The epigenomic landscape of African rainforest hunter-gatherers and farmers

Maud Fagny, Etienne Patin, Julia L. MacIsaac, Maxime Rotival, Timothée Flutre, Meaghan J. Jones, Katherine J. Siddle, Hélène Quach, Christine Harmant, Lisa M. McEwen, Alain Froment, Evelyne Heyer, Antoine Gessain, Edouard Betsem, Patrick Mouguiama-Daouda, Jean-Marie Hombert, George H. Perry, Luis B. Barreiro, Michael S. Kobor and Lluis Quintana-Murci ()
Additional contact information
Maud Fagny: Institut Pasteur, Unit of Human Evolutionary Genetics
Etienne Patin: Institut Pasteur, Unit of Human Evolutionary Genetics
Julia L. MacIsaac: Centre for Molecular Medicine and Therapeutics, University of British Columbia
Maxime Rotival: Institut Pasteur, Unit of Human Evolutionary Genetics
Timothée Flutre: INRA, UMR AGAP
Meaghan J. Jones: Centre for Molecular Medicine and Therapeutics, University of British Columbia
Katherine J. Siddle: Institut Pasteur, Unit of Human Evolutionary Genetics
Hélène Quach: Institut Pasteur, Unit of Human Evolutionary Genetics
Christine Harmant: Institut Pasteur, Unit of Human Evolutionary Genetics
Lisa M. McEwen: Centre for Molecular Medicine and Therapeutics, University of British Columbia
Alain Froment: IRD-MNHN, Sorbonne Universités
Evelyne Heyer: CNRS, MNHN, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Université
Antoine Gessain: Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes
Edouard Betsem: Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes
Patrick Mouguiama-Daouda: Laboratoire Langue, Culture et Cognition (LCC), Université Omar Bongo
Jean-Marie Hombert: CNRS UMR 5596, Université Lumière-Lyon 2
George H. Perry: Pennsylvania State University
Luis B. Barreiro: Université de Montréal, Centre de Recherche CHU Sainte-Justine
Michael S. Kobor: Centre for Molecular Medicine and Therapeutics, University of British Columbia
Lluis Quintana-Murci: Institut Pasteur, Unit of Human Evolutionary Genetics

Nature Communications, 2015, vol. 6, issue 1, 1-11

Abstract: Abstract The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation—particularly that correlated with historical lifestyle—shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time.

Date: 2015
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DOI: 10.1038/ncomms10047

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