UBA2A regulates seed dormancy and the stability of chromatin-retained DOG1 messenger RNA

Multiple factors control primary seed dormancy established during seed maturation and secondary seed dormancy initiated when a non-dormant imbibed seed is exposed to adverse conditions. A key player in the control of primary and secondary dormancy in Arabidopsis thaliana is the Delay of Germination 1 (DOG1) gene, the expression of which is extensively regulated at the transcriptional and co-transcriptional levels. Despite its importance, the influence of post-transcriptional messenger RNA (mRNA) processing and mRNA storage of DOG1 on the determination of dormancy depth remains elusive. Here, we show that the UBA2A protein, a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, negatively regulates primary and secondary seed dormancy through the regulation of the DOG1 gene expression at the post-transcriptional level. uba2a mutants show higher levels of the DOG1 mRNA. Surprisingly, DOG1 gene transcription is not affected, as demonstrated by single-molecule fluorescent in situ hybridization, chromatin-attached mRNA analysis and Pol II chromatin immunoprecipitation (ChIP). Instead, our results show that the UBA2A protein decreases the stability of both chromatin-bound and cytoplasmic DOG1 mRNA pools, and results in higher chromatin retention of DOG1 mRNA in the uba2a mutant. Our study highlights chromatin retention and mRNA stability as important features of DOG1 gene expression regulation with a profound impact on dormancy establishment and shows that UBA2A protein, like its human homolog hnRNPAB, is most likely implicated in mRNA transport in the cell.