TY - JOUR
T1 - Genome-Wide Epigenetic Signatures of Adaptive Developmental Plasticity in the Andes
AU - Childebayeva, Ainash
AU - Goodrich, Jaclyn M.
AU - Leon-Velarde, Fabiola
AU - Rivera-Chira, Maria
AU - Kiyamu, Melisa
AU - Brutsaert, Tom D.
AU - Dolinoy, Dana C.
AU - Bigham, Abigail W.
N1 - Funding Information:
First and foremost, we would like to thank the study participants from Lima and Cerro de Pasco, Peru. We are also thankful to Dr Sudipta Ghosh (NEHU University, Shillong, India), Obed Garcia (University of Michigan), Nate Bartman, Jason Howard, Jacqueline Imse, and Kevin Heffernan (Syracuse University), Mark Olfert (University of West Virginia), and Francisco Villafuerte (Universidad Peruana Cayetano Heredia). We are grateful to physicians Cesar De Albertis, Laura Mori, Josseline Honorio, and Alejandro Zamudio for the help with participant recruitment. We also would like to thank Dr Jennifer Smith (University of Michigan) for assistance with statistical analysis. This work was supported by The National Science Foundation (Grant Nos. BCS-1132310 to T.D.B., F.L., and A.W.B. and BCS-1613415 to A.C. and A.W.B.), The Wenner-Gren Foundation (Dissertation Fieldwork Grant to A.C.), The University of Michigan (A.W.B. and A.C.), and The Michigan Lifestage Environmental Exposures and Disease (M-LEEaD) National Institute of Environmental Health Sciences Core Center (P30 ES017885 to D.C.D.). A.C. was supported by a Baldwin Fellowship from The Leakey Foundation.
Publisher Copyright:
ß The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2021/2/1
Y1 - 2021/2/1
N2 - High-altitude adaptation is a classic example of natural selection operating on the human genome. Physiological and genetic adaptations have been documented in populations with a history of living at high altitude. However, the role of epigenetic gene regulation, including DNA methylation, in high-altitude adaptation is not well understood. We performed an epigenome-wide DNA methylation association study based on whole blood from 113 Peruvian Quechua with differential lifetime exposures to high altitude (>2,500) and recruited based on a migrant study design. We identified two significant differentially methylated positions (DMPs) and 62 differentially methylated regions (DMRs) associated with high-altitude developmental and lifelong exposure statuses. DMPs and DMRs were found in genes associated with hypoxia-inducible factor pathway, red blood cell production, blood pressure, and others. DMPs and DMRs associated with fractional exhaled nitric oxide also were identified. We found a significant association between EPAS1 methylation and EPAS1 SNP genotypes, suggesting that local genetic variation influences patterns of methylation. Our findings demonstrate that DNA methylation is associated with early developmental and lifelong high-altitude exposures among Peruvian Quechua as well as altitude-adaptive phenotypes. Together these findings suggest that epigenetic mechanisms might be involved in adaptive developmental plasticity to high altitude. Moreover, we show that local genetic variation is associated with DNA methylation levels, suggesting that methylation associated SNPs could be a potential avenue for research on genetic adaptation to hypoxia in Andeans.
AB - High-altitude adaptation is a classic example of natural selection operating on the human genome. Physiological and genetic adaptations have been documented in populations with a history of living at high altitude. However, the role of epigenetic gene regulation, including DNA methylation, in high-altitude adaptation is not well understood. We performed an epigenome-wide DNA methylation association study based on whole blood from 113 Peruvian Quechua with differential lifetime exposures to high altitude (>2,500) and recruited based on a migrant study design. We identified two significant differentially methylated positions (DMPs) and 62 differentially methylated regions (DMRs) associated with high-altitude developmental and lifelong exposure statuses. DMPs and DMRs were found in genes associated with hypoxia-inducible factor pathway, red blood cell production, blood pressure, and others. DMPs and DMRs associated with fractional exhaled nitric oxide also were identified. We found a significant association between EPAS1 methylation and EPAS1 SNP genotypes, suggesting that local genetic variation influences patterns of methylation. Our findings demonstrate that DNA methylation is associated with early developmental and lifelong high-altitude exposures among Peruvian Quechua as well as altitude-adaptive phenotypes. Together these findings suggest that epigenetic mechanisms might be involved in adaptive developmental plasticity to high altitude. Moreover, we show that local genetic variation is associated with DNA methylation levels, suggesting that methylation associated SNPs could be a potential avenue for research on genetic adaptation to hypoxia in Andeans.
KW - SNP–DNA methylation interactions
KW - epigenetics
KW - epigenome-wide association study
KW - high-altitude adaptation
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U2 - 10.1093/gbe/evaa239
DO - 10.1093/gbe/evaa239
M3 - Article
C2 - 33185669
AN - SCOPUS:85101433566
SN - 1759-6653
VL - 13
JO - Genome biology and evolution
JF - Genome biology and evolution
IS - 2
M1 - evaa239
ER -