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Prevalence of alternative splicing choices in Arabidopsis thaliana

DOI: 10.1186/1471-2229-10-102

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We investigated prevalence of alternative splicing (AS) events in Arabidopsis thaliana using ESTs. We found that for most AS events with ample EST coverage, the majority of overlapping ESTs strongly supported one major splicing choice, with less than 10% of ESTs supporting the minor form. Analysis of ESTs also revealed a small but noteworthy subset of genes for which alternative choices appeared with about equal prevalence, suggesting that for these genes the variant splicing forms co-occur in the same cell types. Of the AS events in which both forms were about equally prevalent, more than 80% affected untranslated regions or involved small changes to the encoded protein sequence.Currently available evidence from ESTs indicates that alternative splicing in Arabidopsis occurs and affects many genes, but for most genes with documented alternative splicing, one AS choice predominates. To aid investigation of the role AS may play in modulating function of Arabidopsis genes, we provide an on-line resource (ArabiTag) that supports searching AS events by gene, by EST library keyword search, and by relative prevalence of minor and major forms.Most eukaryotic genes contain introns, regions of non-coding sequence that are transcribed into RNA but ultimately removed via a process known as RNA splicing [1]. In alternative splicing (AS), identical transcripts arising from the same locus can undergo multiple splicing programs, in which different segments of the transcribed sequence are removed. The effects on protein sequence and function can be profound [2,3], and there are many examples of genes where AS provides a regulatory mechanism controlling aspects of development and other processes, including flowering in Arabidopsis thaliana (reviewed in [4]), sex determination in Drosophila melanogaster [5], and aspects of neuronal differentiation in mammals (reviewed in [6]). In Arabidopsis, many genes involved in splicing regulation are themselves alternatively spliced and these spl

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