Complexity of the Alternative Splicing Landscape in Plants    

Abstract

Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.

ABA signalling is fine-tuned by antagonistic HAB1 variants

“…RBM proteins are important regulators in pre-mRNA splicing, and many RBM proteins are involved in the regulation of development and stress response 28 . In humans, HsRBM25 is a novel splicing factor that regulates pre-mRNA AS of an apoptotic factor Bcl-x producing the two isoforms, which have opposing roles during apoptosis 31 .…”

“…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 .…”

Eukaryotic Flagella: Variations in Form, Function, and Composition during Evolution

“…Instead, multiple mechanisms contribute to the generation of protein diversity including alternative splicing; in the case of the human genome over 90% of protein-coding genes are alternative spliced, often with tissue-specific dependency, resulting in protein isoforms that differ markedly with regard to function(s) and/or intracellular localisation(s) (Wang et al 2008). In plants, alternative splicing has also emerged as an important mechanism for generating protein diversity (Reddy 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.…”