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

Raquel García-Pérez (), Paula Esteller-Cucala, Glòria Mas, Irene Lobón, Valerio Carlo, Meritxell Riera, Martin Kuhlwilm, Arcadi Navarro, Antoine Blancher, Luciano Croce, José Luis Gómez-Skarmeta, David Juan () and Tomàs Marquès-Bonet ()
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Raquel García-Pérez: Institute of Evolutionary Biology (UPF-CSIC), PRBB
Paula Esteller-Cucala: Institute of Evolutionary Biology (UPF-CSIC), PRBB
Glòria Mas: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology
Irene Lobón: Institute of Evolutionary Biology (UPF-CSIC), PRBB
Valerio Carlo: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology
Meritxell Riera: Institute of Evolutionary Biology (UPF-CSIC), PRBB
Martin Kuhlwilm: Institute of Evolutionary Biology (UPF-CSIC), PRBB
Arcadi Navarro: Institute of Evolutionary Biology (UPF-CSIC), PRBB
Antoine Blancher: Laboratoire d’immunologie, CHU de Toulouse, Institut Fédératif de Biologie, hôpital Purpan
Luciano Croce: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology
José Luis Gómez-Skarmeta: Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía
David Juan: Institute of Evolutionary Biology (UPF-CSIC), PRBB
Tomàs Marquès-Bonet: Institute of Evolutionary Biology (UPF-CSIC), PRBB

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-23397-1

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