A New Exon Derived from a Mammalian Apparent LTR Retrotransposon of theSUPT16HGene

Min-In Bae,Ja-Rang Lee,Yi-Deun Jung,Yun-Ji Kim,Heui-Soo Kim

doi:10.1155/2013/387594

Min-In Bae, Ja-Rang Lee + Show 3 more

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https://doi.org/10.1155/2013/387594

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Abstract

The SUPT16H gene known as FACTP140 is required for the transcription of other genes. For transcription, genes need to be complexed with accessory factors, including transcription factors and RNA polymerase II. One such factor, FACT, interacts with histones H2A/H2B for nucleosome disassembly and transcription elongation. The SUPT16H gene has a transcript and many expressed sequence tags (ESTs). We were especially interested in an MaLR-derived transcript (EST, BX333035) that included a new exon introduced by a transposable element, a mammalian apparent LTR retrotransposon (MaLR). The MaLR was detected ranging from humans to galagos, indicating the MaLR in the SUPT16H gene is integrated into the primate ancestor genome. A new exon was created by alternative donor site provided by the MaLR. The original transcript and the MaLR-derived transcript were expressed in various human, rhesus monkey, and other primate tissues. Additionally, we identified a new alternative transcript that included the MaLR, but there was no significant difference in the expression of the original transcript and the MaLR-derived transcript. Interestingly, the new alternative transcript and the MaLR-derived transcript had the MaLR sequence in the new exon, but they had different structures by adopting different 3′ splice sites. From this study, we verified transposable elements that contributed to transcriptome diversity.

Highlights

Transposable elements (TEs) dispersed in the mammalian genome are on the rise, as completion of the whole human genome sequence
The SUPT16H transcript related to the mammalian apparent long terminal repeat (LTR) retrotransposon (MaLR) (MaLR-derived transcript) has 3 exons, and its last exon was created by the integration of the MaLR LTR element in the opposite direction of the host gene (Figure 1)
MaLRs are considered to function in the mammalian genome by providing alternative splice sites, promoters, and other cis-regulatory elements, similar to other TEs that have been conserved during primate evolution [6]

Summary

Introduction

Transposable elements (TEs) dispersed in the mammalian genome are on the rise, as completion of the whole human genome sequence. TEs can be categorized by various features such as the capacity to mobilize themselves, DNA/RNA intermediation, and the existence of a long terminal repeat (LTR). Endogenous retroviruses (ERVs) and long interspersed elements (LINEs) have gene-encoding enzymatic machinery that could mobilize to other genomic regions as autonomous elements. Nonautonomous elements, especially Alu elements, which are classified as short interspersed elements (SINE) and SINEvariable number tandem repeat-Alu-like sequences (SVA), mobilize using the reverse transcriptase of the LINE. All of the TEs described above are integrated into the host genome by their RNAs, but the integration of DNA transposons is mediated by DNA. These groups can be restructured by the existence of LTRs on both ends. ERVs and LTR retrotransposons have LTRs, but SINEs and LINEs are non-LTR elements [1,2,3]

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