| Polymorphism in microRNA Target Site (PolymiRTS) is a database of naturally occurring DNA variations in putative microRNA (miRNA) target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. Single nucleotide polymorphism (SNP) in miRNA target site may affect the base-pairing between the miRNA and its target site, and hence affect the miRNA-mediated gene repression.
PolymiRTS as genetic variant underlying quantitative trait locus (QTL). Linkage analysis has long been used to discover chromosomal intervals harboring sequence variants that cause individual differences in biological traits. A recent work shows that SNPs in miRNA target sites may be one type of the sequence variants that underlie QTL effects 1. It has been found that miRNA-mediated target mRNA destabilization is widespread in mammals 2,3. Thus, SNPs in miRNA target sites may lead to heritable variations in gene expression. Variations in gene expression across a population can be assessed by a newly developed genetical genomics approach 4. The genetical genomics approach treats gene expression level as quantitative trait. Linkage mapping is then used to discover the genetic loci regulating gene expression traits (eQTLs). PolymiRTS may induce a cis-acting eQTL that coincides with the gene's physical location.This database characterizes PolymiRTS as a new class of sequence variants underlying gene expression traits and/or higher order mammalian traits. We first scan for SNPs in the miRNA target site in the 3'UTR of each gene; then we identify the QTL intervals in which the SNPs are located. Here we consider two types of QTLs: cis-acting eQTLs that regulate gene expression traits and physiological QTLs (pQTLs) that regulate classic higher order traits (physiological/behavioral traits). |