piRTarBase2: an updated C. elegans piRNA binding site database with extensive evidence for piRNA targeting events

Piwi-interacting RNAs (piRNAs) are small non-coding RNAs (ncRNAs) that guide Piwi proteins to complementary RNA targets and trigger gene silencing through secondary 22G siRNA amplification. Accurate identification of piRNA target sites is therefore critical for understanding cellular gene silencing. Previously, we developed piRTarBase to catalog canonical piRNA-mRNA interactions using pirScan, but it was limited to mRNA targets and canonical binding rules. To address these limitations, we developed piRTarBase2, an updated database integrating CLASH-derived interactions processed by ChiRA. piRTarBase2 combined pirScan and RNAup to characterize both canonical and non-canonical binding sites across mRNAs and ncRNAs. It further integrates multiple lines of supporting evidence, including expression fold changes in prg-1 mutants, 22G-RNA signals, and cross-linking-induced mutation sites, for confidence evaluation of the piRNA binding sites. piRTarBase2 provides a comprehensive resource for exploring experimentally supported piRNA-target interactions and is available at https://cosbi7.ee.ncku.edu.tw/pirtarbase_v2/. Database URL: https://cosbi7.ee.ncku.edu.tw/pirtarbase_v2/.