Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals

Bioinformatics
Federico AbascalAlfonso Valencia

Abstract

Transposable elements constitute a large fraction of vertebrate genomes and, during evolution, may be co-opted for new functions. Exonization of transposable elements inserted within or close to host genes is one possible way to generate new genes, and alternative splicing of the new exons may represent an intermediate step in this process. The genes TMPO and ZNF451 are present in all vertebrate lineages. Although they are not evolutionarily related, mammalian TMPO and ZNF451 do have something in common-they both code for splice isoforms that contain LAP2alpha domains. We found that these LAP2alpha domains have sequence similarity to repetitive sequences in non-mammalian genomes, which are in turn related to the first ORF from a DIRS1-like retrotransposon. This retrotransposon domestication happened separately and resulted in proteins that combine retrotransposon and host protein domains. The alternative splicing of the retrotransposed sequence allowed the production of both the new and the untouched original isoforms, which may have contributed to the success of the colonization process. The LAP2alpha-specific isoform of TMPO (LAP2α) has been co-opted for important roles in the cell, whereas the ZNF451 LAP2alpha isoform is evo...Continue Reading

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Citations

Nov 3, 2015·Nature Structural & Molecular Biology·Nathalie EisenhardtAndrea Pichler
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May 29, 2021·NAR Genomics and Bioinformatics·Fernando PozoMichael L Tress
Aug 4, 2021·Cancer Metastasis Reviews·Nianhong ChenPing Shi

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Methods Mentioned

BETA
sumoylation

Software Mentioned

DataMonkey
Phyml
Hmmscan
RepeatModeler
Mafft
Jalview
Ensembl
ProtTest
bedtools
TBLASTN

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