Parent of origin genetic effects on methylation in humans are common and influence complex trait variation

Yanni Zeng, Carmen Amador, Charley Xia, Riccardo Marioni, Duncan Sproul, Rosie M. Walker, Stewart W. Morris, Andrew Bretherick, Oriol Canela-Xandri, Thibaud S. Boutin, David W. Clark, Archie Campbell, Konrad Rawlik, Caroline Hayward, Reka Nagy, Albert Tenesa, David J. Porteous, James F. Wilson, Ian J. Deary, Kathryn L. Evans, Andrew M. McIntosh, Pau Navarro and Chris S. Haley ()
Additional contact information
Yanni Zeng: Institute of Genetics and Molecular Medicine, University of Edinburgh
Carmen Amador: Institute of Genetics and Molecular Medicine, University of Edinburgh
Charley Xia: Institute of Genetics and Molecular Medicine, University of Edinburgh
Riccardo Marioni: University of Edinburgh
Duncan Sproul: Institute of Genetics and Molecular Medicine, University of Edinburgh
Rosie M. Walker: University of Edinburgh
Stewart W. Morris: University of Edinburgh
Andrew Bretherick: Institute of Genetics and Molecular Medicine, University of Edinburgh
Oriol Canela-Xandri: Institute of Genetics and Molecular Medicine, University of Edinburgh
Thibaud S. Boutin: Institute of Genetics and Molecular Medicine, University of Edinburgh
David W. Clark: University of Edinburgh
Archie Campbell: University of Edinburgh
Konrad Rawlik: University of Edinburgh
Caroline Hayward: Institute of Genetics and Molecular Medicine, University of Edinburgh
Reka Nagy: Institute of Genetics and Molecular Medicine, University of Edinburgh
Albert Tenesa: Institute of Genetics and Molecular Medicine, University of Edinburgh
David J. Porteous: University of Edinburgh
James F. Wilson: Institute of Genetics and Molecular Medicine, University of Edinburgh
Ian J. Deary: University of Edinburgh
Kathryn L. Evans: University of Edinburgh
Andrew M. McIntosh: University of Edinburgh
Pau Navarro: Institute of Genetics and Molecular Medicine, University of Edinburgh
Chris S. Haley: Institute of Genetics and Molecular Medicine, University of Edinburgh

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract Parent-of-origin effects (POE) exist when there is differential expression of alleles inherited from the two parents. A genome-wide scan for POE on DNA methylation at 639,238 CpGs in 5,101 individuals identifies 733 independent methylation CpGs potentially influenced by POE at a false discovery rate ≤ 0.05 of which 331 had not previously been identified. Cis and trans methylation quantitative trait loci (mQTL) regulate methylation variation through POE at 54% (399/733) of the identified POE-influenced CpGs. The combined results provide strong evidence for previously unidentified POE-influenced CpGs at 171 independent loci. Methylation variation at 14 of the POE-influenced CpGs is associated with multiple metabolic traits. A phenome-wide association analysis using the POE mQTL SNPs identifies a previously unidentified imprinted locus associated with waist circumference. These results provide a high resolution population-level map for POE on DNA methylation sites, their local and distant regulators and potential consequences for complex traits.

Date: 2019
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DOI: 10.1038/s41467-019-09301-y

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