Humphreys, J. L.; Yates, L. A.; Butler, J. B.; Smith, S. M.

Plant genes can each produce multiple RNA isoforms, but little is known about when and how they are produced, or their functions. We conducted a detailed time course analysis of rapid changes in abundance of RNA isoforms in response to transient water deficit in Arabidopsis thaliana seedlings. We identified 95,104 transcripts in total, 21,935 of which were differentially expressed. Strikingly, 1,258 differentially expressed genes were identified only by means of RNA isoform analysis and would have been missed by conventional analysis. Several hundred genes exhibited a very rapid and reversible switch in the most abundant RNA isoform, with timings corresponding to defined changes in seedling water potential. In most cases it is predicted that RNA isoform switching would generate new protein products. Many of these genes encoded proteins of RNA metabolism and splicing, while others potentially function more directly in the response to water deficit. We propose a model in which very rapid RNA processing mechanisms come into play within minutes of imposition of the stress, changing the RNA isoform population including RNAs that encode components of the RNA processing apparatus itself. These changes together with subsequent changes in transcription facilitate further changes in the RNA isoform population as part of the stress and recovery responses. More broadly we propose that responses to abiotic stress involve substantial changes in gene function through the production of RNA isoforms, and we present a detailed approach to identifying such genome-wide RNA isoform switching.