We sought to comprehensively and systematically characterize the relationship between genetic variation, miRNA expression, and mRNA expression. Genome-wide expression profiling of samples of European and African ancestry identified in each population hundreds of miRNAs whose increased expression is correlated with correspondingly reduced expression of target mRNAs. We scanned 3′ UTR SNPs with a potential functional effect on miRNA binding for cis-acting expression quantitative trait loci (eQTLs) for the corresponding proximal target genes. To extend sequence-based, localized analyses of SNP effect on miRNA binding, we proceeded to dissect the genetic basis of miRNA expression variation; we mapped miRNA expression levels - as quantitative traits - to loci in the genome as miRNA eQTLs, demonstrating that miRNA expression is under significant genetic control. We found that SNPs associated with miRNA expression are significantly enriched with those SNPs already shown to be associated with mRNA. Moreover, we discovered that many of the miRNA-associated genetic variations identified in our study are associated with a broad spectrum of human complex traits from the National Human Genome Research Institute catalog of published genome-wide association studies. Experimentally, we replicated miRNA-induced mRNA expression inhibition and the cis-eQTL relationship to the target gene for several identified relationships among SNPs, miRNAs, and mRNAs in an independent set of samples; furthermore, we conducted miRNA overexpression and inhibition experiments to functionally validate the miRNA-mRNA relationships. This study extends our understanding of the genetic regulation of the transcriptome and suggests that genetic variation might underlie observed relationships between miRNAs and mRNAs more commonly than has previously been appreciated.
Bibliographical noteFunding Information:
We are grateful for the excellent technical support provided by Mr. Ken Hecht in maintaining the cell lines, Mr. Wasim Bleibel for isolating RNA from the discovery samples, Mr. Viren Makhijani for assistance in RNA isolation from the replication samples, and M. Eileen Dolan's lab for generating and depositing Exon-array data (Gene Expression Omnibus accession number GSE7761). This study was supported by the National Institutes of Health (NIH)-National Cancer Institute grant R21 CA139278 and by the NIH-National Institute of General Medical Sciences (NIGMS) grant UO1GM61393. R.S.H. received support from NIH-NIGMS grant K08GM089941, University of Chicago Cancer Center Support Grant P30 CA14599, and the Breast Cancer SPORE (Specialized Program of Research Excellence) Career Development Award.