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Perspectives on ENCODE
Nature ( IF 50.5 ) Pub Date : 2020-07-29 , DOI: 10.1038/s41586-020-2449-8
, Michael P Snyder _{1,

2} , Thomas R Gingeras ₃ , Jill E Moore ₄ , Zhiping Weng _{4,

5,

6} , Mark B Gerstein ₇ , Bing Ren _{8,

9} , Ross C Hardison ₁₀ , John A Stamatoyannopoulos _{11,

12,

13} , Brenton R Graveley ₁₄ , Elise A Feingold ₁₅ , Michael J Pazin ₁₅ , Michael Pagan ₁₅ , Daniel A Gilchrist ₁₅ , Benjamin C Hitz ₁ , J Michael Cherry ₁ , Bradley E Bernstein ₁₆ , Eric M Mendenhall _{17,

18} , Daniel R Zerbino ₁₉ , Adam Frankish ₁₉ , Paul Flicek ₁₉ , Richard M Myers ₁₈

Affiliation

Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA.
Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China.
Bioinformatics Program, Boston University, Boston, MA, USA.
Yale University, New Haven, CT, USA.
Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Department of Medicine, University of Washington, Seattle, WA, USA.
Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA.
HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.

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. 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.

中文翻译：

对编码的看法

DNA 元素百科全书 (ENCODE) 项目于 2003 年启动，其长期目标是开发人类基因组功能元素的综合图谱。这些包括基因、与基因调控相关的生化区域（例如转录因子结合位点、开放染色质和组蛋白标记）和转录亚型。这些标记作为候选顺式调节元件 (cCRE) 的位点，可能在调节基因表达中发挥功能作用1。该项目已扩展到模型生物，特别是小鼠。在ENCODE的第三阶段中，分别为人类和小鼠生成了近100万个和超过30万个cCRE注释，这些为科学界提供了宝贵的资源。作者总结了 ENCODE 项目的历史、ENCODE 1 和 ENCODE 2 的成就，以及 ENCODE 3 中生成和分析的新数据如何补充之前的阶段。

更新日期：2020-07-29

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