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.
Highlights
Production of the right amount of protein in the right cells at the right time is crucial for growth and development of multicellular eukaryotes and their response to the environment
Posttranscriptional gene regulation occurs at many levels, including transcript export, localization, mRNA stability, translation, posttranslational modifications of proteins, and protein stability and degradation, which dictate the amount and functionality of RNAs and proteins within the cell
This review focuses on the current knowledge on splicing and genome-wide alternative splicing (AS) in plants, its regulation and potential functions, and the important outstanding questions and tools to address these
Summary
Production of the right amount of protein in the right cells at the right time is crucial for growth and development of multicellular eukaryotes and their response to the environment. Deep sequencing of human transcriptomes from different organs, tissues, and cell lines indicates that almost every intron-containing gene generates multiple splice variants under certain conditions, and many AS events are regulated in a cell-, tissue-, or condition-specific manner (Pan et al, 2008; Wang et al, 2008; Merkin et al, 2012).
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