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Genome-wide analysis of alternative splicing in Volvox carteri.

Kianianmomeni A, Ong CS, Rätsch G, Hallmann A - BMC Genomics (2014)

Bottom Line: Moreover, many randomly chosen alternatively spliced genes of Volvox do not show alternative splicing in Chlamydomonas.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr, 25, D-33615 Bielefeld, Germany. kianian@uni-bielefeld.de.

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' (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.

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.

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Localization of alternative splicing events in the mRNAs. In the species Volvox(A), Chlamydomonas(B) and Arabidopsis(C) each mRNA was divided into coding region, 5′ UTR or 3′ UTR. The percentage and total number (in parenthesis) of splicing events is given for each of these mRNA regions. The splicing events totaled together 426 events in Volvox, 535 in Chlamydomonas and 8,742 in Arabidopsis.
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Fig3: Localization of alternative splicing events in the mRNAs. In the species Volvox(A), Chlamydomonas(B) and Arabidopsis(C) each mRNA was divided into coding region, 5′ UTR or 3′ UTR. The percentage and total number (in parenthesis) of splicing events is given for each of these mRNA regions. The splicing events totaled together 426 events in Volvox, 535 in Chlamydomonas and 8,742 in Arabidopsis.

Mentions: In Volvox, the majority of all alternative splicing events (66.7%) affect the coding regions. Another 33.3% occur within non-coding regions (14.8% in 5′ UTRs and 18.5% in 3′ UTRs) (Figure 3A). The results from Volvox were again compared with the genome and EST data of Chlamydomonas and Arabidopsis[31, 59], which were treated in the same way as the data from Volvox (see Methods). In Chlamydomonas, 10.8% of the alternative splicing events were detected in 5′ UTRs and 10.1% in 3′ UTRs (Figure 3B). In Arabidopsis, 12.8% of the alternative splicing events were localized in 5′ UTRs and 15.7% in 3′ UTRs (Figure 3C). In both organisms, the majority of alternative splicing events occur within the coding region, just as observed in Volvox. More precisely, it was 79.1% in Chlamydomonas and 71.5% in Arabidopsis (Figures 3B and 3C).Figure 3


Genome-wide analysis of alternative splicing in Volvox carteri.

Kianianmomeni A, Ong CS, Rätsch G, Hallmann A - BMC Genomics (2014)

Localization of alternative splicing events in the mRNAs. In the species Volvox(A), Chlamydomonas(B) and Arabidopsis(C) each mRNA was divided into coding region, 5′ UTR or 3′ UTR. The percentage and total number (in parenthesis) of splicing events is given for each of these mRNA regions. The splicing events totaled together 426 events in Volvox, 535 in Chlamydomonas and 8,742 in Arabidopsis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4378016&req=5

Fig3: Localization of alternative splicing events in the mRNAs. In the species Volvox(A), Chlamydomonas(B) and Arabidopsis(C) each mRNA was divided into coding region, 5′ UTR or 3′ UTR. The percentage and total number (in parenthesis) of splicing events is given for each of these mRNA regions. The splicing events totaled together 426 events in Volvox, 535 in Chlamydomonas and 8,742 in Arabidopsis.
Mentions: In Volvox, the majority of all alternative splicing events (66.7%) affect the coding regions. Another 33.3% occur within non-coding regions (14.8% in 5′ UTRs and 18.5% in 3′ UTRs) (Figure 3A). The results from Volvox were again compared with the genome and EST data of Chlamydomonas and Arabidopsis[31, 59], which were treated in the same way as the data from Volvox (see Methods). In Chlamydomonas, 10.8% of the alternative splicing events were detected in 5′ UTRs and 10.1% in 3′ UTRs (Figure 3B). In Arabidopsis, 12.8% of the alternative splicing events were localized in 5′ UTRs and 15.7% in 3′ UTRs (Figure 3C). In both organisms, the majority of alternative splicing events occur within the coding region, just as observed in Volvox. More precisely, it was 79.1% in Chlamydomonas and 71.5% in Arabidopsis (Figures 3B and 3C).Figure 3

Bottom Line: Moreover, many randomly chosen alternatively spliced genes of Volvox do not show alternative splicing in Chlamydomonas.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr, 25, D-33615 Bielefeld, Germany. kianian@uni-bielefeld.de.

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' (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.

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.

Show MeSH
Related in: MedlinePlus