Perspectives on ENCODE

ENCODE Project Consortium; Michael P Snyder; Thomas R Gingeras; Jill E Moore; Zhiping Weng; Mark B Gerstein; Bing Ren; Ross C Hardison; John A Stamatoyannopoulos; Brenton R Graveley; Elise A Feingold; Michael J Pazin; Michael Pagan; Daniel A Gilchrist; Benjamin C Hitz; J Michael Cherry; Bradley E Bernstein; Eric M Mendenhall; Daniel R Zerbino; Adam Frankish; Paul Flicek; Richard M Myers

doi:10.1038/s41586-020-2449-8

Perspectives on ENCODE

Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29.

Authors

ENCODE Project Consortium; Michael P Snyder^{1

2}, Thomas R Gingeras³, Jill E Moore⁴, Zhiping Weng^{4

5

6}, Mark B Gerstein⁷, Bing Ren^{8

9}, Ross C Hardison¹⁰, John A Stamatoyannopoulos^{11

12

13}, Brenton R Graveley¹⁴, Elise A Feingold¹⁵, Michael J Pazin¹⁵, Michael Pagan¹⁵, Daniel A Gilchrist¹⁵, Benjamin C Hitz¹⁶, J Michael Cherry¹⁶, Bradley E Bernstein¹⁷, Eric M Mendenhall^{18

19}, Daniel R Zerbino²⁰, Adam Frankish²⁰, Paul Flicek²⁰, Richard M Myers¹⁹

Collaborators

ENCODE Project Consortium:
Federico Abascal, Reyes Acosta, Nicholas J Addleman, Jessika Adrian, Veena Afzal, Bronwen Aken, Rizi Ai, Jennifer A Akiyama, Omar Al Jammal, Henry Amrhein, Stacie M Anderson, Gregory R Andrews, Igor Antoshechkin, Kristin G Ardlie, Joel Armstrong, Matthew Astley, Budhaditya Banerjee, Amira A Barkal, If H A Barnes, Iros Barozzi, Daniel Barrell, Gemma Barson, Daniel Bates, Ulugbek K Baymuradov, Cassandra Bazile, Michael A Beer, Samantha Beik, M A Bender, Ruth Bennett, Louis Philip Benoit Bouvrette, Bradley E Bernstein, Andrew Berry, Anand Bhaskar, Alexandra Bignell, Steven M Blue, David M Bodine, Carles Boix, Nathan Boley, Tyler Borrman, Beatrice Borsari, Alan P Boyle, Laurel A Brandsmeier, Alessandra Breschi, Emery H Bresnick, Jason A Brooks, Michael Buckley, Christopher B Burge, Rachel Byron, Eileen Cahill, Lingling Cai, Lulu Cao, Mark Carty, Rosa G Castanon, Andres Castillo, Hassan Chaib, Esther T Chan, Daniel R Chee, Sora Chee, Hao Chen, Huaming Chen, Jia-Yu Chen, Songjie Chen, J Michael Cherry, Surya B Chhetri, Jyoti S Choudhary, Jacqueline Chrast, Dongjun Chung, Declan Clarke, Neal A L Cody, Candice J Coppola, Julie Coursen, Anthony M D'Ippolito, Stephen Dalton, Cassidy Danyko, Claire Davidson, Jose Davila-Velderrain, Carrie A Davis, Job Dekker, Alden Deran, Gilberto DeSalvo, Gloria Despacio-Reyes, Colin N Dewey, Diane E Dickel, Morgan Diegel, Mark Diekhans, Vishnu Dileep, Bo Ding, Sarah Djebali, Alexander Dobin, Daniel Dominguez, Sarah Donaldson, Jorg Drenkow, Timothy R Dreszer, Yotam Drier, Michael O Duff, Douglass Dunn, Catharine Eastman, Joseph R Ecker, Matthew D Edwards, Nicole El-Ali, Shaimae I Elhajjajy, Keri Elkins, Andrew Emili, Charles B Epstein, Rachel C Evans, Iakes Ezkurdia, Kaili Fan, Peggy J Farnham, Nina Farrell, Elise A Feingold, Anne-Maud Ferreira, Katherine Fisher-Aylor, Stephen Fitzgerald, Paul Flicek, Chuan Sheng Foo, Kevin Fortier, Adam Frankish, Peter Freese, Shaliu Fu, Xiang-Dong Fu, Yu Fu, Yoko Fukuda-Yuzawa, Mariateresa Fulciniti, Alister P W Funnell, Idan Gabdank, Timur Galeev, Mingshi Gao, Carlos Garcia Giron, Tyler H Garvin, Chelsea Anne Gelboin-Burkhart, Grigorios Georgolopoulos, Mark B Gerstein, Belinda M Giardine, David K Gifford, David M Gilbert, Daniel A Gilchrist, Shawn Gillespie, Thomas R Gingeras, Peng Gong, Alvaro Gonzalez, Jose M Gonzalez, Peter Good, Alon Goren, David U Gorkin, Brenton R Graveley, Michael Gray, Jack F Greenblatt, Ed Griffiths, Mark T Groudine, Fabian Grubert, Mengting Gu, Roderic Guigó, Hongbo Guo, Yu Guo, Yuchun Guo, Gamze Gursoy, Maria Gutierrez-Arcelus, Jessica Halow, Ross C Hardison, Matthew Hardy, Manoj Hariharan, Arif Harmanci, Anne Harrington, Jennifer L Harrow, Tatsunori B Hashimoto, Richard D Hasz, Meital Hatan, Eric Haugen, James E Hayes, Peng He, Yupeng He, Nastaran Heidari, David Hendrickson, Elisabeth F Heuston, Jason A Hilton, Benjamin C Hitz, Abigail Hochman, Cory Holgren, Lei Hou, Shuyu Hou, Yun-Hua E Hsiao, Shanna Hsu, Hui Huang, Tim J Hubbard, Jack Huey, Timothy R Hughes, Toby Hunt, Sean Ibarrientos, Robbyn Issner, Mineo Iwata, Osagie Izuogu, Tommi Jaakkola, Nader Jameel, Camden Jansen, Lixia Jiang, Peng Jiang, Audra Johnson, Rory Johnson, Irwin Jungreis, Madhura Kadaba, Maya Kasowski, Mary Kasparian, Momoe Kato, Rajinder Kaul, Trupti Kawli, Michael Kay, Judith C Keen, Sunduz Keles, Cheryl A Keller, David Kelley, Manolis Kellis, Pouya Kheradpour, Daniel Sunwook Kim, Anthony Kirilusha, Robert J Klein, Birgit Knoechel, Samantha Kuan, Michael J Kulik, Sushant Kumar, Anshul Kundaje, Tanya Kutyavin, Julien Lagarde, Bryan R Lajoie, Nicole J Lambert, John Lazar, Ah Young Lee, Donghoon Lee, Elizabeth Lee, Jin Wook Lee, Kristen Lee, Christina S Leslie, Shawn Levy, Bin Li, Hairi Li, Nan Li, Shantao Li, Xiangrui Li, Yang I Li, Ying Li, Yining Li, Yue Li, Jin Lian, Maxwell W Libbrecht, Shin Lin, Yiing Lin, Dianbo Liu, Jason Liu, Peng Liu, Tingting Liu, X Shirley Liu, Yan Liu, Yaping Liu, Maria Long, Shaoke Lou, Jane Loveland, Aiping Lu, Yuheng Lu, Eric Lécuyer, Lijia Ma, Mark Mackiewicz, Brandon J Mannion, Michael Mannstadt, Deepa Manthravadi, Georgi K Marinov, Fergal J Martin, Eugenio Mattei, Kenneth McCue, Megan McEown, Graham McVicker, Sarah K Meadows, Alex Meissner, Eric M Mendenhall, Christopher L Messer, Wouter Meuleman, Clifford Meyer, Steve Miller, Matthew G Milton, Tejaswini Mishra, Dianna E Moore, Helen M Moore, Jill E Moore, Samuel H Moore, Jennifer Moran, Ali Mortazavi, Jonathan M Mudge, Nikhil Munshi, Rabi Murad, Richard M Myers, Vivek Nandakumar, Preetha Nandi, Anil M Narasimha, Aditi K Narayanan, Hannah Naughton, Fabio C P Navarro, Patrick Navas, Jurijs Nazarovs, Jemma Nelson, Shane Neph, Fidencio Jun Neri, Joseph R Nery, Amy R Nesmith, J Scott Newberry, Kimberly M Newberry, Vu Ngo, Rosy Nguyen, Thai B Nguyen, Tung Nguyen, Andrew Nishida, William S Noble, Catherine S Novak, Eva Maria Novoa, Briana Nuñez, Charles W O'Donnell, Sara Olson, Kathrina C Onate, Ericka Otterman, Hakan Ozadam, Michael Pagan, Tsultrim Palden, Xinghua Pan, Yongjin Park, E Christopher Partridge, Benedict Paten, Florencia Pauli-Behn, Michael J Pazin, Baikang Pei, Len A Pennacchio, Alexander R Perez, Emily H Perry, Dmitri D Pervouchine, Nishigandha N Phalke, Quan Pham, Doug H Phanstiel, Ingrid Plajzer-Frick, Gabriel A Pratt, Henry E Pratt, Sebastian Preissl, Jonathan K Pritchard, Yuri Pritykin, Michael J Purcaro, Qian Qin, Giovanni Quinones-Valdez, Ines Rabano, Ernest Radovani, Anil Raj, Nisha Rajagopal, Oren Ram, Lucia Ramirez, Ricardo N Ramirez, Dylan Rausch, Soumya Raychaudhuri, Joseph Raymond, Rozita Razavi, Timothy E Reddy, Thomas M Reimonn, Bing Ren, Alexandre Reymond, Alex Reynolds, Suhn K Rhie, John Rinn, Miguel Rivera, Juan Carlos Rivera-Mulia, Brian Roberts, Jose Manuel Rodriguez, Joel Rozowsky, Russell Ryan, Eric Rynes, Denis N Salins, Richard Sandstrom, Takayo Sasaki, Shashank Sathe, Daniel Savic, Alexandra Scavelli, Jonathan Scheiman, Christoph Schlaffner, Jeffery A Schloss, Frank W Schmitges, Lei Hoon See, Anurag Sethi, Manu Setty, Anthony Shafer, Shuo Shan, Eilon Sharon, Quan Shen, Yin Shen, Richard I Sherwood, Minyi Shi, Sunyoung Shin, Noam Shoresh, Kyle Siebenthall, Cristina Sisu, Teri Slifer, Cricket A Sloan, Anna Smith, Valentina Snetkova, Michael P Snyder, Damek V Spacek, Sharanya Srinivasan, Rohith Srivas, George Stamatoyannopoulos, John A Stamatoyannopoulos, Rebecca Stanton, Dave Steffan, Sandra Stehling-Sun, J Seth Strattan, Amanda Su, Balaji Sundararaman, Marie-Marthe Suner, Tahin Syed, Matt Szynkarek, Forrest Y Tanaka, Danielle Tenen, Mingxiang Teng, Jeffrey A Thomas, Dave Toffey, Michael L Tress, Diane E Trout, Gosia Trynka, Junko Tsuji, Sean A Upchurch, Oana Ursu, Barbara Uszczynska-Ratajczak, Mia C Uziel, Alfonso Valencia, Benjamin Van Biber, Arjan G van der Velde, Eric L Van Nostrand, Yekaterina Vaydylevich, Jesus Vazquez, Alec Victorsen, Jost Vielmetter, Jeff Vierstra, Axel Visel, Anna Vlasova, Christopher M Vockley, Simona Volpi, Shinny Vong, Hao Wang, Mengchi Wang, Qin Wang, Ruth Wang, Tao Wang, Wei Wang, Xiaofeng Wang, Yanli Wang, Nathaniel K Watson, Xintao Wei, Zhijie Wei, Hendrik Weisser, Sherman M Weissman, Rene Welch, Robert E Welikson, Zhiping Weng, Harm-Jan Westra, John W Whitaker, Collin White, Kevin P White, Andre Wildberg, Brian A Williams, David Wine, Heather N Witt, Barbara Wold, Maxim Wolf, James Wright, Rui Xiao, Xinshu Xiao, Jie Xu, Jinrui Xu, Koon-Kiu Yan, Yongqi Yan, Hongbo Yang, Xinqiong Yang, Yi-Wen Yang, Galip Gürkan Yardımcı, Brian A Yee, Gene W Yeo, Taylor Young, Tianxiong Yu, Feng Yue, Chris Zaleski, Chongzhi Zang, Haoyang Zeng, Weihua Zeng, Daniel R Zerbino, Jie Zhai, Lijun Zhan, Ye Zhan, Bo Zhang, Jialing Zhang, Jing Zhang, Kai Zhang, Lijun Zhang, Peng Zhang, Qi Zhang, Xiao-Ou Zhang, Yanxiao Zhang, Zhizhuo Zhang, Yuan Zhao, Ye Zheng, Guoqing Zhong, Xiao-Qiao Zhou, Yun Zhu, Jared Zimmerman

Affiliations

¹ Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA. mpsnyder@stanford.edu.
² Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA. mpsnyder@stanford.edu.
³ Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
⁴ University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
⁵ Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China.
⁶ Bioinformatics Program, Boston University, Boston, MA, USA.
⁷ Yale University, New Haven, CT, USA.
⁸ Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
⁹ Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
¹¹ Altius Institute for Biomedical Sciences, Seattle, WA, USA.
¹² Department of Genome Sciences, University of Washington, Seattle, WA, USA.
¹³ Department of Medicine, University of Washington, Seattle, WA, USA.
¹⁴ Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
¹⁵ National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
¹⁶ Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
¹⁷ Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
¹⁸ Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA.
¹⁹ HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
²⁰ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.

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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Binding Sites
Chromatin / genetics
Chromatin / metabolism
DNA Methylation
Databases, Genetic* / standards
Databases, Genetic* / trends
Gene Expression Regulation / genetics
Genome / genetics*
Genome, Human / genetics
Genomics* / standards
Genomics* / trends
Histones / metabolism
Humans
Mice
Molecular Sequence Annotation* / standards
Quality Control
Regulatory Sequences, Nucleic Acid / genetics
Transcription Factors / metabolism

Substances

Chromatin
Histones
Transcription Factors

Abstract

Publication types

MeSH terms

Substances

Grants and funding