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

Abstract

Background: PIWI-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. Results: To 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. Conclusions: Our 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.

Using piRNA interference to quantify acute and inherited silencing in Caenorhabditis elegans with no requirement for genetic crosses: a case study.

“…Third, there are some concerns about using transgenes as a proxy for endogenous gene silencing. For example, most piRNA sensor strains include synthetic piRNA binding sites in the 3' UTR (8)(9)(10)(11) but endogenous genes are resistant to piRNA silencing when targeting their 3' UTRs (16,17). Moreover, transgene insertion site (18), non-coding DNA structures (19), coding sequence (20,21), and transgene structure (22) can influence epigenetic silencing.…”

rde-3 reduces piRNA-mediated silencing and abolishes inherited silencing in C. elegans

“…Third, there are some concerns about using transgenes as a proxy for endogenous gene silencing. For example, most piRNA sensor strains include synthetic piRNA binding sites in the 3’ UTR 8–11 but endogenous genes are resistant to piRNA silencing when targeting their 3’ UTRs 16,17 . Moreover, transgene insertion site 18 , noncoding DNA structures 19 , coding sequence 20,21 , and transgene structure 22 can influence epigenetic silencing.…”