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

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.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)

Paleogenomics of animal domestication

Starting with dogs, over 15,000 years ago, the domestication of animals has been central in the development of modern societies. Because of its importance for a range of disciplines – including archaeology, biology and the humanities – domestication has been studied extensively. This chapter reviews how the field of paleogenomics has revolutionised, and will continue to revolutionise, our understanding of animal domestication. We discuss how the recovery of ancient DNA from archaeological remains is allowing researchers to overcome inherent shortcomings arising from the analysis of modern DNA alone. In particular, we show how DNA, extracted from ancient substrates, has proven to be a crucial source of information to reconstruct the geographic and temporal origin of domestic species. We also discuss how ancient DNA is being used by geneticists and archaeologists to directly observe evolutionary changes linked to artificial and natural selection to generate a richer understanding of this fascinating process