The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly [RNA-seq]

RNAi factors and their catalytic activities are essential for heterochromatin assembly in S. pombe. This has led to the idea that siRNAs can promote H3K9 methylation by recruiting the Cryptic Loci Regulator Complex (CLRC), also known as Recombination In K Complex (RIKC), to the nucleation site. The conserved RNA-binding protein Rct1 (AtCyp59/SIG-7) interacts with splicing factors and with RNA polymerase II. Here we show that Rct1 promotes processing of pericentromeric transcripts into siRNAs, via the RNA recognition motif. Surprisingly, loss of siRNA in rct1 mutant cells has no effect on H3K9 di- or tri-methylation, resembling other splicing mutants, and suggesting post-transcriptional gene silencing per se is not required to maintain heterochromatin. Splicing of the Argonaute gene is also defective in rct1 mutants, and contributes to loss of silencing but not to loss of siRNA. Our results suggest that Rct1 guides transcripts to the RNAi machinery by promoting splicing of elongating non-coding transcripts. rRNA-depleted RNA expression profiling of WT, rct1 KO, rct1-RRM, clr3 KO, ago1 KO, dcr1 KO and rct1 clr3 double KO cells. Two biological replicates are included for all except ago1 KO and dcr1 KO. 12 samples in total.