Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana. (18th May 2020)

• Record Type: Journal Article
• Authors: Romanowski, Andrés; Schlaen, Rubén G.; Perez‐Santangelo, Soledad; Mancini, Estefanía; Yanovsky, Marcelo J.
• Is Part Of: Plant journal. Volume 103:Number 2(2020)
• Page Start: 889
• Page End: 902
• Publication Date: 2020-05-18
• Subjects: circadian clock -- circadian rhythms -- alternative splicing -- splicing factors -- SPF30 -- Arabidopsis thaliana; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.14776
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding of how oscillations in mRNA levels are connected to oscillations in co/post‐transcriptional processes, such as splicing, has remained a challenge. Here we applied a combined approach using deep transcriptome sequencing and bioinformatics tools to identify novel circadian‐regulated genes and splicing events . Using a stringent approach, we identified 300 intron retention, eight exon skipping, 79 alternative 3′ splice site usage, 48 alternative 5′ splice site usage, and 350 multiple (more than one event type) annotated events under circadian regulation. We also found seven and 721 novel alternative exonic and intronic events. Depletion of the circadian‐regulated splicing factor AtSPF30 homologue resulted in the disruption of a subset of clock‐controlled splicing events. Altogether, our global circadian RNA‐seq coupled with an in silico, event‐centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of many circadian‐regulated splicing events broadens our current understanding of the level of control that the circadian clock has over this co/post‐transcriptional regulatory layer. Significance Statement: In this work, we performed a global circadian transcriptomic study on alternative splicing in Arabidopsis thaliana ; the first done on a member of the plant kingdom. Using a stringent approach with an in‐house‐developed bioinformatics tool, we identify novel clock‐controlled genes and 1513 splicing events that are under circadian regulation. Furthermore, we show that disruption of a circadian‐regulated splicing factor (AT2G02570/AtSPF30) affects a specific subset of the circadian‐controlled splicing events.