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Genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants.

Liu LY, Charng YC - Evol. Bioinform. Online (2012)

Bottom Line: Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron.The number of interior protein isoforms would be twice that of C-terminal isoforms, on average.TE exonization provides a promising way for functional expansion of the plant proteome.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, National Taiwan University, Taipei, Taiwan, Republic of China.

ABSTRACT
Insertion of transposable elements (TEs) 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. Previously, we performed the first experimental assessment of TE exonization by inserting a Ds element into each intron of the rice epsps gene. Exonization of Ds in plants was biased toward providing splice donor sites from the beginning of the inserted Ds sequence. Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron. The current study involved genome-wide computational analysis of Ds exonization events in the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice). Up to 71% of the exonized transcripts were putative targets for the nonsense-mediated decay (NMD) pathway. The insertion patterns of Ds and the polymorphic splice donor sites increased the transcripts and subsequent protein isoforms. Protein isoforms contain protein sequence due to unspliced intron-TE region and/or a shift of the reading frame. The number of interior protein isoforms would be twice that of C-terminal isoforms, on average. TE exonization provides a promising way for functional expansion of the plant proteome.

No MeSH data available.


Related in: MedlinePlus

Proportions of 5 types (named 1 to 5) of exonized transcripts for Ds insertion on different chromosomes leading to the nonsense-mediated dacay (NMD) or non-NMD pathway in rice (A) and Arabidopsis (B).Notes: Data are mean (whiskers are range). R = reverse Ds insertion; F = forward Ds insertion. Numbers above 5F and Rs indicate the percentage of corresponding transcripts.
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f2-ebo-8-2012-575: Proportions of 5 types (named 1 to 5) of exonized transcripts for Ds insertion on different chromosomes leading to the nonsense-mediated dacay (NMD) or non-NMD pathway in rice (A) and Arabidopsis (B).Notes: Data are mean (whiskers are range). R = reverse Ds insertion; F = forward Ds insertion. Numbers above 5F and Rs indicate the percentage of corresponding transcripts.

Mentions: Our previous results revealed that Ds is biased toward providing splice donor sites for exonization; the original exon donor site is skipped and transcription proceeds to the donor of Ds for joining the upcoming exons. With the determined donor sites of Ds (Fig. 1A), a genome-wide analysis of TE exonized transcripts in each intron of rice and Arabidopsis genes yielded 58,016,056 and 37,285,244 exonized transcripts, respectively (Supplementary Tables 1 and 2). The resulting exonized transcripts in each genome were classified into 5 types by location of PTC (Fig. 1B). A PTC in the splice donor consensus is represented as CAG/GTAAGT in plants.17,18 Therefore, about one third of the exonized transcripts created by skipping this donor consensus carry a TAA termination codon in frame. For example, the rice epsps gene has 7 introns, with 5 of the splice donor consensuses containing a PTC while 2 (in introns 4 and 5) are in frame. Because Ds is biased to provide a splice donor site, most exonization events for Ds in introns 4 and 5 will undergo NMD. Genome-wide computational analysis of rice revealed that when the TE upstream splice donor sites are skipped, 9.2% of the exonized transcripts contain a PTC in frame, including 6.8% that are putative targets of NMD (Supplementary Table 1 and Fig. 2A). A similar result was obtained for Arabidopsis (Supplementary Table 2 and Fig. 2B). This consequence was termed as type I exonization of Ds. In such case, the PTC in the skipped consensus is the first limitation in expanding the proteome. The resulting transcripts of Type I exonization may undergo NMD or yield truncated protein isoforms without any genetic message of TE. In type II exonization, the PTCs in the TE inserting introns, but outside the original donor consensus, are in frame and allow the resulting exonized transcripts to become targets of NMD. In rice, 49.1% of exonization events are type II, including 36.9% that will undergo NMD. With type I and II events combined, 58.3% of Ds exonized transcripts will undergo the NMD pathway or yield truncated protein isoforms without a genetic message of the TE. In Arabidopsis, type I and II events present 7.2% (1.5% non-NMD) and 27.6% (5.8% non-NMD), respectively, of all events. In Figure 2, the portion of type I and II in sum in rice differs in Arabidopsis (see Discussion section). In Arabidopsis, a larger portion of events are of subsequent types, which show a similar pattern to those events of rice. We present only the results for subsequent types from Arabidopsis in figures.


Genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants.

Liu LY, Charng YC - Evol. Bioinform. Online (2012)

Proportions of 5 types (named 1 to 5) of exonized transcripts for Ds insertion on different chromosomes leading to the nonsense-mediated dacay (NMD) or non-NMD pathway in rice (A) and Arabidopsis (B).Notes: Data are mean (whiskers are range). R = reverse Ds insertion; F = forward Ds insertion. Numbers above 5F and Rs indicate the percentage of corresponding transcripts.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3475393&req=5

f2-ebo-8-2012-575: Proportions of 5 types (named 1 to 5) of exonized transcripts for Ds insertion on different chromosomes leading to the nonsense-mediated dacay (NMD) or non-NMD pathway in rice (A) and Arabidopsis (B).Notes: Data are mean (whiskers are range). R = reverse Ds insertion; F = forward Ds insertion. Numbers above 5F and Rs indicate the percentage of corresponding transcripts.
Mentions: Our previous results revealed that Ds is biased toward providing splice donor sites for exonization; the original exon donor site is skipped and transcription proceeds to the donor of Ds for joining the upcoming exons. With the determined donor sites of Ds (Fig. 1A), a genome-wide analysis of TE exonized transcripts in each intron of rice and Arabidopsis genes yielded 58,016,056 and 37,285,244 exonized transcripts, respectively (Supplementary Tables 1 and 2). The resulting exonized transcripts in each genome were classified into 5 types by location of PTC (Fig. 1B). A PTC in the splice donor consensus is represented as CAG/GTAAGT in plants.17,18 Therefore, about one third of the exonized transcripts created by skipping this donor consensus carry a TAA termination codon in frame. For example, the rice epsps gene has 7 introns, with 5 of the splice donor consensuses containing a PTC while 2 (in introns 4 and 5) are in frame. Because Ds is biased to provide a splice donor site, most exonization events for Ds in introns 4 and 5 will undergo NMD. Genome-wide computational analysis of rice revealed that when the TE upstream splice donor sites are skipped, 9.2% of the exonized transcripts contain a PTC in frame, including 6.8% that are putative targets of NMD (Supplementary Table 1 and Fig. 2A). A similar result was obtained for Arabidopsis (Supplementary Table 2 and Fig. 2B). This consequence was termed as type I exonization of Ds. In such case, the PTC in the skipped consensus is the first limitation in expanding the proteome. The resulting transcripts of Type I exonization may undergo NMD or yield truncated protein isoforms without any genetic message of TE. In type II exonization, the PTCs in the TE inserting introns, but outside the original donor consensus, are in frame and allow the resulting exonized transcripts to become targets of NMD. In rice, 49.1% of exonization events are type II, including 36.9% that will undergo NMD. With type I and II events combined, 58.3% of Ds exonized transcripts will undergo the NMD pathway or yield truncated protein isoforms without a genetic message of the TE. In Arabidopsis, type I and II events present 7.2% (1.5% non-NMD) and 27.6% (5.8% non-NMD), respectively, of all events. In Figure 2, the portion of type I and II in sum in rice differs in Arabidopsis (see Discussion section). In Arabidopsis, a larger portion of events are of subsequent types, which show a similar pattern to those events of rice. We present only the results for subsequent types from Arabidopsis in figures.

Bottom Line: Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron.The number of interior protein isoforms would be twice that of C-terminal isoforms, on average.TE exonization provides a promising way for functional expansion of the plant proteome.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, National Taiwan University, Taipei, Taiwan, Republic of China.

ABSTRACT
Insertion of transposable elements (TEs) 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. Previously, we performed the first experimental assessment of TE exonization by inserting a Ds element into each intron of the rice epsps gene. Exonization of Ds in plants was biased toward providing splice donor sites from the beginning of the inserted Ds sequence. Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron. The current study involved genome-wide computational analysis of Ds exonization events in the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice). Up to 71% of the exonized transcripts were putative targets for the nonsense-mediated decay (NMD) pathway. The insertion patterns of Ds and the polymorphic splice donor sites increased the transcripts and subsequent protein isoforms. Protein isoforms contain protein sequence due to unspliced intron-TE region and/or a shift of the reading frame. The number of interior protein isoforms would be twice that of C-terminal isoforms, on average. TE exonization provides a promising way for functional expansion of the plant proteome.

No MeSH data available.


Related in: MedlinePlus