Circadian regulation of genes contributed by rapid RNA turnover in tomato
Large number of genes whose expression cycles are controlled by circadian rhythm. Circadian period and phase changes were positively selected during domestication in tomato. However, the effect of RNA metabolism on circadian gene oscillations remains largely unclear. In this study, we performed transcriptome and degradome termed genome-wide mapping of uncapped and cleavage transcripts (GMUCT) in tomato leaves at 6 time points in one circadian period. Time-series profiling of RNA-seq data revealed 9342 circadian genes, whose functions enriched in multiple types of metabolic process including RNA metabolism. Proportion Uncapped (PU) metric calculated with normalized GMUCT/RNAseq ratio was used to measure general level of RNA degradation. Using this metric, we found 3885 genes whose PU was rhythmically changed, suggesting they were regulated by circadian RNA degradation. These genes with rhythmic PU were significantly enriched in the gene category with high coordination between mRNA abundance oscillation and PU dynamics. Additionally, we identified 2140 genes undergoing co-translational RNA decay (CTRD) with enriched translational termination stalling of 5' Phosphate end reads. Remarkably, circadian mRNAs with large amplitude tent to be co-translationally decayed. Finally, we found several genes like miR172-targeted AP2, miR398-targeted CSD2 and miR159-targeted MYB125 whose miRNA cleavage efficiency also oscillated in circadian manner. Taken together, these results uncovered the vital roles of RNA metabolism including general RNA degradation, CTRD and miRNA cleavage efficiency in modulating circadian oscillations of RNA abundance. Overall design: GMUCT and RNA-seq profiling in amture leaves of Tomatos