PT - JOURNAL ARTICLE AU - Mulin Jun Li AU - Jiexing Wu AU - Peng Jiang AU - Wei Li AU - Yun Zhu AU - Daniel Fernandez AU - Russell J. H. Ryan AU - Yiwen Chen AU - Junwen Wang AU - Jun S. Liu AU - X. Shirley Liu TI - Exploring functional variation affecting ceRNA regulation in humans AID - 10.1101/016865 DP - 2015 Jan 01 TA - bioRxiv PG - 016865 4099 - http://biorxiv.org/content/early/2015/03/22/016865.short 4100 - http://biorxiv.org/content/early/2015/03/22/016865.full AB - MicroRNA (miRNA) sponges have been shown to function as competing endogenous RNAs (ceRNAs) to regulate the expression of other miRNA targets in the network by sequestering available miRNAs. As the first systematic investigation of the genome-wide genetic effect on ceRNA regulation, we applied multivariate response regression and identified widespread genetic variations that are associated with ceRNA competition using 462 Geuvadis RNA-seq data in multiple human populations. We showed that SNPs in gene 3’UTRs at the miRNA seed binding regions can simultaneously regulate gene expression changes in both cis and trans by the ceRNA mechanism. We termed these loci as endogenous miRNA sponge expression quantitative trait loci or “emsQTLs”, and found that a large number of them were unexplored in conventional eQTL mapping. We identified many emsQTLs are undergoing recent positive selection in different human populations. Using GWAS results, we found that emsQTLs are significantly enriched in traits/diseases associated loci. Functional prediction and prioritization extend our understanding on causality of emsQTL allele in disease pathways. We illustrated that emsQTL can synchronously regulate the expression of tumor suppressor and oncogene through ceRNA competition in angiogenesis. Together these results provide a distinct catalog and characterization of functional noncoding regulatory variants that control ceRNA crosstalk.