Abstract:Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization, which can enrich the complexity of transcriptomes and proteomes. In this study, the first exonization event was detected when the modified rice EPSPS marker gene was inserted with the Ac transposon 5' end, which provided a splice donor site to yield abundant novel transcripts. To assess the contribution of splice donor and acceptor sites of transposon sequences, we in… Show more
“…Our previous studies suggested that the main contribution of Ds exonization to gene diversity is, based on a single transposition event, providing different splice donors for different reading frames rather than providing genetic messages (Huang et al, 2012). According to this, we performed a genome-wide computational approach to assess the role of Ds exonization in plants.…”
Section: Discussionmentioning
confidence: 99%
“…Unlike Ds containing splice sites in both forward and reverse forms (Huang et al, 2012), all splice sites of Ds1 were observed in reverse pattern and locate less than 35 bp from both termini. Additionally, 2 donor sites (D1 and D2, Figure 1) of the Ds1 were identical to those of the Ds , which were determined by RT-PCR experiments to be functional in tobacco and rice (Huang et al, 2012 and unpublished results).Figure 1 Ds1
termini sequences and classification of exonized transcripts. a)
Ds1 termini sequences providing splice donor/acceptor junction (arrows) and premature termination codons (PTCs) in exonized transcripts (bold).…”
Section: Introductionmentioning
confidence: 90%
“…Many results also provided mechanistic insights into the process of exonization, especially 5’ and 3’ splice sites (i.e., splice donor/acceptor) formation in Alu exons (Krull et al, 2007; Lev-Maor et al, 2007; Ram et al, 2008; Sorek et al, 2004). In plants, we had assessed the ability of a TE to provide splice/acceptor sites by inserting a mini Ds transposon into each intron of the epsps gene (Charng et al, 2008; Huang et al, 2012) and found that Ds is biased in favor of providing splice donor sites from the beginning of the inserted Ds sequence. We also performed a genome-wide survey of Ds exonization to enrich transcriptomes and proteomes in plants (Liu and Charng, 2012) and found out up to 71% of the exonized transcripts were putative targets of the nonsense-mediated mRNA decay (NMD) pathway (Chang et al, 2007).…”
BackgroundExonization is an event which an intronic transposed element (TE) provides splice sites and leads to alternatively spliced cassette exons. Without disrupting of the inserted gene’s function, TEs can expand the proteome diversity by adding the splice variant that encodes a different, yet functional protein. Previously, we found that the main contribution of Ds exonization for gene divergence is not providing genetic messages but incorporating the intron sequences with different reading frame patterns to enrich the plant proteome. Ds1, another member of Ac/Ds transposon system, differs from Ds by providing 3 splice donor sites and 2 acceptor sites for alternative splicing, which may greatly increase the extent for proteome expansion.ResultsIn this study, we performed a genome-wide survey of Ds1 exonization events to assess its extent to enrich proteomes in plants. Each Ds1 insertion yielded 11 transcript isoforms by integrating the splice donor and/or acceptor sites, which composed a bulk of all exonized transcript orthologs from the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice). The exonized transcripts were analyzed by the locations of the termination codon (PTC) and the putative targets for the nonsense-mediated decay (NMD) pathway were then excluded. Compared with the Ds element, Ds1 harbors more contents of non-NMD transcripts for protein isoforms.ConclusionsThe contribution of Ds1 exonization for gene divergence is incorporating the intron sequences with different reading frame patterns to enrich the plant proteome. All these simulation results direct new experimental analysis at the molecular level.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-54-14) contains supplementary material, which is available to authorized users.
“…Our previous studies suggested that the main contribution of Ds exonization to gene diversity is, based on a single transposition event, providing different splice donors for different reading frames rather than providing genetic messages (Huang et al, 2012). According to this, we performed a genome-wide computational approach to assess the role of Ds exonization in plants.…”
Section: Discussionmentioning
confidence: 99%
“…Unlike Ds containing splice sites in both forward and reverse forms (Huang et al, 2012), all splice sites of Ds1 were observed in reverse pattern and locate less than 35 bp from both termini. Additionally, 2 donor sites (D1 and D2, Figure 1) of the Ds1 were identical to those of the Ds , which were determined by RT-PCR experiments to be functional in tobacco and rice (Huang et al, 2012 and unpublished results).Figure 1 Ds1
termini sequences and classification of exonized transcripts. a)
Ds1 termini sequences providing splice donor/acceptor junction (arrows) and premature termination codons (PTCs) in exonized transcripts (bold).…”
Section: Introductionmentioning
confidence: 90%
“…Many results also provided mechanistic insights into the process of exonization, especially 5’ and 3’ splice sites (i.e., splice donor/acceptor) formation in Alu exons (Krull et al, 2007; Lev-Maor et al, 2007; Ram et al, 2008; Sorek et al, 2004). In plants, we had assessed the ability of a TE to provide splice/acceptor sites by inserting a mini Ds transposon into each intron of the epsps gene (Charng et al, 2008; Huang et al, 2012) and found that Ds is biased in favor of providing splice donor sites from the beginning of the inserted Ds sequence. We also performed a genome-wide survey of Ds exonization to enrich transcriptomes and proteomes in plants (Liu and Charng, 2012) and found out up to 71% of the exonized transcripts were putative targets of the nonsense-mediated mRNA decay (NMD) pathway (Chang et al, 2007).…”
BackgroundExonization is an event which an intronic transposed element (TE) provides splice sites and leads to alternatively spliced cassette exons. Without disrupting of the inserted gene’s function, TEs can expand the proteome diversity by adding the splice variant that encodes a different, yet functional protein. Previously, we found that the main contribution of Ds exonization for gene divergence is not providing genetic messages but incorporating the intron sequences with different reading frame patterns to enrich the plant proteome. Ds1, another member of Ac/Ds transposon system, differs from Ds by providing 3 splice donor sites and 2 acceptor sites for alternative splicing, which may greatly increase the extent for proteome expansion.ResultsIn this study, we performed a genome-wide survey of Ds1 exonization events to assess its extent to enrich proteomes in plants. Each Ds1 insertion yielded 11 transcript isoforms by integrating the splice donor and/or acceptor sites, which composed a bulk of all exonized transcript orthologs from the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice). The exonized transcripts were analyzed by the locations of the termination codon (PTC) and the putative targets for the nonsense-mediated decay (NMD) pathway were then excluded. Compared with the Ds element, Ds1 harbors more contents of non-NMD transcripts for protein isoforms.ConclusionsThe contribution of Ds1 exonization for gene divergence is incorporating the intron sequences with different reading frame patterns to enrich the plant proteome. All these simulation results direct new experimental analysis at the molecular level.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-54-14) contains supplementary material, which is available to authorized users.
“…4 In contrast, exonization can potentially introduce a portion or portions of a TE into the resulting transcripts, thereby altering the reading frames so as to enhance the complexity of proteomes, as was found, for example, in our previous study involving the insertion of a mini Ds transposon into the modified tobacco marker gene epsps . 5 …”
Section: Introductionmentioning
confidence: 99%
“…In addition, Ds and Ds1 are both biased toward providing splice donor and/or acceptor sites located close to their terminal regions. 5,9
Ds provides only donors (1 forward and 4 reverse insertion patterns), whereas Ds1 provides 3 donors and 2 acceptors associating with 11 possible exonizing patterns (all in reverse insertion patterns). 10,11 These different features between Ds and Ds1 imply possibly independent evolutionary impacts of Ds and Ds1 induced through exonization.…”
In exonization events, Ds1 may provide donor and/or acceptor sites for splicing after inserting into genes and be incorporated into new transcripts with new exon(s). In this study, the protein variants of Ds1 exonization yielding additional functional profile(s) were studied. Unlike Ds exonization, which creates new profiles mostly by incorporating flanking intron sequences with the Ds message, Ds1 exonization additionally creates new profiles through the presence or absence of Ds1 messages. The number of unique functional profiles harboring Ds1 messages is 1.3-fold more than that of functional profiles without Ds1 messages. The highly similar 11 protein isoforms at a single insertion site also contribute to proteome complexity enrichment by exclusively creating new profiles. Particularly, Ds1 exonization produces 459 unique profiles, of which 129 cannot be built by Ds. We thus conclude that Ds and Ds1 are independent but synergistic in their capacity to enrich proteome complexity through exonization.
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