Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy

Abstract

The decay of mRNA plays a vital role in modulating mRNA abundance, which, in turn, influences cellular and organismal processes. In plants and metazoans, three distinct pathways carry out the decay of most cytoplasmic mRNAs: The mRNA decapping complex, which requires the scaffold protein VARICOSE (VCS), removes a protective 5' cap, allowing for 5' to 3' decay via EXORIBONUCLEASE4 (XRN4, XRN1 in metazoans and yeast), and both the exosome and SUPPRESSOR OF VCS (SOV)/DIS3L2 degrade RNAs in the 3' to 5' direction. However, the unique biological contributions of these three pathways, and whether they degrade specialized sets of transcripts, are unknown. In , the participation of SOV in RNA homeostasis is also unclear, because mutants have a normal phenotype. We carried out mRNA decay analyses in wild-type, ,, and seedlings, and used a mathematical modeling approach to determine decay rates and quantify gene-specific contributions of VCS and SOV to decay. This analysis revealed that VCS (decapping) contributes to decay of 68% of the transcriptome, and, while it initiates degradation of mRNAs with a wide range of decay rates, it especially contributes to decay of short-lived RNAs. Only a few RNAs were clear SOV substrates in that they decayed more slowly in mutants. However, 4,506 RNAs showed VCS-dependent feedback in that modulated decay rates, and, by inference, transcription, to maintain RNA abundances, suggesting that these RNAs might also be SOV substrates. This feedback was shown to be independent of siRNA activity.

DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs associated with innate immunity and growth inhibition

“…Triplicate biological samples were sequenced to an average depth of 22.7 million reads. After data normalization and exclusion of low abundance mRNAs, transcript abundances were used to model decay rates for each gene and genotype 11 .…”

“…Since all three RHs colocalize with DCP2 and VCS, we hypothesized that their substrates are degraded in a decapping-dependent manner. A parallel decay experiment was performed in the decapping mutant vcs-7 11 , and co-analysis of rh6812 and vcs-7 effects on decay identified 5,832 out of 6,941 RH substrates (84%) as VCS substrates (Fig. 4e).…”

“…These 5’ and 3’ pathways have substrate specificity, but are not mutually exclusive. When decapping-dependent decay is compromised in Arabidopsis, the 3’-to-5’ exoribonuclease SOV can compensate to control mRNA abundance and homeostasis 10, 11 .…”

Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

“…Previous studies also found that RNA stability correlates with distinct biological 387 functions (Narsai et al, 2007, Sorenson et al, 2018. To test this, we performed a 388 gene classification analysis using MAPMAN on the five different clusters described 389 before (Thimm et al, 2004).…”

Tissue-specific changes in the RNA structurome mediate salinity response inArabidopsis

“…Sequence motifs in the 3'UTR that control transcript degradation are known (Rabani et al, 2017), yet little information exists on how structure plays into this. A recent study on mRNA decay in Arabidopsis showed that transcripts with enriched A content and depleted G content in 5' UTRs exhibited faster decay rates (Sorenson et al 2018). Given that AU base-pairing is weaker than GC base-pairing, these results may implicate saltinduced 5' UTR unfolding (increased reactivity) as a mechanism that exposes transcripts to nucleolytic attack.…”