Expanded encyclopaedias of DNA elements in the human and mouse genomes
Authors:   The ENCODE Project Consortium, Abascal Federico , Acosta Reyes , Addleman Nicholas J. , Adrian Jessika , Afzal Veena , Ai Rizi , Aken Bronwen , Akiyama Jennifer A. , Jammal Omar Al , Amrhein Henry , Anderson Stacie M. , Andrews Gregory R. , Antoshechkin Igor , Ardlie Kristin G. , Armstrong Joel , Astley Matthew , Banerjee Budhaditya , Barkal Amira A. , Barnes If H. A. , Barozzi Iros , Barrell Daniel , Barson Gemma , Bates Daniel , Baymuradov Ulugbek K. , Bazile Cassandra , Beer Michael A. , Beik Samantha , Bender M. A. , Bennett Ruth , Bouvrette Louis Philip Benoit , Bernstein Bradley E. , Berry Andrew , Bhaskar Anand , Bignell Alexandra , Blue Steven M. , Bodine David M. , Boix Carles , Boley Nathan , Borrman Tyler , Borsari Beatrice , Boyle Alan P. , Brandsmeier Laurel A. , Breschi Alessandra , Bresnick Emery H. , Brooks Jason A. , Buckley Michael , Burge Christopher B. , Byron Rachel , Cahill Eileen , Cai Lingling , Cao Lulu , Carty Mark , Castanon Rosa G. , Castillo Andres , Chaib Hassan , Chan Esther T. , Chee Daniel R. , Chee Sora , Chen Hao , Chen Huaming , Chen Jia-Yu , Chen Songjie , Cherry J. Michael , Chhetri Surya B. , Choudhary Jyoti S. , Chrast Jacqueline , Chung Dongjun , Clarke Declan , Cody Neal A. L. , Coppola Candice J. , Coursen Julie , D’Ippolito Anthony M. , Dalton Stephen , Danyko Cassidy , Davidson Claire , Davila-Velderrain Jose , Davis Carrie A. , Dekker Job , Deran Alden , DeSalvo Gilberto , Despacio-Reyes Gloria , Dewey Colin N. , Dickel Diane E. , Diegel Morgan , Diekhans Mark , Dileep Vishnu , Ding Bo , Djebali Sarah , Dobin Alexander , Dominguez Daniel , Donaldson Sarah , Drenkow Jorg , Dreszer Timothy R. , Drier Yotam , Duff Michael O. , Dunn Douglass , Eastman Catharine , Ecker Joseph R. , Edwards Matthew D. , El-Ali Nicole , Elhajjajy Shaimae I. , Elkins Keri , Emili Andrew , Epstein Charles B. , Evans Rachel C. , Ezkurdia Iakes , Fan Kaili , Farnham Peggy J. , Farrell Nina P. , Feingold Elise A. , Ferreira Anne-Maud , Fisher-Aylor Katherine , Fitzgerald Stephen , Flicek Paul , Foo Chuan Sheng , Fortier Kevin , Frankish Adam , Freese Peter , Fu Shaliu , Fu Xiang-Dong , Fu Yu , Fukuda-Yuzawa Yoko , Fulciniti Mariateresa , Funnell Alister P. W. , Gabdank Idan , Galeev Timur , Gao Mingshi , Giron Carlos Garcia , Garvin Tyler H. , Gelboin-Burkhart Chelsea Anne , Georgolopoulos Grigorios , Gerstein Mark B. , Giardine Belinda M. , Gifford David K. , Gilbert David M. , Gilchrist Daniel A. , Gillespie Shawn , Gingeras Thomas R. , Gong Peng , Gonzalez Alvaro , Gonzalez Jose M. , Good Peter , Goren Alon , Gorkin David U. , Graveley Brenton R. , Gray Michael , Greenblatt Jack F. , Griffiths Ed , Groudine Mark T. , Grubert Fabian , Gu Mengting , Guigó Roderic , Guo Hongbo , Guo Yu , Guo Yuchun , Gursoy Gamze , Gutierrez-Arcelus Maria , Halow Jessica , Hardison Ross C. , Hardy Matthew , Hariharan Manoj , Harmanci Arif , Harrington Anne , Harrow Jennifer L. , Hashimoto Tatsunori B. , Hasz Richard D. , Hatan Meital , Haugen Eric , Hayes James E. , He Peng , He Yupeng , Heidari Nastaran , Hendrickson David , Heuston Elisabeth F. , Hilton Jason A. , Hitz Benjamin C. , Hochman Abigail , Holgren Cory , Hou Lei , Hou Shuyu , Hsiao Yun-Hua E. , Hsu Shanna , Huang Hui , Hubbard Tim J. , Huey Jack , Hughes Timothy R. , Hunt Toby , Ibarrientos Sean , Issner Robbyn , Iwata Mineo , Izuogu Osagie , Jaakkola Tommi , Jameel Nader , Jansen Camden , Jiang Lixia , Jiang Peng , Johnson Audra , Johnson Rory , Jungreis Irwin , Kadaba Madhura , Kasowski Maya , Kasparian Mary , Kato Momoe , Kaul Rajinder , Kawli Trupti , Kay Michael , Keen Judith C. , Keles Sunduz , Keller Cheryl A. , Kelley David , Kellis Manolis , Kheradpour Pouya , Kim Daniel Sunwook , Kirilusha Anthony , Klein Robert J. , Knoechel Birgit , Kuan Samantha , Kulik Michael J. , Kumar Sushant , Kundaje Anshul , Kutyavin Tanya , Lagarde Julien , Lajoie Bryan R. , Lambert Nicole J. , Lazar John , Lee Ah Young , Lee Donghoon , Lee Elizabeth , Lee Jin Wook , Lee Kristen , Leslie Christina S. , Levy Shawn , Li Bin , Li Hairi , Li Nan , Li Shantao , Li Xiangrui , Li Yang I. , Li Ying , Li Yining , Li Yue , Lian Jin , Libbrecht Maxwell W. , Lin Shin , Lin Yiing , Liu Dianbo , Liu Jason , Liu Peng , Liu Tingting , Liu X. Shirley , Liu Yan , Liu Yaping , Long Maria , Lou Shaoke , Loveland Jane , Lu Aiping , Lu Yuheng , Lécuyer Eric , Ma Lijia , Mackiewicz Mark , Mannion Brandon J. , Mannstadt Michael , Manthravadi Deepa , Marinov Georgi K. , Martin Fergal J. , Mattei Eugenio , McCue Kenneth , McEown Megan , McVicker Graham , Meadows Sarah K. , Meissner Alex , Mendenhall Eric M. , Messer Christopher L. , Meuleman Wouter , Meyer Clifford , Miller Steve , Milton Matthew G. , Mishra Tejaswini , Moore Dianna E. , Moore Helen M. , Moore Jill E. , Moore Samuel H. , Moran Jennifer , Mortazavi Ali , Mudge Jonathan M. , Munshi Nikhil , Murad Rabi , Myers Richard M. , Nandakumar Vivek , Nandi Preetha , Narasimha Anil M. , Narayanan Aditi K. , Naughton Hannah , Navarro Fabio C. P. , Navas Patrick , Nazarovs Jurijs , Nelson Jemma , Neph Shane , Neri Fidencio Jun , Nery Joseph R. , Nesmith Amy R. , Newberry J. Scott , Newberry Kimberly M. , Ngo Vu , Nguyen Rosy , Nguyen Thai B. , Nguyen Tung , Nishida Andrew , Noble William S. , Novak Catherine S. , Novoa Eva Maria , Nuñez Briana , O’Donnell Charles W. , Olson Sara , Onate Kathrina C. , Otterman Ericka , Ozadam Hakan , Pagan Michael , Palden Tsultrim , Pan Xinghua , Park Yongjin , Partridge E. Christopher , Paten Benedict , Pauli-Behn Florencia , Pazin Michael J. , Pei Baikang , Pennacchio Len A. , Perez Alexander R. , Perry Emily H. , Pervouchine Dmitri D. , Phalke Nishigandha N. , Pham Quan , Phanstiel Doug H. , Plajzer-Frick Ingrid , Pratt Gabriel A. , Pratt Henry E. , Preissl Sebastian , Pritchard Jonathan K. , Pritykin Yuri , Purcaro Michael J. , Qin Qian , Quinones-Valdez Giovanni , Rabano Ines , Radovani Ernest , Raj Anil , Rajagopal Nisha , Ram Oren , Ramirez Lucia , Ramirez Ricardo N. , Rausch Dylan , Raychaudhuri Soumya , Raymond Joseph , Razavi Rozita , Reddy Timothy E. , Reimonn Thomas M. , Ren Bing , Reymond Alexandre , Reynolds Alex , Rhie Suhn K. , Rinn John , Rivera Miguel , Rivera-Mulia Juan Carlos , Roberts Brian S. , Rodriguez Jose Manuel , Rozowsky Joel , Ryan Russell , Rynes Eric , Salins Denis N. , Sandstrom Richard , Sasaki Takayo , Sathe Shashank , Savic Daniel , Scavelli Alexandra , Scheiman Jonathan , Schlaffner Christoph , Schloss Jeffery A. , Schmitges Frank W. , See Lei Hoon , Sethi Anurag , Setty Manu , Shafer Anthony , Shan Shuo , Sharon Eilon , Shen Quan , Shen Yin , Sherwood Richard I. , Shi Minyi , Shin Sunyoung , Shoresh Noam , Siebenthall Kyle , Sisu Cristina , Slifer Teri , Sloan Cricket A. , Smith Anna , Snetkova Valentina , Snyder Michael P. , Spacek Damek V. , Srinivasan Sharanya , Srivas Rohith , Stamatoyannopoulos George , Stamatoyannopoulos John A. , Stanton Rebecca , Steffan Dave , Stehling-Sun Sandra , Strattan J. Seth , Su Amanda , Sundararaman Balaji , Suner Marie-Marthe , Syed Tahin , Szynkarek Matt , Tanaka Forrest Y. , Tenen Danielle , Teng Mingxiang , Thomas Jeffrey A. , Toffey Dave , Tress Michael L. , Trout Diane E. , Trynka Gosia , Tsuji Junko , Upchurch Sean A. , Ursu Oana , Uszczynska-Ratajczak Barbara , Uziel Mia C. , Valencia Alfonso , Biber Benjamin Van , van der Velde Arjan G. , Van Nostrand Eric L. , Vaydylevich Yekaterina , Vazquez Jesus , Victorsen Alec , Vielmetter Jost , Vierstra Jeff , Visel Axel , Vlasova Anna , Vockley Christopher M. , Volpi Simona , Vong Shinny , Wang Hao , Wang Mengchi , Wang Qin , Wang Ruth , Wang Tao , Wang Wei , Wang Xiaofeng , Wang Yanli , Watson Nathaniel K. , Wei Xintao , Wei Zhijie , Weisser Hendrik , Weissman Sherman M. , Welch Rene , Welikson Robert E. , Weng Zhiping , Westra Harm-Jan , Whitaker John W. , White Collin , White Kevin P. , Wildberg Andre , Williams Brian A. , Wine David , Witt Heather N. , Wold Barbara , Wolf Maxim , Wright James , Xiao Rui , Xiao Xinshu , Xu Jie , Xu Jinrui , Yan Koon-Kiu , Yan Yongqi , Yang Hongbo , Yang Xinqiong , Yang Yi-Wen , Yardımcı Galip Gürkan , Yee Brian A. , Yeo Gene W. , Young Taylor , Yu Tianxiong , Yue Feng , Zaleski Chris , Zang Chongzhi , Zeng Haoyang , Zeng Weihua , Zerbino Daniel R. , Zhai Jie , Zhan Lijun , Zhan Ye , Zhang Bo , Zhang Jialing , Zhang Jing , Zhang Kai , Zhang Lijun , Zhang Peng , Zhang Qi , Zhang Xiao-Ou , Zhang Yanxiao , Zhang Zhizhuo , Zhao Yuan , Zheng Ye , Zhong Guoqing , Zhou Xiao-Qiao , Zhu Yun , Zimmerman Jared , Moore Jill E. , Purcaro Michael J. , Pratt Henry E. , Epstein Charles B. , Shoresh Noam , Adrian Jessika , Kawli Trupti , Davis Carrie A. , Dobin Alexander , Kaul Rajinder , Halow Jessica , Van Nostrand Eric L. , Freese Peter , Gorkin David U. , Shen Yin , He Yupeng , Mackiewicz Mark , Pauli-Behn Florencia , Williams Brian A. , Mortazavi Ali , Keller Cheryl A. , Zhang Xiao-Ou , Elhajjajy Shaimae I. , Huey Jack , Dickel Diane E. , Snetkova Valentina , Wei Xintao , Wang Xiaofeng , Rivera-Mulia Juan Carlos , Rozowsky Joel , Zhang Jing , Chhetri Surya B. , Zhang Jialing , Victorsen Alec , White Kevin P. , Visel Axel , Yeo Gene W. , Burge Christopher B. , Lécuyer Eric , Gilbert David M. , Dekker Job , Rinn John , Mendenhall Eric M. , Ecker Joseph R. , Kellis Manolis , Klein Robert J. , Noble William S. , Kundaje Anshul , Guigó Roderic , Farnham Peggy J. , Cherry J. Michael , Myers Richard M. , Ren Bing , Graveley Brenton R. , Gerstein Mark B. , Pennacchio Len A. , Snyder Michael P. , Bernstein Bradley E. , Wold Barbara , Hardison Ross C. , Gingeras Thomas R. , Stamatoyannopoulos John A. , Weng Zhiping 
Published: July 2020

AbstractThe human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.