Analysis of Col-0 and sgs3-1 transcriptome profile treated with cordycepin in Arabidopsis

In plant cytoplasm, transcriptome homeostasis and active RNA degradation rely on two principal turnover pathways: exonucleolytic RNA decay and endonucleolytic RNA silencing. Although RNA decay is recognized to dampen silencing efficacy, whether RNA silencing exerts a reciprocal effect on decay remain key unresolved questions. Here we shown that RNA silencing represses RNA decay activity. mRNA-seq approach was used to investigate the RNA decay activity in Col-0 wild-type and sgs3-1 mutant. Seedlings (7 days old) were exposed to the transcriptional inhibitor cordycepin, and total RNA was collected for RNA-seq analysis at 0, 30, 60, and 120 minutes post-treatment. RNA stability analysis revealed 3,372 transcripts with significantly altered decay rates in sgs3-1 versus Col-0. Of these 1,951 genes showing faster degradation in the sgs3-1 mutant and 1,421 genes showing slower degradation, suggesting RNA silencing represses decay efficiency of endogenous transcripts in Arabidopsis.