Transcriptome-wide analysis suggests piRNAs preferentially recognize the coding region of mRNAs in C. elegans

BackgroundPIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposon mRNAs and some endogenous mRNAs in various animals. However, C. elegans piRNAs fail to trigger gene silencing at many sequence-based predicted targeting sites. ResultsTo gain insights into the mechanisms that control piRNA silencing capability, we compared the transcriptome-wide predicted piRNA targeting sites to the in vivo piRNA binding sites. Surprisingly, while predicted piRNA targeting sites are enriched in 3 UTRs, we found that C. elegans piRNAs preferentially bind to coding regions (CDS) of target mRNAs, leading to preferential production of secondary silencing small RNAs in the CDS. Furthermore, our analyses suggest that Argonaute protein CSR-1 protects mRNAs from piRNA silencing through two distinct mechanisms - by inhibiting piRNA binding across the entire CSR-1 targeted transcript, and by inhibiting secondary silencing small RNA production locally at CSR-1 bound sites. However, CSR-1 is not responsible for the piRNA binding preference for the CDS. ConclusionsOur work identifies the CDS as the critical region that is uniquely competent for piRNA silencing in C. elegans. We speculate that the preference for CDS recognition by piRNAs may represent a mechanism to counteract the evolution of foreign protein-coding RNAs that evade piRNA surveillance.