How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY)

• Published in: Plant, cell and environment Vol. 41; no. 7; pp. 1539 - 1550
• Main Authors: James, Allan B., Calixto, Cristiane P.G., Tzioutziou, Nikoleta A., Guo, Wenbin, Zhang, Runxuan, Simpson, Craig G., Jiang, Wenying, Nimmo, Gillian A., Brown, John W.S., Nimmo, Hugh G.
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.07.2018; John Wiley and Sons Inc
• Subjects: 5′UTR; Alternative splicing; Alternative Splicing - genetics; Alternative Splicing - physiology; Arabidopsis; Arabidopsis - genetics; Arabidopsis - physiology; circadian; Circadian Rhythm - genetics; Circadian rhythms; Clock gene; Coupling (molecular); DNA-Binding Proteins - genetics; DNA-Binding Proteins - physiology; Elongation; Gene Expression Regulation, Plant; Gene regulation; isoform switch; Isoforms; Molecular chains; Mutants; Original; Real-Time Polymerase Chain Reaction; Ribonucleic acid; RNA; RNA Isoforms - genetics; RNA Isoforms - physiology; signalling; Splicing; Splicing factors; Switching; Temperature; Temperature effects; Temperature perception; thermostat; Transcription; Transcription Factors - genetics; Transcription Factors - physiology; splicing factors; circadian; alternative splicing; thermostat; Arabidopsis; isoform switch; 5′UTR; temperature; signalling
• ISSN: 0140-7791; 1365-3040
• DOI: 10.1111/pce.13193

One of the ways in which plants can respond to temperature is via alternative splicing (AS). Previous work showed that temperature changes affected the splicing of several circadian clock gene transcripts. Here, we investigated the role of RNA‐binding splicing factors (SFs) in temperature‐sensitive AS of the clock gene LATE ELONGATED HYPOCOTYL (LHY). We characterized, in wild type plants, temperature‐associated isoform switching and expression patterns for SF transcripts from a high‐resolution temperature and time series RNA‐seq experiment. In addition, we employed quantitative RT‐PCR of SF mutant plants to explore the role of the SFs in cooling‐associated AS of LHY. We show that the splicing and expression of several SFs responds sufficiently, rapidly, and sensitively to temperature changes to contribute to the splicing of the 5′UTR of LHY. Moreover, the choice of splice site in LHY was altered in some SF mutants. The splicing of the 5′UTR region of LHY has characteristics of a molecular thermostat, where the ratio of transcript isoforms is sensitive to temperature changes as modest as 2 °C and is scalable over a wide dynamic range of temperature. Our work provides novel insight into SF‐mediated coupling of the perception of temperature to post‐transcriptional regulation of the clock. The mechanisms involved in the early responses of plants to temperature remain largely elusive. Here, we investigated the role of RNA‐binding splicing factors (SFs) in temperature‐sensitive alternative splicing of the clock gene LATE ELONGATED HYPOCOTYL. We demonstrate that temperature‐associated isoform switching of SF transcripts is sufficiently rapid and sensitive to temperature changes to contribute to the splicing of the 5′UTR of LATE ELONGATED HYPOCOTYL. This work establishes a role for “splicing of splicing factors” in the coupling of the perception of temperature to post‐transcriptional regulation of the clock.