Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting post-transcriptional transgene silencing

Besides regulating splicing, the conserved spliceosome component SmD1b promotes posttranscriptional silencing of sense transgenes (S-PTGS)¹. Here, the « Epigenetics and small RNAs » EpiARN team in collaboration with the Institute of Plant Sciences Paris-Saclay (IPS2) and the Max Plank Institute, Germany, show that the conserved spliceosome component PRP39a also plays a role in S-PTGS in Arabidopsis thaliana (Bazin et al, 2023). However, PRP39a and SmD1b actions appear distinct in both splicing and S-PTGS. Indeed, RNAseq-based analysis of expression level and alternative splicing in prp39a and smd1b mutants identified different sets of deregulated transcripts and non-coding RNAs. Moreover, double mutant analyses involving prp39a or smd1b and RNA quality control (RQC) mutants revealed distinct genetic interactions for SmD1b and PRP39a with nuclear RQC machineries, suggesting non-redundant roles in the RQC/PTGS interplay. Supporting this hypothesis, a prp39a smd1b double mutant exhibited enhanced suppression of S-PTGS compared to the single mutants. Because the prp39a and smd1b mutants (i) show no major changes in the expression of PTGS or RQC components, (ii) accumulate endogenous small RNAs at wildtype level, and (iii) do not alter PTGS triggered by inverted-repeat transgenes directly producing dsRNA (IR-PTGS), PRP39a and SmD1b appear to synergistically promote a step specific to S-PTGS. Together, these results suggest that, independently of their specific roles in splicing, PRP39a and SmD1b limit 3'-to-5' and/or 5'-to-3' degradation of transgene-derived aberrant RNAs in the nucleus, thus favoring the export of aberrant RNAs to the cytoplasm where their conversion into double-stranded RNA initiates S-PTGS.

¹ Elvira-Matelot E, Bardou F, Ariel F, Jauvion V, Bouteiller N, Le Masson I, Cao J, Crespi MD, Vaucheret H. (2016). The Nuclear Ribonucleoprotein SmD1
Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis. Plant Cell 28, 426-438