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/ .
