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A comparison of gene expression and DNA methylation patterns across tissues and species

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dc.contributor.author Blake, Lauren E.
dc.contributor.author Roux, Julien
dc.contributor.author Hernando Herráez, Irene, 1985-
dc.contributor.author Banovich, Nicholas E.
dc.contributor.author García Pérez, Raquel, 1989-
dc.contributor.author Hsiao, Chiaowen Joyce
dc.contributor.author Eres, Ittai
dc.contributor.author Cuevas, Claudia
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.contributor.author Gilad, Yoav
dc.date.accessioned 2020-04-17T06:59:37Z
dc.date.available 2020-04-17T06:59:37Z
dc.date.issued 2020
dc.identifier.citation Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Perez RG, Hsiao CJ, Eres I, Cuevas C, Marques-Bonet T, Gilad Y. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Res. 2020; 30(2):250-62. DOI: 10.1101/gr.254904.119
dc.identifier.issn 1088-9051
dc.identifier.uri http://hdl.handle.net/10230/44259
dc.description.abstract Previously published comparative functional genomic data sets from primates using frozen tissue samples, including many data sets from our own group, were often collected and analyzed using nonoptimal study designs and analysis approaches. In addition, when samples from multiple tissues were studied in a comparative framework, individuals and tissues were confounded. We designed a multitissue comparative study of gene expression and DNA methylation in primates that minimizes confounding effects by using a balanced design with respect to species, tissues, and individuals. We also developed a comparative analysis pipeline that minimizes biases attributable to sequence divergence. Thus, we present the most comprehensive catalog of similarities and differences in gene expression and DNA methylation levels between livers, kidneys, hearts, and lungs, in humans, chimpanzees, and rhesus macaques. We estimate that overall, interspecies and inter-tissue differences in gene expression levels can only modestly be accounted for by corresponding differences in promoter DNA methylation. However, the expression pattern of genes with conserved inter-tissue expression differences can be explained by corresponding interspecies methylation changes more often. Finally, we show that genes whose tissue-specific regulatory patterns are consistent with the action of natural selection are highly connected in both gene regulatory and protein-protein interaction networks.
dc.description.sponsorship This project was funded in part by the Office of Research Infrastructure/Office of the Director (ORIP/OD) P51OD011132 grant. T.M.-B. is supported by BFU2017-86471-P (Ministry of Economy and Competitiveness/European Regional Development Fund, European Union), NIH U01 MH106874 grant, Howard Hughes Medical Institute: International Early Career, Obra Social “La Caixa” and Secretaria d'Universitats i Recerca and Centres de Recerca de Catalunya Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)
dc.relation.ispartof Genome Res. 2020; 30(2):250-62
dc.rights © 2020 Blake et al.; Published by Cold Spring Harbor Laboratory Press. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.title A comparison of gene expression and DNA methylation patterns across tissues and species
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1101/gr.254904.119
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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