The surveillance of pre-mRNA splicing is an early step in C. elegans RNA interference of endogenous genes.

Here we examine the role of mRNA splicing in Caenorhabditis elegans RNAi. We find that viable null mutations in U1 and U2-snRNP-specific splicing factor genes cause defects in RNAi. The U1A orthologue rnp-2 is required for normal ERGO-1 Argonaute-class 26G siRNA biogenesis, trans-splicing of the eri-6/7 transcript and targeting of poorly conserved gene transcripts by WAGO Argonaute-class 22G siRNAs. We find that poorly spliced gene transcripts engaged by the siRNA generating machinery are poorly conserved, possess few introns, and often have introns that are divergent from introns found in highly conserved genes. Analysis of small RNA populations in wildtype and splicing mutant embryos using next-generation sequencing