RNA-Seq of C. elegans tagged with UMI exposed to 30 minute HeatShock
Piwi-interacting RNAs (piRNAs), best known for silencing transposons and other non-self-sequences through transcriptional and post-transcriptional silencing, also pervasively target endogenous mRNAs in diverse species, and most germline transcripts in Caenorhabditis elegans1-8. The functions of this broad targeting remain unclear. Here, we uncovered a surprising role for the piRNA pathway in regulating the splicing and fidelity of nascent mRNAs induced during stress. Upon heat shock, piRNAs target essential heat-shock protein (hsps) RNAs—normally absent but massively upregulated upon stress—and generate abundant sequence-specific secondary RNA (22G-RNAs) antisense to these transcripts. Instead of enforcing silencing, these 22G-RNAs selectively associate with nascent hsp transcripts and RNA polymerase II at the transcription complex, delaying splicing and preserving a pool of pre-mRNAs for processing during recovery from stress. This role of the piRNA pathway in enforcing splicing delays extends beyond hsps to alternatively spliced genes and ensures the proper expression of long-intron-containing genes in the genome. In piRNA-deficient prde-1 mutants, splicing is precocious, hsp pre-mRNAs are depleted, expression of long-genes is impaired, transcripts accumulate errors, and consequently, embryos become critically dependent on nonsense-mediated decay (NMD) for survival. Downregulating NMD components in piRNA-deficient animals results in the accumulation of polyubiquitinated proteins and embryonic lethality. Thus, by safeguarding splicing under stress, the piRNA pathway complements NMD as a mechanism of RNA quality control, linking RNA fidelity to genome surveillance.