The extent of Ds1 transposon to enrich transcriptomes and proteomes by exonization.

Yuh-Chyang Charng,Li-Yu Daisy Liu

doi:10.1186/1999-3110-54-14

Abstract

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.

Highlights

Exonization is an event which an intronic transposed element (TE) provides splice sites and leads to alternatively spliced cassette exons
Previous study had revealed that an exonic Ds1 can provide splice donor as well as acceptor sites for alternative splicing (Wessler, 1991)
This indicates that those exonized transcripts resulted from Ds1 merely offering acceptors will not yield type I transcripts

Summary

Introduction

Exonization 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. 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. A well-known effect of TEs is to disrupt the function of the inserted gene, mostly in exons. TEs inserted into intronic sequences may not disrupt the target gene but, by alternative splicing (AS) and exonization, alter the regular splicing pattern of a pre-mRNA and result in the translation of new protein isoforms (Feschotte, 2008). While the prevailing original splice variant maintains functionality, the additional sequence, free from selection pressure, evolves a

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