Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome

Abstract

Antisense long noncoding (aslnc)RNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNAi. Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive aslncRNAs levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for Xrn1-sensitive aslncRNAs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared with S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.

Translation is a key determinant controlling the fate of cytoplasmic long non-coding RNAs

“…The xut0741-a, -b, -d and -f alleles, flanked by NaeI sites, were produced as synthetic gBlocks DNA fragments (IDT – Integrated DNA Technologies), and then cloned between the KpnI and XbaI sites of the pAM376 backbone vector (Szachnowski et al, 2019), giving the pAM594, pAM596, pAM598 and pAM600 vectors, respectively. The xut0741-c and xut0741-e mutants were constructed by site-directed mutagenesis from xut0741-d and then cloned into the same backbone vector, giving the pAM724 and pAM723 vectors, respectively.…”

RNA-Mediated Regulation of Meiosis in Budding Yeast

“…Non-coding RNA are found across species, including viruses, prokaryotes, yeast, plants and animals [ 27 , 28 , 29 , 30 , 31 ]. Different classes of lncRNA species, viz., CUT, XUT and SUTs, have been identified in diverse fungi, including S. pombe and Naumovozyma castellii [ 32 , 33 ]. The long non-coding RNAs are evolving as interesting subjects of study as they play important biological roles in several organisms.…”

From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory

“…In budding and fission yeasts, cytoplasmic lncRNAs are extensively degraded by the 5 -3 exoribonuclease Xrn1/Exo2 [124,[137][138][139]. Inactivation of Xrn1 leads to the stabilization of Xrn1-sensititve Unstable Transcripts (XUTs), the majority of which are antisense to protein-coding genes [124,[138][139][140].…”

“…In budding and fission yeasts, cytoplasmic lncRNAs are extensively degraded by the 5 -3 exoribonuclease Xrn1/Exo2 [124,[137][138][139]. Inactivation of Xrn1 leads to the stabilization of Xrn1-sensititve Unstable Transcripts (XUTs), the majority of which are antisense to protein-coding genes [124,[138][139][140]. Strikingly, in S. cerevisiae, 70% of these XUTs are targeted to Xrn1 through NMD [56,124], indicating that most XUTs are translated and that translation constitutes a prerequisite for their degradation.…”