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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

(A) Ds termini sequences (forward and reverse) providing splice donor junction (slash) and premature termination codons (PTCs) in exonized transcripts (bold). (B) Classification of exonized transcripts (black line) according to location of the PTC.Notes: Normal transcript is shown as a dashed line. The corresponding DNAs of the TE-inserted target are shown in the center. Black box indicates the unspliced intron. Exonization occurs by using the splice donor (arrow) of TE to join the upcoming exon. The existence and location of an in-frame PTC determines the type of the exonized transcripts, classified into 5 types. As an example, for type I, a PTC (UAA in bold) locates in the skipped exon/intron consensus: italics indicate exonic sequences. Brackets indicate the boundaries of PTC location for classification. Type V transcripts have no in-frame PTC until the end of the gene.
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f1-ebo-8-2012-575: (A) Ds termini sequences (forward and reverse) providing splice donor junction (slash) and premature termination codons (PTCs) in exonized transcripts (bold). (B) Classification of exonized transcripts (black line) according to location of the PTC.Notes: Normal transcript is shown as a dashed line. The corresponding DNAs of the TE-inserted target are shown in the center. Black box indicates the unspliced intron. Exonization occurs by using the splice donor (arrow) of TE to join the upcoming exon. The existence and location of an in-frame PTC determines the type of the exonized transcripts, classified into 5 types. As an example, for type I, a PTC (UAA in bold) locates in the skipped exon/intron consensus: italics indicate exonic sequences. Brackets indicate the boundaries of PTC location for classification. Type V transcripts have no in-frame PTC until the end of the gene.

Mentions: Ds is a non-autonomous (transposase defective) transposon which is composed of 11 bp terminal-inverted repeats and about 250 bp of both ends (terminal regions) of its full form transposon, Activator (Ac). Previously, we found the first exonization event of Ds in transgenic tobacco containing an inducible transposon system to terminate the marker of transgenic plants. In this system, the marker epsps gene was accompanied by the Ac-based inducible transposon, KCEH. However, the 5′ end of the Ac transposon was located in intron 1 of the modified epsps marker gene.13 We observed abundant exonized transcripts, with the 5′ Ac end of KCEH providing a splice donor site instead of the original site. Since a truncated (one end of) TE located in a plant gene’s intron occurs rarely, we assessed the exonization potential of an intact TE, specifically a mini Ds transposon inserted in the forward or reverse direction in each intron of the epsps gene. Exonization of Ds in epsps was biased in favor of providing splice donor sites from the beginning of the inserted Ds sequence.14 Furthermore, Ds existing in an intron in a reverse pattern could offer 4 donor sites, which can result in the new transcript isoforms having different reading frames according to the different splice junction sites (Fig. 1). However, exonized transcripts may contain a premature termination codon (PTC), which can trigger the decay of the transcript through the nonsense-mediated mRNA decay (NMD) pathway.15 Although our RT-PCR analysis indicated that many PTC-containing transcripts remained abundant,14 the fact that NMD limits AS in expanding the proteome encouraged us to study the role of TE exonization.


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

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

(A) Ds termini sequences (forward and reverse) providing splice donor junction (slash) and premature termination codons (PTCs) in exonized transcripts (bold). (B) Classification of exonized transcripts (black line) according to location of the PTC.Notes: Normal transcript is shown as a dashed line. The corresponding DNAs of the TE-inserted target are shown in the center. Black box indicates the unspliced intron. Exonization occurs by using the splice donor (arrow) of TE to join the upcoming exon. The existence and location of an in-frame PTC determines the type of the exonized transcripts, classified into 5 types. As an example, for type I, a PTC (UAA in bold) locates in the skipped exon/intron consensus: italics indicate exonic sequences. Brackets indicate the boundaries of PTC location for classification. Type V transcripts have no in-frame PTC until the end of the gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3475393&req=5

f1-ebo-8-2012-575: (A) Ds termini sequences (forward and reverse) providing splice donor junction (slash) and premature termination codons (PTCs) in exonized transcripts (bold). (B) Classification of exonized transcripts (black line) according to location of the PTC.Notes: Normal transcript is shown as a dashed line. The corresponding DNAs of the TE-inserted target are shown in the center. Black box indicates the unspliced intron. Exonization occurs by using the splice donor (arrow) of TE to join the upcoming exon. The existence and location of an in-frame PTC determines the type of the exonized transcripts, classified into 5 types. As an example, for type I, a PTC (UAA in bold) locates in the skipped exon/intron consensus: italics indicate exonic sequences. Brackets indicate the boundaries of PTC location for classification. Type V transcripts have no in-frame PTC until the end of the gene.
Mentions: Ds is a non-autonomous (transposase defective) transposon which is composed of 11 bp terminal-inverted repeats and about 250 bp of both ends (terminal regions) of its full form transposon, Activator (Ac). Previously, we found the first exonization event of Ds in transgenic tobacco containing an inducible transposon system to terminate the marker of transgenic plants. In this system, the marker epsps gene was accompanied by the Ac-based inducible transposon, KCEH. However, the 5′ end of the Ac transposon was located in intron 1 of the modified epsps marker gene.13 We observed abundant exonized transcripts, with the 5′ Ac end of KCEH providing a splice donor site instead of the original site. Since a truncated (one end of) TE located in a plant gene’s intron occurs rarely, we assessed the exonization potential of an intact TE, specifically a mini Ds transposon inserted in the forward or reverse direction in each intron of the epsps gene. Exonization of Ds in epsps was biased in favor of providing splice donor sites from the beginning of the inserted Ds sequence.14 Furthermore, Ds existing in an intron in a reverse pattern could offer 4 donor sites, which can result in the new transcript isoforms having different reading frames according to the different splice junction sites (Fig. 1). However, exonized transcripts may contain a premature termination codon (PTC), which can trigger the decay of the transcript through the nonsense-mediated mRNA decay (NMD) pathway.15 Although our RT-PCR analysis indicated that many PTC-containing transcripts remained abundant,14 the fact that NMD limits AS in expanding the proteome encouraged us to study the role of TE exonization.

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