Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

Abstract

High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely.

ABA signalling is fine-tuned by antagonistic HAB1 variants

“…The percentage of genes showing AS will dramatically increase when plants are subjected to abiotic stresses. Thus, AS plays a fundamental role in plant development and stress adaptation 27,28 . We are beginning to understand the potential control of AS over hormone signalling 23,25 .…”

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

“…The control of these alternative splicing differences among different tissues is thought to be the result of differential splicing factor expression and is likely also influenced by tissue-specific methylation patterns (Regulski et al, 2013). Alternative splicing has also been tied closely with nonsensemediated decay (NMD) and has been shown to increase or decrease a transcript's sensitivity to this decay mechanism under a variety of conditions (Kalyna et al, 2012;Drechsel et al, 2013;Staiger and Brown, 2013).…”

“…Alternative splicing has been shown to play a role in a variety of different plant processes, including tissue identity (Staiger and Brown, 2013). Genes involved in processes ranging from auxin biosynthesis to iron transport have tissue-specific alternative splicing patterns that affect both protein localization and function (Kriechbaumer et al, 2012;Li et al, 2013).…”

Changes in cell wall polysaccharide composition, gene transcription and alternative splicing in germinating barley embryos

“…Alternative splicing occurs at a post-transcriptional regulatory stage and controls many developmental processes in planta (Eckardt, 2013, Reddy, Marquez, 2013, Staiger and Brown, 2013. It generates more than one mRNA variant from precursor mRNA transcripts and regulates transcript levels by introducing premature termination codons leading to a nonsense-mediated decay , Liu et al , 2013.…”

“…It regulates many biological processes including hormone-mediated signal transduction and stress-or light-induced responses (Eckardt, 2013, Reddy et al , 2013, Staiger and Brown, 2013, Wu et al , 2014. It determines tissue-specific differentiation patterns and controls plant development and adaptation to environmental conditions.…”