Genome-Wide Characterization Of Differential Transcript Usage In Arabidopsis thaliana

Abstract

SUMMARYAlternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express one isoform at a significantly higher level than others, but under specific conditions this expression dominance can switch to different isoforms. These isoform switches have been observed for thousands of Zea mays and Vitis vinifera genes and have been linked to development and stress response. In Arabidopsis thaliana however, isoform switches have only been reported for 812 genes and the characteristics of these genes, nor the implications of the isoform switches on their protein functions, are currently well understood. Here we present a dataset of isoform dominance and switching for all genes in the AtRTD2 annotation based on a protocol that was benchmarked on simulated data and validated through comparison with a published RT-PCR panel. We report 138,722 isoform switches for 8,162 genes across 206 public RNA-Seq samples and find that these switches change the protein sequences in 23% of the cases. The observed isoform switches show high consistency across replicates and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different ages, expression breadths, and functions show large differences in the frequency at which they switch isoforms and in the effect that these isoform switches have on their protein sequences. Finally, we showcase how the detected isoform switches can be applied to gain further insight in the regulation of a genes expression and function.\n\nSIGNIFICANCE STATEMENTIsoform switching 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 switching for Arabidopsis thaliana based on 206 public RNA-Seq samples and provide novel insights in the regulation and functional consequences of alternative splicing.