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Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms.

Wang H, You C, Chang F, Wang Y, Wang L, Qi J, Ma H - Front Genet (2014)

Bottom Line: We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants.Moreover, 337 novel transcribed regions were identified and most of them have a single exon.Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai, China ; Institutes of Biomedical Sciences, Fudan University Shanghai, China.

ABSTRACT
Alternative splicing (AS) is a process in eukaryotic gene expression, in which the primary transcript of a multi-exon gene is spliced into two or more different mature transcripts, thereby increasing proteome diversity. AS is often regulated differentially between different tissues or developmental stages. Recent studies suggested that up to 60% of intron-containing genes in Arabidopsis thaliana undergo AS. Yet little is known about this complicated and important process during floral development. To investigate the preferential expression of different isoforms of individual alternatively spliced genes, we used high throughput RNA-Seq technology to explore the transcriptomes of three floral development stages of Arabidopsis thaliana and obtained information of various AS events. We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants. This is less frequent than the previously reported 40-60% for multiple organs and stages of A. thaliana, indicating that many genes expressed in floral development function with a single predominant isoform. On the other hand, 1716 isoforms were differentially expressed between the three stages, suggesting that AS might still play important roles in stage transition during floral development. Moreover, 337 novel transcribed regions were identified and most of them have a single exon. Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.

No MeSH data available.


An example of alternative spliced isoforms (of AT2G30940) expressed specifically at F12 stage. The fourth exons of the two isoforms end at different sites (pointed out in a red triangle) according to gene annotations in TAIR10, and this alternative donor event was further confirmed by PCR validation on flower tissues. Each bar (middle panel) represents a short read mapped to the reference genome. Two ends of a split read, indicting a cleavage of an intron, are connected by a gray line. One of the two transcripts, AT2G30940.1, is only expressed in F12, revealed both by alignment details of reads mapped to an exon-exon junction and by RT-PCR validation (relative ratio approximately 220.5, consistent with that of FPKM).
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Figure 4: An example of alternative spliced isoforms (of AT2G30940) expressed specifically at F12 stage. The fourth exons of the two isoforms end at different sites (pointed out in a red triangle) according to gene annotations in TAIR10, and this alternative donor event was further confirmed by PCR validation on flower tissues. Each bar (middle panel) represents a short read mapped to the reference genome. Two ends of a split read, indicting a cleavage of an intron, are connected by a gray line. One of the two transcripts, AT2G30940.1, is only expressed in F12, revealed both by alignment details of reads mapped to an exon-exon junction and by RT-PCR validation (relative ratio approximately 220.5, consistent with that of FPKM).

Mentions: Among the 66 genes with specific splicing isoform(s) at F12 stage, AT2G30940, encoding a protein kinase, has two isoforms due to an AD event. As shown in Figure 4, the presence/absence of six nucleotides at the end of the fourth exon was observed in different isoforms, which were distinguished by 18 reads mapped to the exon-exon junction. Compared with the first transcript (AT2G30940.1), the second transcript (AT2G30940.2) encodes a protein with 2 extra amino acids. In addition, both transcripts were expressed at stage F12 only, with AT2G30940.1 more highly expressed than AT2G30940.2 (FPKM values: 1.9 vs. 0.01), suggesting that they provide different levels of function for Arabidopsis flower development. Similar phenomenon was observed for another gene (AT5G11400) encoding kinase and a gene (AT4G16162) coding for a Leucine-rich repeat (LRR) protein. Interestingly, many genes coding for protein kinases were found to be involved in the regulation of constitutive and AS in plants and animals through phosphorylation and interaction with serine/arginine-rich proteins (Birney et al., 2007), the regulation of several kinase genes by usage of alternative promoters and/or AS has been studied in animals (Duncan et al., 1995, 1997). Still, AS events of kinase genes and their effects on flower development of plants are little known, thus calling for further studies (Marquez et al., 2012).


Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms.

Wang H, You C, Chang F, Wang Y, Wang L, Qi J, Ma H - Front Genet (2014)

An example of alternative spliced isoforms (of AT2G30940) expressed specifically at F12 stage. The fourth exons of the two isoforms end at different sites (pointed out in a red triangle) according to gene annotations in TAIR10, and this alternative donor event was further confirmed by PCR validation on flower tissues. Each bar (middle panel) represents a short read mapped to the reference genome. Two ends of a split read, indicting a cleavage of an intron, are connected by a gray line. One of the two transcripts, AT2G30940.1, is only expressed in F12, revealed both by alignment details of reads mapped to an exon-exon junction and by RT-PCR validation (relative ratio approximately 220.5, consistent with that of FPKM).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3921568&req=5

Figure 4: An example of alternative spliced isoforms (of AT2G30940) expressed specifically at F12 stage. The fourth exons of the two isoforms end at different sites (pointed out in a red triangle) according to gene annotations in TAIR10, and this alternative donor event was further confirmed by PCR validation on flower tissues. Each bar (middle panel) represents a short read mapped to the reference genome. Two ends of a split read, indicting a cleavage of an intron, are connected by a gray line. One of the two transcripts, AT2G30940.1, is only expressed in F12, revealed both by alignment details of reads mapped to an exon-exon junction and by RT-PCR validation (relative ratio approximately 220.5, consistent with that of FPKM).
Mentions: Among the 66 genes with specific splicing isoform(s) at F12 stage, AT2G30940, encoding a protein kinase, has two isoforms due to an AD event. As shown in Figure 4, the presence/absence of six nucleotides at the end of the fourth exon was observed in different isoforms, which were distinguished by 18 reads mapped to the exon-exon junction. Compared with the first transcript (AT2G30940.1), the second transcript (AT2G30940.2) encodes a protein with 2 extra amino acids. In addition, both transcripts were expressed at stage F12 only, with AT2G30940.1 more highly expressed than AT2G30940.2 (FPKM values: 1.9 vs. 0.01), suggesting that they provide different levels of function for Arabidopsis flower development. Similar phenomenon was observed for another gene (AT5G11400) encoding kinase and a gene (AT4G16162) coding for a Leucine-rich repeat (LRR) protein. Interestingly, many genes coding for protein kinases were found to be involved in the regulation of constitutive and AS in plants and animals through phosphorylation and interaction with serine/arginine-rich proteins (Birney et al., 2007), the regulation of several kinase genes by usage of alternative promoters and/or AS has been studied in animals (Duncan et al., 1995, 1997). Still, AS events of kinase genes and their effects on flower development of plants are little known, thus calling for further studies (Marquez et al., 2012).

Bottom Line: We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants.Moreover, 337 novel transcribed regions were identified and most of them have a single exon.Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai, China ; Institutes of Biomedical Sciences, Fudan University Shanghai, China.

ABSTRACT
Alternative splicing (AS) is a process in eukaryotic gene expression, in which the primary transcript of a multi-exon gene is spliced into two or more different mature transcripts, thereby increasing proteome diversity. AS is often regulated differentially between different tissues or developmental stages. Recent studies suggested that up to 60% of intron-containing genes in Arabidopsis thaliana undergo AS. Yet little is known about this complicated and important process during floral development. To investigate the preferential expression of different isoforms of individual alternatively spliced genes, we used high throughput RNA-Seq technology to explore the transcriptomes of three floral development stages of Arabidopsis thaliana and obtained information of various AS events. We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants. This is less frequent than the previously reported 40-60% for multiple organs and stages of A. thaliana, indicating that many genes expressed in floral development function with a single predominant isoform. On the other hand, 1716 isoforms were differentially expressed between the three stages, suggesting that AS might still play important roles in stage transition during floral development. Moreover, 337 novel transcribed regions were identified and most of them have a single exon. Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.

No MeSH data available.