Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome

Abstract

Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four early AS splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, Such factors likely drive cascades of AS of downstream genes that, alongside transcription, modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.

Patterns of alternative splicing in response to cold acclimation in fish

“…For example, there was enriched alternative splicing for genes involved in RNA splicing (GO:0008380), poly(A) RNA binding (GO:0044822) and the tricarboxylic acid cycle (GO:0006099), suggesting AS genes associated with changes in splicing patterns, RNA chaperoning and metabolic pathways in killifish, stickleback and zebrafish, respectively. Similar temperature-mediated changes in exon usage associated with RNA splicing and binding are also common in plants (Capovilla et al, 2015;Filichkin et al, 2015;Calixto et al, 2018). Even at the level of specific genes, variation in splicing patterns in killifish and zebrafish was observed for genes that have previously been highlighted for their responses and roles in cold acclimation, such as cold-inducible RNA binding protein (cirbp; Gracey et al, 2004;Sano et al, 2015).…”

“…In contrast, alternative splicing, a process in which variation in exon usage produces different mature mRNA transcripts from the pre-mRNA transcript of a gene (Modrek and Lee, 2002), is widespread across taxa (Tapial et al, 2017), and thus has the potential to be a common mechanism underlying phenotypic plasticity in many species. Alternative splicing in the response to environmental stress is widely observed in plants (Reddy et al, 2013;Capovilla et al, 2015;Filichkin et al, 2015;Thatcher et al, 2015;Calixto et al, 2018), but this mechanism has rarely been examined in animals (although see Polley et al, 2003;Marden, 2008;Huang et al, 2016;Jakšićand Schlötterer, 2016;Hopkins et al, 2018;Tan et al, 2018;Xia et al, 2018), and much remains unknown about its importance.…”

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

“…Tissue was immediately frozen in liquid nitrogen and stored at −80 °C until further use. For the RNA‐seq diel and temperature time series experiment (Figure S1 and Calixto et al, ), plants were harvested at 3‐hr intervals over 24 hr at 20 °C and on Days 1 and 4 after transfer to 4 °C. Transfer to 4 °C was initiated at dusk, unless otherwise stated.…”

“…After standard quality control and trimming of reads, transcript expression was determined using Salmon version 0.82 (Patro, Duggal, Love, Irizarry, & Kingsford, ) in conjunction with AtRTD2‐QUASI (Zhang et al, ). Expression profiles for the specific genes used in this study were extracted from the total RNA‐seq dataset of Calixto et al ().…”

Cold induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm

“…At the heart of this regulation is the chaperone activity of the cold shock protein cspA and its 5'UTR that acts as a thermosensor (Giuliodori et al, 2010) and auto-regulates its own abundance in a temperature-dependent way . In plants, cold adaptation is more complex, involving temperature-induced adjustments of the chromatin (Zeng et al, 2019;Park et al, 2018), transcriptional (Nagano et al, 2019), pre-mRNA processing (Calixto et al, 2018), post-transcriptional and posttranslational landscapes (Zhu, 2016). The transcriptional response to cold acclimatization in plants is beginning to be unraveled and entire signaling networks such as the C-repeat binding transcription factor (CBFs) regulon have been exposed (Zhao et al, 2015).…”