Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana

The circadian clock ofArabidopsis thalianacontrols many physiological and molecular processes, allowingplants to anticipate daily changes in their environment. However, developing a detailed understanding ofhow oscillations in mRNA levels are connected to oscillations in co/post-transcriptional processes, such assplicing, has remained a challenge. Here we applied a combined approach using deep transcriptomesequencing and bioinformatics tools to identify novel circadian-regulated genes and splicing events.Using astringent approach, we identified 300 intron retention, eight exon skipping, 79 alternative 30splice siteusage, 48 alternative 50splice site usage, and 350 multiple (more than one event type) annotated eventsunder circadian regulation. We also found seven and 721 novel alternative exonic and intronic events. Deple-tion of the circadian-regulated splicing factor AtSPF30 homologue resulted in the disruption of a subset ofclock-controlled splicing events. Altogether, our global circadian RNA-seq coupled with anin silico, event-centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clockand the splicing machinery at a global scale. The identification of many circadian-regulated splicing eventsbroadens our current understanding of the level of control that the circadian clock has over this co/post-transcriptional regulatory layer.