CLASHub is an integrated database and analytical platform for microRNA-target interactions

Abstract

Abstract MicroRNAs (miRNAs) are short RNAs that regulate gene expression, critical for development and disease. Residing in Argonaute (AGO) proteins, miRNAs target messenger RNAs via complementary base-pairing. Current miRNA-target databases rely on indirect data from AGO crosslinking immunoprecipitation (AGO-CLIP). In contrast, CLASH (Crosslinking, Ligation, and Sequencing of Hybrids) employs proximity ligation within AGO complexes, providing direct miRNA-target interaction evidence. Existing CLASH datasets remain limited to a few human and mouse samples. Here, we present CLASHub, which integrates CLASH-defined interactions with gene and miRNA expression data from human, mouse, Drosophila , and C. elegans , spanning 25 cell types and tissues, including 91 new CLASH datasets generated from 17 cell types/tissues. The datasets also include samples with knockout of ZSWIM8 , an essential component in target-directed miRNA degradation (TDMD), providing insights into miRNA turnover mechanisms. CLASHub features a user-friendly Analyzer interface for CLASH, RNA-seq, miRNA-seq, and cumulative fraction curve analyses. Leveraging these tools, we uncover a TDMD trigger in the ATP6V1G1 3′ UTR for miR-335-3p degradation, as well as multiple targets of miR-18a-5p. Thus, CLASHub is an online platform that enables cell/tissue-specific exploration of miRNA-target interactions, supporting miRNA and broader RNA biology research. The platform is publicly accessible at https://clashub.rc.ufl.edu/ .