Abstract
Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery. This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. To assess the potential of RNAi activation on endogenous transcripts, we sequenced small RNAs from a set of Arabidopsis thaliana mutants with defects in various RNA metabolism pathways. We observed a global production of siRNAs caused by inefficient pre-mRNA cleavage and polyadenylation leading to read-through transcription into downstream antisense genes. In addition, in the lsm1a lsm1b double mutant, we identified NIA1, SMXL5, and several miRNA-targeted mRNAs as producing siRNAs, a group of transcripts suggested being especially sensitive to deficiencies in RNA metabolism. However, in most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules. This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways.
Highlights
Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery
Several studies have demonstrated the existence of a new class of small RNA (sRNA) called rqcsiRNA (RNA quality control small interfering RNA)[7] or ct-siRNA8, which are generated mainly due to defects in RNA degradation machinery from mRNAs that do not normally produce siRNAs
It has been observed that many defects in mRNA maturation or degradation can lead to the accumulation of aberrant endogenous or transgenic transcripts that are recognised by RNA interference (RNAi) Âpathways[23â25,30,31,62]
Summary
Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. In most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways. These results suggest that different RNA degradation pathways may substitute for each other or that the rqc-siRNA generating mechanisms are limited only to a specific group of aberrant transcripts
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