Alternative splicing (AS) has been implicated in a wide range of developmental and physiological processes including stress responses but there is little information on the impact or dynamics of the AS response and its relationship to the well-characterised transcriptional cold response. To analyse dynamic reprogramming of the cold transcriptome, we have a high resolution ultra-deep RNA-seq time-course of Arabidopsis plants transferred from 20°C to the cold. Transcript-specific expression was quantified using Salmon and AtRTD2 (a comprehensive, non-redundant Reference Transcript Dataset with ca. 82k unique transcripts; Zhang et al, 2017).
Almost 7k genes were differentially expressed (DE) at the gene level and ca. 2.5k significantly differentially alternatively spliced (DAS). We identified over 3,000 novel cold-response genes of which 1,600 were only regulated at the level of AS (DAS). We show rapidly induced parallel waves of transcriptional and AS activity (within the first 3-9h) involving thousands of genes where the DE and DAS gene sets are largely different. The sensitive temperature-dependent AS of some genes may contribute to temperature perception and signalling. AS therefore makes a previously unrecognised but profound contribution to re-programming of the cold transcriptome.
This analysis has only been possible because of the development of a comprehensive Reference Transcript Dataset (AtRTD2) and computational methods to produce the RTD and to analyse time-course data which we are beginning to apply to crop species.
Zhang et al (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Research 45: 5061-5073.
Schlaen et al (2015) A splicing factor modulates temperature compensation of circadian rhythms in Arabidopsis. Proc Natl Acad Sci U S A. 112, 9382-9387.
Staiger, D. and Brown, J.W.S. (2013) Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses. Plant Cell 25, 3640-56.