Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

Abstract

Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species

“…These differences in the regulation of AS and GE reflect divergent evolutionary processes of gene expression and AS level regulation in plants. A recent study investigating the regulation of AS and GE in Arabidopsis under stress conditions (Martín et al, 2021 ) found the core genes regulated by AS and GE in response to internal and external stimuli shared few common members. One clear difference is that RNA binding proteins (RBPs) were significantly enriched in the AS core sets, whereas GE core gene sets were depleted in RBPs but significantly enriched in DNA‐binding proteins.…”

“…Similarly, in this study, a batch of RNA binding proteins and RNA recognition motif‐containing family proteins enriched in identified AS event sets, including tissue‐, stage‐, species‐specific, biased and polyploidization‐altered AS events, indicating this regulatory specialization is widespread. Moreover, this AS landscapes study in Arabidopsis discovered that the different AS event types were differentially regulated under stress or in different tissues with RI showing the most diverse changes (Martín et al, 2021 ). This is similar to our conclusion on the comparison of AS event types among developmental stages, tissues and subgenomes (Figure 1 ), revealing the complexity of AS spatiotemporal regulation as a key element in gene expression.…”

ExOrthist: a tool to infer exon orthologies at any evolutionary distance

“…Neural regulation (difference in average PSI of neural and non-neural samples) for each Nova -regulated exon was calculated using data from VastDB for mm10 and dm6 [ 29 ], and through the script Get_Tissue_Specific_AS.pl [ 66 ]. Analysis of splicing-related features was performed with matt cmpr_exons [ 51 ] v1.3.0 and a selection of features was plotted in Additional file 1 : Figure S3.…”

A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

“…More importantly, the defined TSS and TES clearly demonstrated variation in TSS and TES for many genes and re-analysis of the cold time-series data with AtRTD3 identified differential TSS and TES usage due to low temperature and light/dark conditions. It will now be possible to examine transcriptional and post-transcriptional regulation of gene expression involving differential TSS and TES usage demonstrated here and the impact of AS in UTRs [53,67] during development and in response to abiotic and biotic stresses. Differential TSS and TES usage illustrates novel regulatory mechanisms.…”