Title: Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms.
Authors: Pierce, Brandon L; Tong, Lin; Argos, Maria; Demanelis, Kathryn; Jasmine, Farzana; Rakibuz-Zaman, Muhammad; Sarwar, Golam; Islam, Md Tariqul; Shahriar, Hasan; Islam, Tariqul; Rahman, Mahfuzar; Yunus, Md; Kibriya, Muhammad G; Chen, Lin S; Ahsan, Habibul
Published In Nat Commun, (2018 02 23)
Abstract: Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as a methylation QTL (cis-meQTL), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing evidence of a causal relationship between expression and methylation (i.e., shared mechanism) with many additional pairs we are underpowered to detect. These co-localized pairs are enriched for SNPs showing opposite associations with expression and methylation, although many SNPs affect multiple CpGs in opposite directions. This work demonstrates the pervasiveness of co-regulated expression and methylation in the human genome. Applying this approach to other types of molecular QTLs can enhance our understanding of regulatory mechanisms.
PubMed ID:
29476079
MeSH Terms: Adult; Bangladesh; DNA Methylation*; Female; Gene Expression; Genetic Variation*; Genome, Human; Genome-Wide Association Study; Genomics; Humans; Male; Middle Aged; Polymorphism, Single Nucleotide; Quantitative Trait Loci*; Young Adult