A comparison of gene expression and DNA methylation patterns across tissues and species
Blake, Lauren E. (University of Chicago. Department of Human Genetics (USA))
Roux, Julien (Swiss Institute of Bioinformatics (Switzerland))
Hernando-Herraez, Irene (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Banovich, Nicholas E. (University of Chicago. Department of Human Genetics (USA))
García Perez, Raquel (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Hsiao, Chiaowen Joyce (University of Chicago. Department of Human Genetics (USA))
Eres, Ittai (University of Chicago. Department of Human Genetics (USA))
Cuevas, Claudia (University of Chicago. Department of Human Genetics (USA))
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Gilad, Yoav (University of Chicago. Department of Medicine (USA))

Fecha:	2020
Resumen:	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.
Ayudas:	Ministerio de Economía y Competitividad BFU2017-86471-P
Nota:	Altres ajuts: Obra Social "LaCaixa" and Secretaria d'Universitats i Recerca and Centres de Recerca de Catalunya Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Publicado en:	Genome research, Vol. 30, Issue 2 (February 2020) , p. 250-262, ISSN 1549-5469

DOI: 10.1101/gr.254904.119
PMID: 31953346

14 p, 2.4 MB

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Documentos de investigación > Documentos de los grupos de investigación de la UAB > Centros y grupos de investigación (producción científica) > Ciencias > Institut Català de Paleontologia Miquel Crusafont (ICP)
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