Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Animals
Chromatin
/ genetics
DNA
/ chemistry
DNA Footprinting
DNA Methylation
/ genetics
DNA Replication Timing
Databases, Genetic
Deoxyribonuclease I
/ metabolism
Genome
/ genetics
Genome, Human
Genomics
Histones
/ metabolism
Humans
Mice
Mice, Transgenic
Molecular Sequence Annotation
RNA-Binding Proteins
/ genetics
Registries
Regulatory Sequences, Nucleic Acid
/ genetics
Transcription, Genetic
/ genetics
Transposases
/ metabolism
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
07 2020
07 2020
Historique:
received:
26
08
2017
accepted:
27
05
2020
entrez:
31
7
2020
pubmed:
31
7
2020
medline:
12
1
2021
Statut:
ppublish
Résumé
The 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 ENCODE
Identifiants
pubmed: 32728249
doi: 10.1038/s41586-020-2493-4
pii: 10.1038/s41586-020-2493-4
pmc: PMC7410828
doi:
Substances chimiques
Chromatin
0
Histones
0
RNA-Binding Proteins
0
DNA
9007-49-2
Transposases
EC 2.7.7.-
Deoxyribonuclease I
EC 3.1.21.1
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
699-710Subventions
Organisme : NHGRI NIH HHS
ID : U24 HG009397
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG006991
Pays : United States
Organisme : NHGRI NIH HHS
ID : F32 HG006993
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM087237
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG007036
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009390
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG009446
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009442
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA014195
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG007004
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009380
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG007033
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG006996
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009431
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG003143
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG007037
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG007005
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG007002
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG006992
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000044
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA045508
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK068634
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG007019
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG007010
Pays : United States
Organisme : NIDDK NIH HHS
ID : R24 DK106766
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG006994
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG006997
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM083337
Pays : United States
Organisme : NIDDK NIH HHS
ID : R37 DK050107
Pays : United States
Organisme : NHGRI NIH HHS
ID : K99 HG009530
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG007000
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009411
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG006998
Pays : United States
Investigateurs
Federico Abascal
(F)
Reyes Acosta
(R)
Nicholas J Addleman
(NJ)
Jessika Adrian
(J)
Veena Afzal
(V)
Rizi Ai
(R)
Bronwen Aken
(B)
Jennifer A Akiyama
(JA)
Omar Al Jammal
(OA)
Henry Amrhein
(H)
Stacie M Anderson
(SM)
Gregory R Andrews
(GR)
Igor Antoshechkin
(I)
Kristin G Ardlie
(KG)
Joel Armstrong
(J)
Matthew Astley
(M)
Budhaditya Banerjee
(B)
Amira A Barkal
(AA)
If H A Barnes
(IHA)
Iros Barozzi
(I)
Daniel Barrell
(D)
Gemma Barson
(G)
Daniel Bates
(D)
Ulugbek K Baymuradov
(UK)
Cassandra Bazile
(C)
Michael A Beer
(MA)
Samantha Beik
(S)
M A Bender
(MA)
Ruth Bennett
(R)
Louis Philip Benoit Bouvrette
(LPB)
Bradley E Bernstein
(BE)
Andrew Berry
(A)
Anand Bhaskar
(A)
Alexandra Bignell
(A)
Steven M Blue
(SM)
David M Bodine
(DM)
Carles Boix
(C)
Nathan Boley
(N)
Tyler Borrman
(T)
Beatrice Borsari
(B)
Alan P Boyle
(AP)
Laurel A Brandsmeier
(LA)
Alessandra Breschi
(A)
Emery H Bresnick
(EH)
Jason A Brooks
(JA)
Michael Buckley
(M)
Christopher B Burge
(CB)
Rachel Byron
(R)
Eileen Cahill
(E)
Lingling Cai
(L)
Lulu Cao
(L)
Mark Carty
(M)
Rosa G Castanon
(RG)
Andres Castillo
(A)
Hassan Chaib
(H)
Esther T Chan
(ET)
Daniel R Chee
(DR)
Sora Chee
(S)
Hao Chen
(H)
Huaming Chen
(H)
Jia-Yu Chen
(JY)
Songjie Chen
(S)
J Michael Cherry
(JM)
Surya B Chhetri
(SB)
Jyoti S Choudhary
(JS)
Jacqueline Chrast
(J)
Dongjun Chung
(D)
Declan Clarke
(D)
Neal A L Cody
(NAL)
Candice J Coppola
(CJ)
Julie Coursen
(J)
Anthony M D'Ippolito
(AM)
Stephen Dalton
(S)
Cassidy Danyko
(C)
Claire Davidson
(C)
Jose Davila-Velderrain
(J)
Carrie A Davis
(CA)
Job Dekker
(J)
Alden Deran
(A)
Gilberto DeSalvo
(G)
Gloria Despacio-Reyes
(G)
Colin N Dewey
(CN)
Diane E Dickel
(DE)
Morgan Diegel
(M)
Mark Diekhans
(M)
Vishnu Dileep
(V)
Bo Ding
(B)
Sarah Djebali
(S)
Alexander Dobin
(A)
Daniel Dominguez
(D)
Sarah Donaldson
(S)
Jorg Drenkow
(J)
Timothy R Dreszer
(TR)
Yotam Drier
(Y)
Michael O Duff
(MO)
Douglass Dunn
(D)
Catharine Eastman
(C)
Joseph R Ecker
(JR)
Matthew D Edwards
(MD)
Nicole El-Ali
(N)
Shaimae I Elhajjajy
(SI)
Keri Elkins
(K)
Andrew Emili
(A)
Charles B Epstein
(CB)
Rachel C Evans
(RC)
Iakes Ezkurdia
(I)
Kaili Fan
(K)
Peggy J Farnham
(PJ)
Nina P Farrell
(NP)
Elise A Feingold
(EA)
Anne-Maud Ferreira
(AM)
Katherine Fisher-Aylor
(K)
Stephen Fitzgerald
(S)
Paul Flicek
(P)
Chuan Sheng Foo
(CS)
Kevin Fortier
(K)
Adam Frankish
(A)
Peter Freese
(P)
Shaliu Fu
(S)
Xiang-Dong Fu
(XD)
Yu Fu
(Y)
Yoko Fukuda-Yuzawa
(Y)
Mariateresa Fulciniti
(M)
Alister P W Funnell
(APW)
Idan Gabdank
(I)
Timur Galeev
(T)
Mingshi Gao
(M)
Carlos Garcia Giron
(CG)
Tyler H Garvin
(TH)
Chelsea Anne Gelboin-Burkhart
(CA)
Grigorios Georgolopoulos
(G)
Mark B Gerstein
(MB)
Belinda M Giardine
(BM)
David K Gifford
(DK)
David M Gilbert
(DM)
Daniel A Gilchrist
(DA)
Shawn Gillespie
(S)
Thomas R Gingeras
(TR)
Peng Gong
(P)
Alvaro Gonzalez
(A)
Jose M Gonzalez
(JM)
Peter Good
(P)
Alon Goren
(A)
David U Gorkin
(DU)
Brenton R Graveley
(BR)
Michael Gray
(M)
Jack F Greenblatt
(JF)
Ed Griffiths
(E)
Mark T Groudine
(MT)
Fabian Grubert
(F)
Mengting Gu
(M)
Roderic Guigó
(R)
Hongbo Guo
(H)
Yu Guo
(Y)
Yuchun Guo
(Y)
Gamze Gursoy
(G)
Maria Gutierrez-Arcelus
(M)
Jessica Halow
(J)
Ross C Hardison
(RC)
Matthew Hardy
(M)
Manoj Hariharan
(M)
Arif Harmanci
(A)
Anne Harrington
(A)
Jennifer L Harrow
(JL)
Tatsunori B Hashimoto
(TB)
Richard D Hasz
(RD)
Meital Hatan
(M)
Eric Haugen
(E)
James E Hayes
(JE)
Peng He
(P)
Yupeng He
(Y)
Nastaran Heidari
(N)
David Hendrickson
(D)
Elisabeth F Heuston
(EF)
Jason A Hilton
(JA)
Benjamin C Hitz
(BC)
Abigail Hochman
(A)
Cory Holgren
(C)
Lei Hou
(L)
Shuyu Hou
(S)
Yun-Hua E Hsiao
(YE)
Shanna Hsu
(S)
Hui Huang
(H)
Tim J Hubbard
(TJ)
Jack Huey
(J)
Timothy R Hughes
(TR)
Toby Hunt
(T)
Sean Ibarrientos
(S)
Robbyn Issner
(R)
Mineo Iwata
(M)
Osagie Izuogu
(O)
Tommi Jaakkola
(T)
Nader Jameel
(N)
Camden Jansen
(C)
Lixia Jiang
(L)
Peng Jiang
(P)
Audra Johnson
(A)
Rory Johnson
(R)
Irwin Jungreis
(I)
Madhura Kadaba
(M)
Maya Kasowski
(M)
Mary Kasparian
(M)
Momoe Kato
(M)
Rajinder Kaul
(R)
Trupti Kawli
(T)
Michael Kay
(M)
Judith C Keen
(JC)
Sunduz Keles
(S)
Cheryl A Keller
(CA)
David Kelley
(D)
Manolis Kellis
(M)
Pouya Kheradpour
(P)
Daniel Sunwook Kim
(DS)
Anthony Kirilusha
(A)
Robert J Klein
(RJ)
Birgit Knoechel
(B)
Samantha Kuan
(S)
Michael J Kulik
(MJ)
Sushant Kumar
(S)
Anshul Kundaje
(A)
Tanya Kutyavin
(T)
Julien Lagarde
(J)
Bryan R Lajoie
(BR)
Nicole J Lambert
(NJ)
John Lazar
(J)
Ah Young Lee
(AY)
Donghoon Lee
(D)
Elizabeth Lee
(E)
Jin Wook Lee
(JW)
Kristen Lee
(K)
Christina S Leslie
(CS)
Shawn Levy
(S)
Bin Li
(B)
Hairi Li
(H)
Nan Li
(N)
Shantao Li
(S)
Xiangrui Li
(X)
Yang I Li
(YI)
Ying Li
(Y)
Yining Li
(Y)
Yue Li
(Y)
Jin Lian
(J)
Maxwell W Libbrecht
(MW)
Shin Lin
(S)
Yiing Lin
(Y)
Dianbo Liu
(D)
Jason Liu
(J)
Peng Liu
(P)
Tingting Liu
(T)
X Shirley Liu
(XS)
Yan Liu
(Y)
Yaping Liu
(Y)
Maria Long
(M)
Shaoke Lou
(S)
Jane Loveland
(J)
Aiping Lu
(A)
Yuheng Lu
(Y)
Eric Lécuyer
(E)
Lijia Ma
(L)
Mark Mackiewicz
(M)
Brandon J Mannion
(BJ)
Michael Mannstadt
(M)
Deepa Manthravadi
(D)
Georgi K Marinov
(GK)
Fergal J Martin
(FJ)
Eugenio Mattei
(E)
Kenneth McCue
(K)
Megan McEown
(M)
Graham McVicker
(G)
Sarah K Meadows
(SK)
Alex Meissner
(A)
Eric M Mendenhall
(EM)
Christopher L Messer
(CL)
Wouter Meuleman
(W)
Clifford Meyer
(C)
Steve Miller
(S)
Matthew G Milton
(MG)
Tejaswini Mishra
(T)
Dianna E Moore
(DE)
Helen M Moore
(HM)
Jill E Moore
(JE)
Samuel H Moore
(SH)
Jennifer Moran
(J)
Ali Mortazavi
(A)
Jonathan M Mudge
(JM)
Nikhil Munshi
(N)
Rabi Murad
(R)
Richard M Myers
(RM)
Vivek Nandakumar
(V)
Preetha Nandi
(P)
Anil M Narasimha
(AM)
Aditi K Narayanan
(AK)
Hannah Naughton
(H)
Fabio C P Navarro
(FCP)
Patrick Navas
(P)
Jurijs Nazarovs
(J)
Jemma Nelson
(J)
Shane Neph
(S)
Fidencio Jun Neri
(FJ)
Joseph R Nery
(JR)
Amy R Nesmith
(AR)
J Scott Newberry
(JS)
Kimberly M Newberry
(KM)
Vu Ngo
(V)
Rosy Nguyen
(R)
Thai B Nguyen
(TB)
Tung Nguyen
(T)
Andrew Nishida
(A)
William S Noble
(WS)
Catherine S Novak
(CS)
Eva Maria Novoa
(EM)
Briana Nuñez
(B)
Charles W O'Donnell
(CW)
Sara Olson
(S)
Kathrina C Onate
(KC)
Ericka Otterman
(E)
Hakan Ozadam
(H)
Michael Pagan
(M)
Tsultrim Palden
(T)
Xinghua Pan
(X)
Yongjin Park
(Y)
E Christopher Partridge
(EC)
Benedict Paten
(B)
Florencia Pauli-Behn
(F)
Michael J Pazin
(MJ)
Baikang Pei
(B)
Len A Pennacchio
(LA)
Alexander R Perez
(AR)
Emily H Perry
(EH)
Dmitri D Pervouchine
(DD)
Nishigandha N Phalke
(NN)
Quan Pham
(Q)
Doug H Phanstiel
(DH)
Ingrid Plajzer-Frick
(I)
Gabriel A Pratt
(GA)
Henry E Pratt
(HE)
Sebastian Preissl
(S)
Jonathan K Pritchard
(JK)
Yuri Pritykin
(Y)
Michael J Purcaro
(MJ)
Qian Qin
(Q)
Giovanni Quinones-Valdez
(G)
Ines Rabano
(I)
Ernest Radovani
(E)
Anil Raj
(A)
Nisha Rajagopal
(N)
Oren Ram
(O)
Lucia Ramirez
(L)
Ricardo N Ramirez
(RN)
Dylan Rausch
(D)
Soumya Raychaudhuri
(S)
Joseph Raymond
(J)
Rozita Razavi
(R)
Timothy E Reddy
(TE)
Thomas M Reimonn
(TM)
Bing Ren
(B)
Alexandre Reymond
(A)
Alex Reynolds
(A)
Suhn K Rhie
(SK)
John Rinn
(J)
Miguel Rivera
(M)
Juan Carlos Rivera-Mulia
(JC)
Brian S Roberts
(BS)
Jose Manuel Rodriguez
(JM)
Joel Rozowsky
(J)
Russell Ryan
(R)
Eric Rynes
(E)
Denis N Salins
(DN)
Richard Sandstrom
(R)
Takayo Sasaki
(T)
Shashank Sathe
(S)
Daniel Savic
(D)
Alexandra Scavelli
(A)
Jonathan Scheiman
(J)
Christoph Schlaffner
(C)
Jeffery A Schloss
(JA)
Frank W Schmitges
(FW)
Lei Hoon See
(LH)
Anurag Sethi
(A)
Manu Setty
(M)
Anthony Shafer
(A)
Shuo Shan
(S)
Eilon Sharon
(E)
Quan Shen
(Q)
Yin Shen
(Y)
Richard I Sherwood
(RI)
Minyi Shi
(M)
Sunyoung Shin
(S)
Noam Shoresh
(N)
Kyle Siebenthall
(K)
Cristina Sisu
(C)
Teri Slifer
(T)
Cricket A Sloan
(CA)
Anna Smith
(A)
Valentina Snetkova
(V)
Michael P Snyder
(MP)
Damek V Spacek
(DV)
Sharanya Srinivasan
(S)
Rohith Srivas
(R)
George Stamatoyannopoulos
(G)
John A Stamatoyannopoulos
(JA)
Rebecca Stanton
(R)
Dave Steffan
(D)
Sandra Stehling-Sun
(S)
J Seth Strattan
(JS)
Amanda Su
(A)
Balaji Sundararaman
(B)
Marie-Marthe Suner
(MM)
Tahin Syed
(T)
Matt Szynkarek
(M)
Forrest Y Tanaka
(FY)
Danielle Tenen
(D)
Mingxiang Teng
(M)
Jeffrey A Thomas
(JA)
Dave Toffey
(D)
Michael L Tress
(ML)
Diane E Trout
(DE)
Gosia Trynka
(G)
Junko Tsuji
(J)
Sean A Upchurch
(SA)
Oana Ursu
(O)
Barbara Uszczynska-Ratajczak
(B)
Mia C Uziel
(MC)
Alfonso Valencia
(A)
Benjamin Van Biber
(BV)
Arjan G van der Velde
(AG)
Eric L Van Nostrand
(EL)
Yekaterina Vaydylevich
(Y)
Jesus Vazquez
(J)
Alec Victorsen
(A)
Jost Vielmetter
(J)
Jeff Vierstra
(J)
Axel Visel
(A)
Anna Vlasova
(A)
Christopher M Vockley
(CM)
Simona Volpi
(S)
Shinny Vong
(S)
Hao Wang
(H)
Mengchi Wang
(M)
Qin Wang
(Q)
Ruth Wang
(R)
Tao Wang
(T)
Wei Wang
(W)
Xiaofeng Wang
(X)
Yanli Wang
(Y)
Nathaniel K Watson
(NK)
Xintao Wei
(X)
Zhijie Wei
(Z)
Hendrik Weisser
(H)
Sherman M Weissman
(SM)
Rene Welch
(R)
Robert E Welikson
(RE)
Zhiping Weng
(Z)
Harm-Jan Westra
(HJ)
John W Whitaker
(JW)
Collin White
(C)
Kevin P White
(KP)
Andre Wildberg
(A)
Brian A Williams
(BA)
David Wine
(D)
Heather N Witt
(HN)
Barbara Wold
(B)
Maxim Wolf
(M)
James Wright
(J)
Rui Xiao
(R)
Xinshu Xiao
(X)
Jie Xu
(J)
Jinrui Xu
(J)
Koon-Kiu Yan
(KK)
Yongqi Yan
(Y)
Hongbo Yang
(H)
Xinqiong Yang
(X)
Yi-Wen Yang
(YW)
Galip Gürkan Yardımcı
(GG)
Brian A Yee
(BA)
Gene W Yeo
(GW)
Taylor Young
(T)
Tianxiong Yu
(T)
Feng Yue
(F)
Chris Zaleski
(C)
Chongzhi Zang
(C)
Haoyang Zeng
(H)
Weihua Zeng
(W)
Daniel R Zerbino
(DR)
Jie Zhai
(J)
Lijun Zhan
(L)
Ye Zhan
(Y)
Bo Zhang
(B)
Jialing Zhang
(J)
Jing Zhang
(J)
Kai Zhang
(K)
Lijun Zhang
(L)
Peng Zhang
(P)
Qi Zhang
(Q)
Xiao-Ou Zhang
(XO)
Yanxiao Zhang
(Y)
Zhizhuo Zhang
(Z)
Yuan Zhao
(Y)
Ye Zheng
(Y)
Guoqing Zhong
(G)
Xiao-Qiao Zhou
(XQ)
Yun Zhu
(Y)
Jared Zimmerman
(J)
Commentaires et corrections
Type : ErratumIn
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