Expanded encyclopaedias of DNA elements in the human and mouse genomes

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...

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Autores: ENCODE Project Consortium, Moore, Jill E., Guigó Serra, Roderic, Weng, Zhiping
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/45354
Acceso en línea:http://hdl.handle.net/10230/45354
http://dx.doi.org/10.1038/s41586-020-2493-4
Access Level:acceso abierto
Palabra clave:Data integration
Epigenomics
Functional genomics
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spelling Expanded encyclopaedias of DNA elements in the human and mouse genomesENCODE Project ConsortiumMoore, Jill E.Guigó Serra, RodericWeng, ZhipingData integrationEpigenomicsFunctional genomicsThe 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.Nature Research202020202020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/45354http://dx.doi.org/10.1038/s41586-020-2493-4reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésNature. 2020; 583(7818):699-710© The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/453542026-06-12T07:21:37Z
dc.title.none.fl_str_mv Expanded encyclopaedias of DNA elements in the human and mouse genomes
title Expanded encyclopaedias of DNA elements in the human and mouse genomes
spellingShingle Expanded encyclopaedias of DNA elements in the human and mouse genomes
ENCODE Project Consortium
Data integration
Epigenomics
Functional genomics
title_short Expanded encyclopaedias of DNA elements in the human and mouse genomes
title_full Expanded encyclopaedias of DNA elements in the human and mouse genomes
title_fullStr Expanded encyclopaedias of DNA elements in the human and mouse genomes
title_full_unstemmed Expanded encyclopaedias of DNA elements in the human and mouse genomes
title_sort Expanded encyclopaedias of DNA elements in the human and mouse genomes
dc.creator.none.fl_str_mv ENCODE Project Consortium
Moore, Jill E.
Guigó Serra, Roderic
Weng, Zhiping
author ENCODE Project Consortium
author_facet ENCODE Project Consortium
Moore, Jill E.
Guigó Serra, Roderic
Weng, Zhiping
author_role author
author2 Moore, Jill E.
Guigó Serra, Roderic
Weng, Zhiping
author2_role author
author
author
dc.subject.none.fl_str_mv Data integration
Epigenomics
Functional genomics
topic Data integration
Epigenomics
Functional genomics
description 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 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.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/45354
http://dx.doi.org/10.1038/s41586-020-2493-4
url http://hdl.handle.net/10230/45354
http://dx.doi.org/10.1038/s41586-020-2493-4
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nature. 2020; 583(7818):699-710
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Research
publisher.none.fl_str_mv Nature Research
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
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