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Review
. 2012 Oct;17(10):616-23.
doi: 10.1016/j.tplants.2012.06.001. Epub 2012 Jun 27.

Alternative splicing in plants--coming of age

Affiliations
Review

Alternative splicing in plants--coming of age

Naeem H Syed et al. Trends Plant Sci. 2012 Oct.

Abstract

More than 60% of intron-containing genes undergo alternative splicing (AS) in plants. This number will increase when AS in different tissues, developmental stages, and environmental conditions are explored. Although the functional impact of AS on protein complexity is still understudied in plants, recent examples demonstrate its importance in regulating plant processes. AS also regulates transcript levels and the link with nonsense-mediated decay and generation of unproductive mRNAs illustrate the need for both transcriptional and AS data in gene expression analyses. AS has influenced the evolution of the complex networks of regulation of gene expression and variation in AS contributed to adaptation of plants to their environment and therefore will impact strategies for improving plant and crop phenotypes.

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Figures

Figure 1
Figure 1
Increasing frequency of occurrence of alternative splicing (AS) in Arabidopsis with time. In 2003, a study using EST (expressed sequence tag) libraries estimated that only 1.2% of the genes in Arabidopsis undergo AS . Subsequently, greater coverage of ESTs and cDNAs libraries allowed the discovery of many more AS events (2004–2006, [7,102–104]). The advent of high-throughput technologies has resulted in significant increases in the frequency of AS (almost 60-fold over the past 10 years).
Figure 2
Figure 2
Main types of alternative splicing (AS) events and frequency in Arabidopsis. (a) Splicing of pre-mRNA is directed by cis elements which include splice sites, branch point, and polypyrimidine tract sequences. Selection of alternative splice sites is affected by trans-acting factors binding to auxiliary exonic and intronic cis elements, termed splicing enhancers and silencers. (b) Types of AS events. (c) Frequency of occurrence of intron retention in Arabidopsis. Intron retention is the most frequent AS event in Arabidopsis (40%) but its contribution to transcript diversity is much lower . Of the 61% of Arabidopsis intron-containing genes with AS, 51% produce AS transcripts which do not involve intron retention (–IR). Among alternatively spliced transcripts, 23.6% contain one or more retained introns (+IR), whereas the rest (74.6%) are produced by other AS events. Colored boxes, exons; lines, introns; GU, 5′ splice site which includes highly conserved GU dinucleotide; AG, 3′ splice site which includes highly conserved AG dinucleotide; A, branch point adenosine; (Y)n, polypyrimidine tract; ovals, positive and negative splicing regulators; carets, splicing events; thick gray line, unspliced (retained) intron. Abbreviations: ESE, exonic splicing enhancers; ESS, exonic splicing silencers; ISE, intronic splicing enhancers; ISS, intronic splicing silencers; Alt 3′ ss, alternative 3′ splice sites; Alt 5′ ss, alternative 5′ splice sites; ES, exon skipping; IR, intron retention.
Figure 3
Figure 3
Dynamic regulation of expression by alternative splicing. Developmental or environmental cues activate signaling pathways which can directly modulate splicing factor activity by post-translational modifications, relocalization, etc. Signaling also directs changes in transcription of splicing factor genes and alternative splicing of these genes changes the abundance, composition, and activity of the splicing factor population. Expression of other target genes including transcription factors is also modulated by alternative splicing responding to the dynamic changes in splicing factor profiles. Changes in the proteome feedback to transcription and alternative splicing (and other post-transcriptional mechanisms) ultimately generating the cellular and organismal phenotype and response. Boxes of colored bars, abundance and/or composition of SFs. Abbreviations: AS, alternative splicing; SF, splicing factor.

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