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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

Flow chart of the steps for analyzing the exonized transcripts.
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Related In: Results  -  Collection


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f6-ebo-8-2012-575: Flow chart of the steps for analyzing the exonized transcripts.

Mentions: The construction of the exonized transcripts involved use of R.26 For each gene, we simulate Ds insertion events for every intron. A flow chart for the analytic steps was shown in Figure 6. Let a target gene, G, have I introns (and, of course, I + 1 exons), with the ith intron of length ni. First, the sequence of the 512 bp Ds was inserted in a forward or reverse direction after the jth nt (j = si, ..., ni) of the ith intron of G. Usually, si = 0, meaning “before the first nucleotide.” When the ith exon of G has length mi < 9, let si be 9 − mi to avoid exonic insertions. Furthermore, if mi > ni, the ith intron of G was skipped for the analyses. The insertion we describe here refers to the insertion of the letters of Ds after the jth nucleotide. This insertion was equivalent to a biological event of Ds inserted at 8 bp before the assigned position. Biologically, the insertion of Ds causes the duplication of 8 bp of G right after the insertion position, and the sequence of the Ds starts at the 9th nt after the insertion position.


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

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

Flow chart of the steps for analyzing the exonized transcripts.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6-ebo-8-2012-575: Flow chart of the steps for analyzing the exonized transcripts.
Mentions: The construction of the exonized transcripts involved use of R.26 For each gene, we simulate Ds insertion events for every intron. A flow chart for the analytic steps was shown in Figure 6. Let a target gene, G, have I introns (and, of course, I + 1 exons), with the ith intron of length ni. First, the sequence of the 512 bp Ds was inserted in a forward or reverse direction after the jth nt (j = si, ..., ni) of the ith intron of G. Usually, si = 0, meaning “before the first nucleotide.” When the ith exon of G has length mi < 9, let si be 9 − mi to avoid exonic insertions. Furthermore, if mi > ni, the ith intron of G was skipped for the analyses. The insertion we describe here refers to the insertion of the letters of Ds after the jth nucleotide. This insertion was equivalent to a biological event of Ds inserted at 8 bp before the assigned position. Biologically, the insertion of Ds causes the duplication of 8 bp of G right after the insertion position, and the sequence of the Ds starts at the 9th nt after the insertion position.

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