Abstract

Alternative splicing (AS) is implicated in a wide range of developmental and physiological processes including stress responses. RNA -seq data show extensive AS but give virtually no idea of the impact or dynamics of the AS response and its relationship to the fairly well-characterised transcriptional cold response. To analyse dynamic reprogramming of the cold transcriptome, we have a high resolution RNA -seq time-course of Arabidopsis plants grown at 20°C and transferred to the cold. We quantified expression at the transcript level using Salmon and AtRTD2 (a comprehensive, non-redundant Reference Transcript Dataset with ca. 82k unique transcripts) which we constructed and optimised.

Almost 9k genes had significantly altered expression in response to lowering temperature. Of these, 6.5k were differentially expressed (DE) at the gene level and ca. 2.5k are 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). Cold treatment induces waves of transcriptional and AS activity (within the first 9h) involving thousands of genes. 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.