Tissue-specific RNA-seq of Atsdr4l-5 dig2 mutant seeds

Arabidopsis thaliana SEED DORMANCY 4-LIKE (AtSDR4L) and its paralog Dynamic Influencer of Gene Expression 2 (DIG2) act as transcriptional co-repressors to promote seed-to-seedling phase transition. Their regulatory roles at the temporal and tissue-specific scales remain elusive. Here, we show that mutant phenotypes of Atsdr4l dig2 are alleviated by abscisic acid (ABA) antagonists and gibberellin (GA). Dissected mutant embryos exhibit stunted growth, reduced cell expansion and differentiation. The double mutant results in many similar changes in gene expression in the seed coat and the embryo, with a subset of the genes differentially expressed tissue-specifically. Transcriptomes of Atsdr4l-5 dig2 seed compartments form a distinct cluster from those of the mutant seedlings of Atsdr4l and Polycomb Repressive Complex-related genes, suggesting developmental stage-specific role of these regulators.Together, these results demonstrated that AtSDR4L and DIG2 work in concert to launch the growth potential in embryo and alleviate the constraints in seed coat to prepare seeds for germination. Overall design: Embryo and seed coat were isolated from mature seeds of Atsdr4l-5 dig2 mutant and Col-0 wildtype with three biological replicates each. Total RNA was extracted and mRNA was enriched by polyA selection for RNA-seq profiling of the differentially expressed genes between the mutant and the wildtype in both tissues .