PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways

TLDR

Polymorphisms in microRNAs and their target sites can disrupt miRNA function, causing disease and phenotypic variation, and recent genomic technologies such as CLASH now enable direct mapping of miRNA–mRNA binding sites. The study updates the PolymiRTS database to provide an integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and target sites. The database now incorporates CLASH‑derived miRNA–mRNA interactions and adds features such as small indels, TargetScan context+ score differences, and pathway annotations to assess polymorphic miRNA effects. Users can browse and search PolymiRTS to explore relationships between polymorphisms and gene expression, phenotypes, diseases, and pathways.

Abstract

Polymorphisms in microRNAs (miRNAs) and their target sites (PolymiRTS) are known to disrupt miRNA function, leading to the development of disease and variation in physiological and behavioral phenotypes. Here, we describe recent updates to the PolymiRTS database (http://compbio.uthsc.edu/miRSNP), an integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites. Recent advances in genomic technologies have made it possible to identify miRNA–mRNA binding sites from direct mapping experiments such as CLASH (cross linking, ligation and sequencing of hybrids). We have integrated data from CLASH experiments in the PolymiRTS database to provide more complete and accurate miRNA–mRNA interactions. Other significant new features include (i) small insertions and deletions in miRNA seed regions and miRNA target sites, (ii) TargetScan context + score differences for assessing the impact of polymorphic miRNA–mRNA interactions and (iii) biological pathways. The browse and search pages of PolymiRTS allow users to explore the relations between the PolymiRTSs and gene expression traits, physiological and behavioral phenotypes, human diseases and biological pathways.