Systemic interindividual Epigenetic Variation in Humans Is associated With Transposable Elements and Under Strong Genetic Control

Authors

Chathura J Gunasekara
Harry MacKay
C Anthony Scott
Shaobo Li
Eleonora Laritsky
Maria S Baker
Sandra L Grimm
Goo Jun
Yumei Li
Rui Chen
Joseph L Wiemels
Cristian Coarfa
Robert A Waterland

Publication Date

1-12-2023

Journal

Genome Biology

Abstract

BACKGROUND: Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition.

RESULTS: We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of 188 donors in the NIH Gene-Tissue Expression (GTEx) program. At CoRSIVs, DNA methylation in peripheral blood correlates with methylation and gene expression in internal organs. We also discover unprecedented mQTL at these regions. Genetic influences on CoRSIV methylation are extremely strong (median R

CONCLUSIONS: A focus on systemic interindividual epigenetic variants, clearly enhanced in mQTL content, should likewise benefit studies attempting to link human epigenetic variation to the risk of disease.

Keywords

Humans, DNA Transposable Elements, Gene Expression Regulation, DNA Methylation, Quantitative Trait Loci, CpG Islands, Epigenesis, Genetic