Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3’ splice site usage

Abstract

RNA helicases drive necessary rearrangements and ensure fidelity during the pre-mRNA splicing cycle. DEAD-box helicase DDX41 has been linked to human disease and has recently been shown to interact with DEAH-box helicase PRP22 in the spliceosomal C* complex, yet its function in splicing remains unknown. Depletion of DDX41 homolog SACY-1 from somatic cells has been previously shown to lead to changes in alternative 3’ splice site usage. Here, we show by transcriptomic analysis of published and novel datasets that SACY-1 perturbation causes a previously unreported pattern in alternative 3’ splicing in introns with pairs of 3’ splice sites ≤ 18 nucleotides away from each other. We find that both SACY-1 depletion and the allele sacy-1(G533R) lead to a striking unidirectional increase in the usage of the proximal (upstream) 3’ splice site. We previously discovered a similar alternative splicing pattern between germline tissue and somatic tissue, in which there is a unidirectional increase in proximal 3’ splice site usage in the germline for ~200 events; many of the somatic SACY-1 alternative 3’ splicing events overlap with these developmentally regulated events. We generated targeted mutant alleles of the C. elegans homolog of PRP22, mog-5, in the region of MOG-5 that is predicted to interact with SACY-1 based on the human C* structure. These viable alleles, and a mimic of the myelodysplastic syndrome-associated allele DDX41(R525H), all promote usage of proximal alternative adjacent 3’ splice sites. We show that PRP22/MOG-5 and DDX41/SACY-1 have overlapping roles in proofreading the 3’ splice site.