Genome‐wide characterization of differential transcript usage in Arabidopsis thaliana

Abstract

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, neither 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 reverse transciptase-polymerase chain reaction panel. We report DTU events for 8148 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.

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information

“…For the unknown Brassicaceae genes, detailed expression information was obtained from Vaneechoutte et.al. 2017 ( 56 ). Gene family and phylostrata data was retrieved from the PLAZA 3.0 Dicots comparative genomics database ( 57 ).…”

Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants

“…5, Supplementary Material online). Starting from the transcript counts for 206 public RNA-Seq experiments, a gene-expression matrix was generated by summing transcript counts per locus (Vaneechoutte et al. 2017).…”

“…Only a subset of 25 samples is shown. Expression data for all 206 samples in the Vaneechoutte et al. (2017) data set are available in supplementary figure 4, Supplementary Material online.…”

Alternative Splicing as a Regulator of Early Plant Development

“…Numerous plant large-scale studies have focused on gene expression and AS patterns in different tissues and during development, identifying many novel organ- or stage-specific mRNAs with dynamic expression changes and a stage-dependent switch in isoform dominance for many genes ( Zhang et al, 2010 ; Thatcher et al, 2014 ; Klepikova et al, 2016 ; Vaneechoutte et al, 2017 ). Notably, genes encoding alternatively spliced transcripts are not necessarily differentially expressed during developmental transitions, suggesting that AS shapes the transcriptome independently from transcriptional regulation ( Srinivasan et al, 2016 ).…”