Abstract
BackgroundAlternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress.ResultsTo analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS.ConclusionsOur study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-431) contains supplementary material, which is available to authorized users.
Highlights
Alternative splicing (AS) of precursor mRNA is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress
To evaluate the quality of the RNA sequencing (RNA-seq) data, we investigated the proportion of read alignments in the genome, the continuity of reads (3'/5' bias) along transcriptional units (TUs) and sequencing saturation
Through analyzing global changes in AS under salt stress, we firstly identified ~49% of all intron-containing genes that were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS)
Summary
Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress. Another study using a whole-genome tiling array in Arabidopsis with various stress treatments identified a group of AS events that were associated with stressresponsive genes and some essential regulatory genes [9]. These and other studies revealed the involvement of AS in response to abiotic stress [7]. That study mainly focused on the complexity of AS rather than on a detailed description of the global changes from AS under salt stress conditions [10]
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