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Journal articles
The epigenomic landscape of African rainforest hunter-gatherers and farmers
Maud Fagny
1
Etienne Patin
1
Maxime Rotival
1
Julia L. Macisaac
2
Timothée Flutre
3
Meaghan J. Jones
2
Katherine J. Siddle
1
Hélène Quach
1
Christine Harmant
1
Lisa M. Mcewen
2
Alain Froment
4
Evelyne Heyer
4
Antoine Gessain
5
Edouard Betsem
6, 5
Patrick Mouguiama-Daouda
7
Jean-Marie Hombert
8
Luis B. Barreiro
9
Michael S. Kobor
2
George H. Perry
10
Lluis Quintana-Murci
1
Maud Fagny 1
Author IdHAL : maud-fagny ResearcherId : http://www.researcherid.com/rid/ O-5415-2017 ORCID : https://orcid.org/0000-0002-7740-2521
Etienne Patin 1
Author IdHAL : etienne-patin ORCID : https://orcid.org/0000-0002-9911-4459
Maxime Rotival 1
Author IdHAL : maxime-rotival ORCID : https://orcid.org/0000-0003-2519-8044
Julia L. Macisaac 2
Author
Timothée Flutre 3
Author IdHAL : timothee-flutre arXiv : https://arxiv.org/a/flutre_t_1 ORCID : https://orcid.org/0000-0003-4489-4782
Meaghan J. Jones 2
Author
Katherine J. Siddle 1
Author
Hélène Quach 1
Author
Christine Harmant 1
Author
Lisa M. Mcewen 2
Author
Alain Froment 4
Author
Evelyne Heyer 4
Author IdHAL : evelyne-heyer ORCID : https://orcid.org/0000-0002-0266-3196
Antoine Gessain 5
Author
Edouard Betsem 6, 5
Author
Patrick Mouguiama-Daouda 7
Author
Jean-Marie Hombert 8
Author
Luis B. Barreiro 9
Author
Michael S. Kobor 2
Author
George H. Perry 10
Author
Lluis Quintana-Murci 1
Author
1
Génétique Evolutive Humaine - Human Evolutionary Genetics (Département Génomes et Génétique - 25-28 rue du Docteur Roux, F-75724 Paris Cedex 15 - France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
- CNRS - Centre National de la Recherche Scientifique : URA3012 (France)
2
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics (Vancouver - Canada)
- UBC - University of British Columbia (Vancouver Campus, , 2329 West Mall, Vancouver, BC, V6T 1Z4 / Okanagan Campus, 3333 University Way, Kelowna, BC, V1V 1V7 - Canada)
3
UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (TA A-108 / 03 - Avenue Agropolis - 34398 Montpellier Cedex 5 France - France)
- Cirad - Centre de Coopération Internationale en Recherche Agronomique pour le Développement : UMR108 (Siège 42, rue Scheffer 75116 Paris - France)
- INRA - Institut National de la Recherche Agronomique (France)
- Montpellier SupAgro - Centre international d'études supérieures en sciences agronomiques (2, place Pierre Viala - 34060 Montpellier Cedex 02 - France)
- Montpellier SupAgro - Institut national d’études supérieures agronomiques de Montpellier (2, place Viala 34060 Montpellier Cédex 2 - France)
4
Département des Jardins botaniques et zoologiques (57 rue Cuvier - 75005 Paris - France)
- MNHN - Muséum national d'Histoire naturelle (57, rue Cuvier - 75231 Paris Cedex 05 - France)
5
EPVO (UMR_3569 / U-Pasteur_3) - Epidémiologie et Physiopathologie des Virus Oncogènes (Département de Virologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR_3569 (France)
- UPD7 - Université Paris Diderot - Paris 7 : UMR_3569 (5 rue Thomas-Mann - 75205 Paris cedex 13 - France)
- Institut Pasteur [Paris] : U-Pasteur_3 (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
6
Faculty of Medicine and Biomedical Sciences (Yaounde - Cameroon)
- University of Yaounde I (Cameroon)
7
LCC - Laboratoire Langue, Culture et Cognition [Libreville, Gabon] (Université Omar Bongo B.P. 13131 Libreville - Gabon)
8
EMC - Laboratoire d'Etude des Mécanismes Cognitifs (5, avenue Pierre Mendès-France 69676 Bron cedex - France)
- UL2 - Université Lumière - Lyon 2 : EA3082 (86, rue Pasteur - 69007 Lyon - France)
- CNRS - Centre National de la Recherche Scientifique : UMR5596 (France)
10
Departments of Anthropology and Biology (Pennsylvania 16802 - United States)
- Penn State - Pennsylvania State University (201 Old Main, University Park, Pennsylvania 16802 - United States)
- Penn State System (Pennsylvania, PA, USA, Etats-Unis - United States)
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.
Document type :
Journal articles
Complete list of metadatas
https://hal-pasteur.archives-ouvertes.fr/pasteur-01238387
Contributor : Anne Lassailly-Bondaz <>
Submitted on : Friday, December 4, 2015 - 5:45:09 PM
Last modification on : Friday, December 18, 2020 - 5:30:03 PM
Long-term archiving on: : Saturday, April 29, 2017 - 5:51:39 AM
Contributor : Anne Lassailly-Bondaz <>
Submitted on : Friday, December 4, 2015 - 5:45:09 PM
Last modification on : Friday, December 18, 2020 - 5:30:03 PM
Long-term archiving on: : Saturday, April 29, 2017 - 5:51:39 AM
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ncomms10047.pdf
Publication funded by an institution
Licence
Distributed under a Creative Commons Attribution 4.0 International License
Identifiers
- HAL Id : pasteur-01238387, version 1
- DOI : 10.1038/ncomms10047
- PUBMED : 26616214
- PRODINRA : 341972
- WOS : 000366376400002
Collections
PASTEUR | CNRS | INRA | CIRAD | AGROPOLIS | MNHN | UNIV-LYON2 | MONTPELLIER-SUPAGRO | UDL | UNIV-PARIS7 | USPC | INRAE | UNIV-PARIS | UP-SCIENCES | AFRIQ
Citation
Maud Fagny, Etienne Patin, Maxime Rotival, Julia L. Macisaac, Timothée Flutre, et al.. The epigenomic landscape of African rainforest hunter-gatherers and farmers. Nature Communications, Nature Publishing Group, 2015, 6, 11 p. ⟨10.1038/ncomms10047⟩. ⟨pasteur-01238387⟩
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