.

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UR - http://www.scopus.com/inward/citedby.url?scp=85088796908&partnerID=8YFLogxK

U2 - 10.1038/s41586-020-2449-8

DO - 10.1038/s41586-020-2449-8

M3 - Review article

C2 - 32728248

AN - SCOPUS:85088796908

SN - 0028-0836

VL - 583

SP - 693

EP - 698

JO - Nature

JF - Nature

IS - 7818

ER -

Perspectives on ENCODE

Abstract

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