Complexity of the Alternative Splicing Landscape in Plants

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...

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Bibliographic Details
Published in:The Plant cell 2013-10, Vol.25 (10), p.3657-3683
Main Authors: Reddy, Anireddy S.N., Marquez, Yamile, Kalyna, Maria, Barta, Andrea
Format: Article
Language:English
Subjects:
Alternative Splicing
chromatin
Epigenesis, Genetic
Exons
functional diversity
gene expression
Gene expression regulation
Gene Expression Regulation, Plant
Genes
Introns
Messenger RNA
ornamental plants
Plant Development
Plants
REVIEW
RNA
RNA Precursors - genetics
RNA, Plant - genetics
sequence analysis
Sequencing
Signal Transduction
Spliceosomes - metabolism
Splicing
stress response
translation (genetics)
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Summary: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.
ISSN:1040-4651
1532-298X
DOI:10.1105/tpc.113.117523