Genome-wide analysis of alternative splicing in Volvox carteri.

Arash Kianianmomeni,Cheng Ong,Gunnar Rätsch,Armin Hallmann

doi:10.1186/1471-2164-15-1117

Arash Kianianmomeni, Cheng Ong + Show 2 more

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https://doi.org/10.1186/1471-2164-15-1117

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Abstract

BackgroundAlternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes. Particularly in multicellular eukaryotes, this mechanism is involved in the regulation of developmental and physiological processes like growth, differentiation and signal transduction.ResultsHere we report the genome-wide analysis of alternative splicing in the multicellular green alga Volvox carteri. The bioinformatic analysis of 132,038 expressed sequence tags (ESTs) identified 580 alternative splicing events in a total of 426 genes. The predominant type of alternative splicing in Volvox is intron retention (46.5%) followed by alternative 5′ (17.9%) and 3′ (21.9%) splice sites and exon skipping (9.5%). Our analysis shows that in Volvox at least ~2.9% of the intron-containing genes are subject to alternative splicing. Considering the total number of sequenced ESTs, the Volvox genome seems to provide more favorable conditions (e.g., regarding length and GC content of introns) for the occurrence of alternative splicing than the genome of its close unicellular relative Chlamydomonas. Moreover, many randomly chosen alternatively spliced genes of Volvox do not show alternative splicing in Chlamydomonas. Since the Volvox genome contains about the same number of protein-coding genes as the Chlamydomonas genome (~14,500 protein-coding genes), we assumed that alternative splicing may play a key role in generation of genomic diversity, which is required to evolve from a simple one-cell ancestor to a multicellular organism with differentiated cell types (Mol Biol Evol 31:1402-1413, 2014). To confirm the alternative splicing events identified by bioinformatic analysis, several genes with different types of alternatively splicing have been selected followed by experimental verification of the predicted splice variants by RT-PCR.ConclusionsThe results show that our approach for prediction of alternative splicing events in Volvox was accurate and reliable. Moreover, quantitative real-time RT-PCR appears to be useful in Volvox for analyses of relationships between the appearance of specific alternative splicing variants and different kinds of physiological, metabolic and developmental processes as well as responses to environmental changes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1117) contains supplementary material, which is available to authorized users.

Highlights

Alternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes
The results indicated that 11.6% of the alternative splicing events in Chlamydomonas are alternative 5′ splice sites, 25.8% are alternative 3′ splice sites, 0.7% show both alternative 5′ and 3′ splice sites and 11.9% show exon skipping
After bioinformatic analysis of 132,038 Expressed sequence tags (EST), we identified 580 alternative splicing events corresponding to 426 genes

Summary

Introduction

Alternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes. Alternative splicing of precursor messenger RNA (premRNA) is an important post-transcriptional regulatory mechanism that enhances the transcriptome plasticity and proteome diversity. Alternative splicing produces multiple transcripts from a single gene by varying the selection of the include/exclude regions. The real percentages might even be higher than reported, because they correlate with the number of sequenced ESTs. An increased number of sequenced ESTs frequently reveal additional alternative splicing events because more and more rare splicing variants from genes with low expression become sequenced. For Arabidopsis the reported percentage of alternatively spliced genes increased dramatically within a decade: it was 1.2% in 2003 [22], 11.6% in 2004 [23], more than 30% in 2006 [24], 42% in 2010 [18] and 61% in 2012 [19]

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