Perspectives on ENCODE

编码基因计算生物学人类基因组生物基因组遗传学组蛋白染色质转录因子进化生物学

作者

Jill Moore,Michael Purcaro,Henry Pratt,Jessika Adrian,Veena Afzal,Bronwen Aken,Rizi Ai,Jennifer A. Akiyama,Alexander Dobin,Rajinder Kaul,Stacie M. Anderson,Gregory R. Andrews,Igor Antoshechkin,Kristin Ardlie,Quan Shen,Matthew Astley,Budhaditya Banerjee,Amira Barkal,Brian A. Yee,Iros Barozzi,Daniel Barrell,Gemma Barson,Daniel J. Bates,Ulugbek K. Baymuradov,Diane E. Dickel,M Beer,Samantha Beik,M. A. Bender,Ruth Bennett,Louis Philip Benoit Bouvrette,B Bernstein,Andrew Berry,Anand Bhaskar,Alexandra Bignell,Steven M. Blue,Axel Visel,G Yeo,Christoph N. Schlaffner,Tyler Borrman,Beatrice Borsari,Alan P. Boyle,Laurel A. Brandsmeier,Eric M. Mendenhall,José Manuel Rodrı́guez,Jason A. Brooks,Michael Buckley,Christopher B. Burge,Rachel Byron,Eileen Cahill,Lingling Cai,J. Michael Cherry,Mark Carty,Rosa Castanon,Andrés Castillo,Hassan Chaı̈b,Esther T. Chan,M Snyder,Sora Chee,Hao Chen,Huaming Chen,Jiayu Chen,Songjie Chen,J. Michael Cherry,Surya B. Chhetri,Jyoti S. Choudhary,Jacqueline Chrast,Dongjun Chung,Declan Clarke,New Cody,Candice J. Coppola,Julie Coursen,Anthony D’Ippolito,Stephen Dalton,Cassidy Danyko,Claire Davidson,José Dávila-Velderrain,Carrie 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 Domı́nguez,Sarah Donaldson,Jörg Hackermüller,Laurence D. Rowe,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 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,Y. Fukuda,Mariateresa Fulciniti,Alister P. W. Funnell,Benjamin C. Hitz,Timur R. Galeev,Mingshi Gao,Carlos García Girón,Tyler H. Garvin,Chelsea Gelboin-Burkhart,Grigorios Georgolopoulos,Mark Gerstein,Belinda Giardine,David K. Gifford,David M. Gilbert,Daniel A. Gilchrist,Shawn Gillespie,Thomas R. Gingeras,Peng Gong,Álvaro González,José M. González,Peter J. Good,Alon Goren,David U. Gorkin,Bing Ren,Michael Gray,Jack Greenblatt,Ed Griffiths,Mark Groudine,Fabian Grubert,Mengting Gu,Roderic Guigó,Hongbo Guo,Yuming Guo,Yuchun Guo,Gamze Gürsoy,María Gutiérrez‐Arcelus,Jessica Halow,Ross C. Hardison,Matthew P. Hardy,Manoj Hariharan,Arif Harmanci,Anne Harrington,Jennifer Harrow,Tatsunori Hashimoto,Richard Hasz,Meital Hatan,Eric Haugen,James E. Hayes,Peng He,Yupeng He,Nastaran Heidari,David G. Hendrickson,Elisabeth F. Heuston,Jason A. Hilton,Benjamin C. Hitz,Abigail Hochman,Cory Holgren,Lei Hou,Shuyu Hou,Yun-Hua Esther Hsiao,Shanna Hsu,Hui Huang,Tim 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,Carrie Davis,Mike Kay,Judith C. Keen,Sündüz Keleş,Cheryl A. Keller,David R. Kelley,Jiewei Xu,Pouya Kheradpour,Daniel Sunwook Kim,Anthony Kirilusha,Robert J. Klein,Birgit Knoechel,Samantha Kuan,Michael Kulik,Sushant Kumar,Anshul Kundaje,Tanya Kutyavin,Julien Lagarde,Bryan R. Lajoie,Nicole Lambert,John Lazar,Ah Young Lee,Donghoon Lee,Elizabeth Lee,Jin Wook Lee,Kristen Lee,Christina Leslie,Shawn Levy,Bin Li,Hairi Li,Nan Li,Shantao Li,Xiangrui Li,Yang Li,Ying Li,Yining Li,Yue Li,Lian Jin,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 Lü,Yuheng Lu,Éric 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,C. Luke Messer,Wouter Meuleman,Clifford A. Meyer,Steve Miller,Matthew G. Milton,Tejaswini Mishra,Dianna E. Moore,Helen M. Moore,Jill Moore,Samuel H. Moore,Jennifer Moran,A Mortazavi,Jonathan M. Mudge,Nikhil Munshi,Rabi Murad,R Myers,Vivek Nandakumar,Preetha Nandi,Anil Narasimha,Aditi K. Narayanan,Hannah Naughton,Fábio C. P. Navarro,Patrick A. Navas,Jurijs Nazarovs,Jemma Nelson,Shane Neph,Fidencio Neri,Joseph R. Nery,Amy R. Nesmith,J. Scott Newberry,Kimberly M. Newberry,Vu N. Ngo,Rosy Nguyen,Thai B. Nguyen,Tung Thanh Nguyen,Andrew Nishida,William Stafford Noble,Catherine S. Novak,Eva Maria Novoa,Briana Nuñez,Colm P. O’Donnell,Sara Olson,M. Kathrina Oñate,Ericka Otterman,Hakan Özadam,Michael Pagan,Tsultrim Palden,Xinghua Pan,Yongjin Park,E. Christopher Partridge,Benedict Paten,Florencia Pauli,Michael J. Pazin,Baikang Pei,L Pennacchio,Alexander R. Perez,Emily Perry,Dmitri D. Pervouchine,Nishigandha Phalke,Quan Pham,Doug Phanstiel,Ingrid Plajzer-Frick,Gabriel A. Pratt,Henry Pratt,Sebastian Preißl,Jonathan K. Pritchard,Yuri Pritykin,Michael Purcaro,Qian Qin,Giovanni Quinones-Valdez,Ines Rabano,Ernest Radovani,Anil Raj,Nisha Rajagopal,Oren Ram,Lucı́a Ramı́rez,Ricardo N. Ramírez,Dylan Rausch,Soumya Raychaudhuri,Joseph J. Raymond,Rozita Razavi,Timothy E. Reddy,Thomas Reimonn,Bing Ren,Alexandre Reymond,Alex Reynolds,Suhn K. Rhie,John L. Rinn,Miguel N. Rivera,Juan Carlos Rivera‐Mulia,Brian S. Roberts,José Manuel Rodrı́guez,Joel Rozowsky,Russell J.H. Ryan,Eric Rynes,Denis Salins,Richard Sandstrom,Takayo Sasaki,Shashank Sathe,Daniel Savic,Alexandra Scavelli,Jonathan Scheiman,Christoph N. 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,T Slifer,Cricket A. Sloan,Mark I. McCarthy,Valentina Snetkova,M Snyder,Damek V. Spacek,Sharanya Srinivasan,Rohith Srivas,George Stamatoyannopoulos,J Stamatoyannopoulos,Rebecca Stanton,Dave Steffan,Sandra Stehling-Sun,Venkat S. Malladi,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 Trout,Gosia Trynka,Junko Tsuji,Sean A. Upchurch,Oana Ursu,Barbara Uszczyńska-Ratajczak,Mia C. Uziel,Alfonso Valencia,Benjamin Van Biber,Arjan G. van der Velde,Eric L. Van Nostrand,Yekaterina Vaydylevich,Jesús Vázquez,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 Watson,Xintao Wei,Zhijie Wei,Hendrik Weisser,Sherman M. Weissman,Rene Welch,Robert E. Welikson,Zhiping Weng,Harm-Jan Westra,John W. Whitaker,Collin C. White,Kevin P. White,André Wildberg,Brian A. Williams,David Wine,Heather Witt,B Wold,Maxim Y. Wolf,James C. Wright,Rui Xiao,Xinshu Xiao,Jie Xu,Jinrui Xu,Koon‐Kiu Yan,Yongqi Yan,Hongbo Yang,Xinqiong Yang,Yiwen Yang,Galip Gürkan Yardımcı,Brian A. Yee,G 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,Xiaoqiao Zhou,Yun Zhu,Jared Zimmerman,M Snyder,Thomas R. Gingeras,Jill Moore,Zhiping Weng,Mark Gerstein,Bing Ren,Ross C. Hardison,J Stamatoyannopoulos,Bing Ren,Elise A. Feingold,Michael J. Pazin,Michael Pagan,Daniel A. Gilchrist,Benjamin C. Hitz,J. Michael Cherry,B Bernstein,Eric M. Mendenhall,Daniel R. Zerbino,Adam Frankish,Paul Flicek,R Myers

出处

期刊：Nature [Springer Nature]
日期：2020-07-29 卷期号：583 (7818): 693-698 被引量：141

链接

nature.com osti.gov handle.net upf.edu ac.uk ac.uk unibe.ch unibe.ch unil.ch nih.gov nih.govdoi.org

标识

DOI：10.1038/s41586-020-2449-8

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 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.

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Perspectives on ENCODE

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