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Perspectives on ENCODE

An Author Correction to this article was published on 26 April 2022

This article has been updated

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.

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Fig. 1: ENCODE assays by year.
Fig. 2: Progress in annotating the human genome.
Fig. 3: Publications using ENCODE data.
Fig. 4: An overview of the mouse ENCODE Project in the current phase.

Change history

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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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Contributions

The role of the NHGRI Project Management Group in the preparation of this paper was limited to coordination and scientific management of the ENCODE consortium. All other authors contributed to the concepts, writing and/or revisions of this manuscript.

Corresponding author

Correspondence to Michael P. Snyder.

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Competing interests

B.E.B. declares outside interests in Fulcrum Therapeutics, 1CellBio, HiFiBio, Arsenal Biosciences, Cell Signaling Technologies, BioMillenia, and Nohla Therapeutics. P.F. is a member of the Scientific Advisory Boards of Fabric Genomics, Inc. and Eagle Genomics, Ltd. M.P.S. is cofounder and scientific advisory board member of Personalis, SensOmics, Mirvie, Qbio, January, Filtricine, and Genome Heart. He serves on the scientific advisory board of these companies and Genapsys and Jupiter. Z.W. is a cofounder of Rgenta Therapeutics and she serves on its scientific advisory board. R.M.M. is an advisor to DNAnexus and Decheng Capital, and has outside interests in IMIDomics, Accuragen and ReadCoor, Inc. The authors declare no other competing financial interests.

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Extended data figures and tables

Extended Data Fig. 1 ENCODE timeline.

Pilot phase: September 2003–September 2007; ENCODE 2: September 2007–September 2012; ENCODE 3: September 2012–January 2017; ENCODE 4: February 2017–present; modENCODE: April 2007–April 2012; mouse ENCODE: 2009–2012.

Supplementary information

Supplementary Information

This file contains the full author list for The ENCODE Project Consortium, and Supplementary Note 1 (Useful URLs).

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The ENCODE Project Consortium., Snyder, M.P., Gingeras, T.R. et al. Perspectives on ENCODE. Nature 583, 693–698 (2020). https://doi.org/10.1038/s41586-020-2449-8

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