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

Allan B James,Wenying Jiang,Craig G Simpson,Hugh G Nimmo,Cristiane P.G Calixto,Gillian A Nimmo,Wenbin Guo,Runxuan Zhang,John W.S Brown,Nikoleta A Tzioutziou

doi:10.1111/pce.13193

Allan B James, Wenying Jiang + Show 8 more

Open Access

https://doi.org/10.1111/pce.13193

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Abstract

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.

Highlights

Plants respond to daily and seasonal changes in temperature
To obtain quantitative data for PTB1, PTB2, SUPPRESSOR OF ABI3‐5 (SUA), and U2AF65A, we examined transcript isoform‐specific expression profiles from an RNA‐seq experiment for Arabidopsis shoot tissue harvested across 3 days before, during, and after a low temperature transition (20 to 4 °C; Figure S1)
The nature of the signal transduction mechanism(s) through which temperature changes are detected and how specific splicing events are regulated is of great interest

Summary

| INTRODUCTION

AS of pre‐mRNAs is strongly associated with the responses of plants to their changing environment (Cui & Xiong, 2015; Filichkin et al, 2015; Reddy, Marquez, Kalyna, & Barta, 2013; Shang, Cao, & Ma, 2017; Staiger & Brown, 2013), less clear is an understanding of the factors influencing co‐transcriptional splice site choice. The Arabidopsis homolog of RNA Binding Motif Protein 5, SUPPRESSOR OF ABI3‐5 (SUA) is involved in the regulated splicing of plant immunity factors (Ding et al, 2014) and some “exitrons” (exon‐like introns), which contain pY (“UCUUCU[U/C]C”) recognition elements for SUA (Marquez, Hopfler, Ayatollahi, Barta, & Kalyna, 2015). We identify some elements of the machinery that links the perception of temperature to the circadian clock and to temperature‐dependent outputs of the clock

| MATERIALS AND METHODS

| RESULTS

Findings

| DISCUSSION