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Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures

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dc.contributor.author García Pérez, Raquel, 1989-
dc.contributor.author Esteller-Cucala, Paula
dc.contributor.author Mas, Glòria
dc.contributor.author Lobón, Irene
dc.contributor.author Di Carlo, Valerio
dc.contributor.author Riera, Meritxell
dc.contributor.author Kuhlwilm, Martin
dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-
dc.contributor.author Blancher, Antoine
dc.contributor.author Di Croce, Luciano
dc.contributor.author Gómez Skarmeta, José Luis
dc.contributor.author Juan, David
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.date.accessioned 2021-08-03T06:18:40Z
dc.date.available 2021-08-03T06:18:40Z
dc.date.issued 2021
dc.identifier.citation García-Pérez R, Esteller-Cucala P, Mas G, Lobón I, Di Carlo V, Riera M, Kuhlwilm M, Navarro A, Blancher A, Di Croce L, Gómez-Skarmeta JL, Juan D, Marquès-Bonet T. Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures. Nat Commun. 2021;12(1):3116. DOI: 10.1038/s41467-021-23397-1
dc.identifier.issn 2041-1723
dc.identifier.uri http://hdl.handle.net/10230/48306
dc.description.abstract Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ChIP-seq for five histone marks, ATAC-seq and RNA-seq, further complemented with whole genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS). We annotated regulatory elements (RE) and integrated chromatin contact maps to define gene regulatory architectures, creating the largest catalog of RE in primates to date. We report that epigenetic conservation and its correlation with sequence conservation in primates depends on the activity state of the regulatory element. Our gene regulatory architectures reveal the coordination of different types of components and highlight the role of promoters and intragenic enhancers (gE) in the regulation of gene expression. We observe that most regulatory changes occur in weakly active gE. Remarkably, novel human-specific gE with weak activities are enriched in human-specific nucleotide changes. These elements appear in genes with signals of positive selection and human acceleration, tissue-specific expression, and particular functional enrichments, suggesting that the regulatory evolution of these genes may have contributed to human adaptation.
dc.description.sponsorship R.G.-P. was supported by a fellowship from MICINN (FPU13/01823). P.E.-C. was supported by a Formació de Personal Investigador fellowship from Generalitat de Catalunya (FI_B00122). M.K. was supported by a Deutsche Forschungsgemeinschaft (DFG) fellowship (KU 3467/1-1) and the Postdoctoral Junior Leader Fellowship Program from “la Caixa” Banking Foundation (LCF/BQ/PR19/11700002). D.J. was supported by a Juan de la Cierva fellowship (FJCI2016-29558) from MICINN. T.M-B. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement EC-H2020-ERC-CoG-ApeGenomeDiversity-864203), BFU2017-86471-P (AEI/FEDER, UE), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career, NIH 1R01HG010898-01A1, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Program del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). G.M., V.D.C., and L.D.C. were supported by grants from the Spanish of Economy, Industry, and Competitiveness (MEIC) (BFU2016-75008-P) and G.M. was also supported by the “Convocatoria de Ayudas Fundación BBVA a Investigadores, Innovadores y Creadores Culturales”. J.L.G.-S. was supported by the Spanish government (grants BFU2016-74961-P), an institutional grant Unidad de Excelencia María de Maeztu (MDM-2016-0687) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 740041). A.N. was supported by Fondo Europeo de Desarrollo Regional (FEDER) with project grants BFU2016-77961-P and PGC2018- 101927-B-I00 and by the Spanish National Institute of Bioinformatics (PT17/0009/0020).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Nature Research
dc.relation.ispartof Nat Commun. 2021;12(1):3116
dc.rights © The Author(s) 2021. 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/.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1038/s41467-021-23397-1
dc.subject.keyword Epigenomics
dc.subject.keyword Molecular evolution
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2017-86471-P
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016-75008-P
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016-74961-P
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/740041
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016-77961-P
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-101927-B-I00
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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