Genome-wide characterization of differential transcript usage in Arabidopsis thaliana

SUMMARY Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of Differential Transcript Usage (DTU) have been observed for thousands of Arabidopsis thaliana , Zea mays and Vitis vinifera genes and have been linked to development and stress response. However, the characteristics of these genes, nor the implications of DTU on their protein coding sequences or functions, are currently well understood. Here we present a dataset of isoform dominance and DTU for all genes in the AtRTD2 reference transcriptome based on a protocol that was benchmarked on simulated data and validated through comparison with a published RT-PCR panel. We report DTU events for 8,148 genes across 206 public RNA-Seq samples and find that protein sequences are affected in 22% of the cases. The observed DTU events show high consistency across replicates and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different evolutionary ages, expression breadths, and functions show large differences in the frequency at which they undergo DTU and in the effect that these events have on their protein sequences. Finally, we showcase how the generated dataset can be used to explore DTU events for genes of interest or to find genes with specific DTU in samples of interest. SIGNIFICANCE STATEMENT Differential transcript usage through alternative splicing has been reported for thousands of genes in plants, yet genome-wide datasets to study the implications for gene functions are thus far not available. Here we present the first reference dataset of isoform dominance and differential transcript usage for Arabidopsis thaliana based on 206 public RNA-Seq samples and provide insights in the occurrence and functional consequences of alternative splicing.