| Description |
The regulation of mRNA levels is achieved by balancing two opposing and dynamic processes: transcription and degradation. While our understanding of transcription to regulate mRNA levels has expanded, our understanding of RNA degradation is still limited. The relative contributions of known mRNA decay pathways and their respective substrates remains poorly understood. The work presented here provides insight into the functions of two mRNA turnover pathways: the decapping complex, which removes the 5' cap prior to 5'-3' degradation, and the 3'-5' exoribonuclease SOV, orthologous to DIS3L2 in metazoans. We use Arabidopsis as a model organism to expand our knowledge of the contributions of the decapping complex and SOV to management of cytoplasmic RNA levels. The contributions of SOV to mRNA degradation in plants is overlooked in most studies, primarily because the widely-used Arabidopsis laboratory accession, Columbia (Col-0), is an sov mutant. We previously discovered that when SOV is introduced via a transgene driven by the endogenous promoter, it suppresses the seedling-lethal phenotype of mRNA decapping-deficient vcs sov mutants. This finding prompted us to carry out a genome-wide mRNA decay kinetics assay to uncover the relative importance of mRNA decapping and SOV for shaping the transcriptome. We also investigated possible additional functions of SOV in comparison with its metazoan ortholog DIS3L2, which was shown to prefer RNA substrates modified with poly-uridine additions. The work presented here addresses questions about the roles of mRNA decapping and SOV in Arabidopsis: (1) what are the contributions of SOV and mRNA decapping to genome-wide mRNA decay? and (2) what are possible additional substrates of SOV? Our genome-wide mRNA decay assay revealed that short-lived RNAs are among the primary substrates of the decapping complex, and we identified an RNA-feedback mechanism in sov mutants that was reminiscent of RNA buffering identified in yeast. I also found that SOV is not a general suppressor of all decapping mutants, and evidence that uridylated substrate preference could be shared in plants and metazoans by using a multidisciplinary genetic and homology modeling approach. Additionally, I present findings that suggest SOV gain and rdr6 impairment additively suppresses decapping mutant phenotypes. |
