Abstract
Alternative splicing is a molecular tool of the cell to generate more than one messenger RNA from the same gene. Through variable combinations of exons blueprints for different proteins are assembled from one and the same pre-messenger RNA, thus increasing the complexity of the proteome. Moreover, through alternative splicing different transcript variants with different stabilities and different regulatory motifs can be generated, leading to variation in the transcriptome. The importance of alternative splicing in plants has been increasingly recognized in the last decade. Alternative splicing has been found during abiotic and biotic stress and during development. Here, recent advancements in the understanding of alternative splicing in higher plants are presented. Mechanistic details and functional consequences of alternative splicing are discussed with a focus on the model plant Arabidopsis thaliana.
Highlights
The realization of the information encoded in the eukaryotic genome can be fine-tuned at multiple steps once transcription has been initiated in the nucleus
Alternative splicing has emerged as a versatile strategy to increase the functionality and regulatory potential of the Arabidopsis genome in the last decade
The ongoing identification of a wealth of novel splice variants will lead to more refined gene models not present in the current version of the Arabidopsis genome (TAIR10) and will have to be incorporated in future databases [168]
Summary
The realization of the information encoded in the eukaryotic genome can be fine-tuned at multiple steps once transcription has been initiated in the nucleus This layer of regulation includes capping of the mRNA 5 end, splicing, processing at the 3 end including addition of the poly(A) tail, RNA editing, covalent modification of bases, export from the nucleus to the cytoplasm, mRNA degradation, and localization of mRNAs, as well as the control of translation initiation [1]. Through the variable use of splice sites exonic sequences can be lost or intronic sequences can remain in the mRNA, changing the composition of the mRNA and affecting the open reading frames of the encoded proteins (Figure 2(a)) This variation in the pre-mRNA splicing patterns is designated as alternative splicing [15, 16]. Model plants including rice, Brachypodium, or the moss Physcomitrella patens, readers are referred to recent excellent summaries [17,18,19,20]
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