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Data for: Genetic architecture modulates diet induced hepatic mRNA and miRNA expression profiles

Citation

Que, Excel et al. (2020), Data for: Genetic architecture modulates diet induced hepatic mRNA and miRNA expression profiles, Dryad, Dataset, https://doi.org/10.25338/B87K75

Abstract

Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically-relevant traits. More recently, these analyses have been extended to other molecular traits such as protein abundance, metabolite levels, and miRNA expression. Here we performed global hepatic eQTL and miRNA expression quantitative trait loci (mirQTL) analysis in a population of Diversity Outbred (DO) mice fed two different diets. We identified several key features of eQTL and mirQTL, namely differences in the mode of genetic regulation (cis or trans) between mRNA and miRNA. Approximately 50% of mirQTL are regulated by a trans-acting factor compared to ~25% of eQTL. We note differences in the heritability of mRNA and miRNA expression and variance explained by each eQTL or mirQTL. In general, cis-acting variants affecting mRNA or miRNA expression explain more phenotypic variance than trans-acting variants. Lastly, we investigated the effect of diet on the genetic architecture of eQTL and mirQTL highlighting the critical effects of environment on both eQTL and mirQTL. Overall, these data underscore the complex genetic regulation of two well-characterized RNA classes (mRNA and miRNA) that have critical roles in the regulation of clinical traits and disease susceptibility.

Usage Notes

DOeQTL_DataDictionary.xlsx file accompanies the Master Results file, masterRes_3_12_20.rds. 

Phenotypes in mirCross.rds are expressed miRNA. 

Phenotypes in are DO2_cross2.rds are expressed mRNA. 

Funding

NIH, Award: 5R01HL128572

NIH, Award: P30DK056350

NIH, Award: R01DK105965

NIH, Award: R01DK105965

USDA, Award: 2032-51000-022-00D