Genome-wide analysis of alternative splicing in Volvox carteri

Kianianmomeni A, Ong CS, Rätsch G, Hallmann A (2014)
BMC Genomics 15: 1117.

Download
OA
Journal Article | Published | English
Author
; ; ;
Abstract
BACKGROUND: Alternative 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. RESULTS: Here 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[prime] (17.9%) and 3[prime] (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 [1]. 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. CONCLUSIONS: The 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.
Publishing Year
ISSN
Financial disclosure
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
PUB-ID

Cite this

Kianianmomeni A, Ong CS, Rätsch G, Hallmann A. Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics. 2014;15:1117.
Kianianmomeni, A., Ong, C. S., Rätsch, G., & Hallmann, A. (2014). Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics, 15, 1117. doi:10.1186/1471-2164-15-1117
Kianianmomeni, A., Ong, C. S., Rätsch, G., and Hallmann, A. (2014). Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics 15, 1117.
Kianianmomeni, A., et al., 2014. Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics, 15, p 1117.
A. Kianianmomeni, et al., “Genome-wide analysis of alternative splicing in Volvox carteri”, BMC Genomics, vol. 15, 2014, pp. 1117.
Kianianmomeni, A., Ong, C.S., Rätsch, G., Hallmann, A.: Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics. 15, 1117 (2014).
Kianianmomeni, Arash, Ong, Cheng Soon, Rätsch, Gunnar, and Hallmann, Armin. “Genome-wide analysis of alternative splicing in Volvox carteri”. BMC Genomics 15 (2014): 1117.
Main File(s)
Access Level
OA Open Access
Last Uploaded
2015-01-27 08:33:30

This data publication is cited in the following publications:
This publication cites the following data publications:

2 Citations in Europe PMC

Data provided by Europe PubMed Central.

Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii.
Jakalski M, Takeshita K, Deblieck M, Koyanagi KO, Makalowska I, Watanabe H, Makalowski W., Biol. Direct 11(), 2016
PMID: 27487948
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data.
Kahles A, Ong CS, Zhong Y, Ratsch G., Bioinformatics 32(12), 2016
PMID: 26873928

164 References

Data provided by Europe PubMed Central.

Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific.
Taneri B, Snyder B, Novoradovsky A, Gaasterland T., Genome Biol. 5(10), 2004
PMID: 15461794
Control of cell division by a retinoblastoma protein homolog in Chlamydomonas.
Umen JG, Goodenough UW., Genes Dev. 15(13), 2001
PMID: 11445540
Evolution of sex and mating loci: an expanded view from Volvocine algae.
Umen JG., Curr. Opin. Microbiol. 14(6), 2011
PMID: 22035946
Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants.
Xiao YL, Smith SR, Ishmael N, Redman JC, Kumar N, Monaghan EL, Ayele M, Haas BJ, Wu HC, Town CD., Plant Physiol. 139(3), 2005
PMID: 16244158
Stochastic noise in splicing machinery.
Melamud E, Moult J., Nucleic Acids Res. 37(14), 2009
PMID: 19546110
Noisy splicing drives mRNA isoform diversity in human cells.
Pickrell JK, Pai AA, Gilad Y, Pritchard JK., PLoS Genet. 6(12), 2010
PMID: 21151575
Patterns of organellar and nuclear inheritance among progeny of two geographically isolated strains of Volvox carteri.
Adams CR, Stamer KA, Miller JK, McNally JG, Kirk MM, Kirk DL., Curr. Genet. 18(2), 1990
PMID: 1977526
Artificial media for fresh-water algae: problems and suggestions
Provasoli L, Pintner IJ., 1959

Sambrook J, Russell DW., 2001
Structure and expression of a single actin gene in Volvox carteri.
Cresnar B, Mages W, Muller K, Salbaum JM, Schmitt R., Curr. Genet. 18(4), 1990
PMID: 2253273

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 25516378
PubMed | Europe PMC

Search this title in

Google Scholar