Exon-trapping mediated by the human retrotransposon SVA

Hancks, Dustin C., Ewing, Adam D., Chen, Jesse E., Tokunaga, Katsushi and Kazazian, Haig H. (2009) Exon-trapping mediated by the human retrotransposon SVA. Genome Research, 19 11: 1983-1991. doi:10.1101/gr.093153.109

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Author Hancks, Dustin C.
Ewing, Adam D.
Chen, Jesse E.
Tokunaga, Katsushi
Kazazian, Haig H.
Title Exon-trapping mediated by the human retrotransposon SVA
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2009-11
Sub-type Article (original research)
DOI 10.1101/gr.093153.109
Open Access Status File (Publisher version)
Volume 19
Issue 11
Start page 1983
End page 1991
Total pages 9
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Abstract Although most human retrotransposons are inactive, both inactive and active retrotransposons drive genome evolution and may influence transcription through various mechanisms. In humans, three retrotransposon families are still active, but one of these, SVA, remains mysterious. Here we report the identification of a new subfamily of SVA, which apparently formed after an alternative splicing event where the first exon of the MAST2 gene spliced into an intronic SVA and subsequently retrotransposed. Additional examples of SVA retrotransposing upstream exons due to splicing into SVA were also identified in other primate genomes. After molecular and computational experiments, we found a number of functional 3′ splice sites within many different transcribed SVAs across the human and chimpanzee genomes. Using a minigene splicing construct containing an SVA, we observed splicing in cell culture, along with SVA exonization events that introduced premature termination codons (PTCs). These data imply that an SVA residing within an intron in the same orientation as the gene may alter normal gene transcription either by gene-trapping or by introducing PTCs through exonization, possibly creating differences within and across species.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Mater Research Institute-UQ (MRI-UQ)
 
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