Perspectives on ENCODE

被引：133

作者：

Snyder, Michael P. ^{[1
,2
]}

Gingeras, Thomas R. ^{[3
]}

Moore, Jill E. ^{[4
]}

Weng, Zhiping ^{[4
,5
,6
]}

Gerstein, Mark B. ^{[7
]}

Ren, Bing ^{[8
,9
]}

Hardison, Ross C. ^{[10
]}

Stamatoyannopoulos, John A. ^{[11
,12
,13
]}

Graveley, Brenton R. ^{[14
]}

Feingold, Elise A. ^{[15
]}

Pazin, Michael J. ^{[15
]}

Pagan, Michael ^{[15
]}

Gilchrist, Daniel A. ^{[15
]}

Hitz, Benjamin C. ^{[1
]}

Cherry, J. Michael ^{[1
]}

Bernstein, Bradley E. ^{[16
,17
,18
]}

Mendenhall, Eric M. ^{[19
,20
]}

Zerbino, Daniel R. ^{[21
]}

Frankish, Adam ^{[21
]}

Flicek, Paul ^{[21
]}

Myers, Richard M. ^{[20
]}

机构：

[1] Stanford Univ, Sch Med, Dept Genet, Palo Alto, CA 94304 USA

[2] Stanford Sch Med, Cardiovasc Inst, Stanford, CA 94305 USA

[3] Cold Spring Harbor Lab, Funct Genom, POB 100, Cold Spring Harbor, NY 11724 USA

[4] Univ Massachusetts, Sch Med, Program Bioinformat & Integrat Biol, Worcester, MA USA

[5] Tongji Univ, Shanghai Pulm Hosp, Sch Life Sci & Technol, Dept Thorac Surg,Clin Translat Res Ctr, Shanghai, Peoples R China

[6] Boston Univ, Bioinformat Program, Boston, MA 02215 USA

[7] Yale Univ, New Haven, CT USA

[8] Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA USA

[9] Univ Calif San Diego, Ctr Epigenom, La Jolla, CA 92103 USA

[10] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA

[11] Altius Inst Biomed Sci, Seattle, WA USA

[12] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[13] Univ Washington, Dept Med, Seattle, WA USA

[14] UConn Hlth, Inst Syst Genom, Dept Genet & Genome Sci, Farmington, CT USA

[15] NHGRI, NIH, Bethesda, MD 20892 USA

[16] Massachusetts Gen Hosp, Broad Inst, Boston, MA 02114 USA

[17] Massachusetts Gen Hosp, Dept Pathol, Boston, MA 02114 USA

[18] Harvard Med Sch, Boston, MA 02115 USA

[19] Univ Alabama, Biol Sci, Huntsville, AL 35899 USA

[20] HudsonAlpha Inst Biotechnol, Huntsville, AL USA

[21] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge, England

来源：

NATURE | 2020年 / 583卷 / 7818期

基金：

英国医学研究理事会; 英国生物技术与生命科学研究理事会;

关键词：

DNA ELEMENTS; REGULATORY INFORMATION; TRANSCRIPTION FACTORS; FUNCTIONAL ELEMENTS; HUMAN GENOME; MOUSE; IDENTIFICATION; ENCYCLOPEDIA; PRINCIPLES; DROSOPHILA;

D O I：

10.1038/s41586-020-2449-8

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 candidatecis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression(1). 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. The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

引用

页码：693 / +

页数：9

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