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

Abascal F, Tress ML, Valencia A - Bioinformatics (2015)

Bottom Line: 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 LAP2alpha-specific isoform of TMPO (LAP2α) has been co-opted for important roles in the cell, whereas the ZNF451 LAP2alpha isoform is evolving under strong purifying selection but remains uncharacterized.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid 28029, Spain.

No MeSH data available.


(A) A multiple sequence alignment including the LAP2alpha domains of mammalian LAP2α and ZNF451-L2a and homologous sequences from non-mammalian DIRS1-like elements. The phylogenetic tree in (B) was built with Phyml for the LAP2alpha domains of LAP2α and ZNF451-L2a. Overall dN/dS ratios were calculated with the SLAC method in DataMonkey (see Supplementary Appendix). (C) A schematic structure of the DIRS1-like element from which the LAP2alpha domain originated
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btv132-F2: (A) A multiple sequence alignment including the LAP2alpha domains of mammalian LAP2α and ZNF451-L2a and homologous sequences from non-mammalian DIRS1-like elements. The phylogenetic tree in (B) was built with Phyml for the LAP2alpha domains of LAP2α and ZNF451-L2a. Overall dN/dS ratios were calculated with the SLAC method in DataMonkey (see Supplementary Appendix). (C) A schematic structure of the DIRS1-like element from which the LAP2alpha domain originated

Mentions: In contrast, we found numerous significant similarity hits (TBLASTN e value < 1e-05) within the genomes of anole lizard (6), Chinese soft-shell turtle (9) and coelacanth (11; Fig 2A). With further sequence searches, we found that these genomes in fact contained hundreds or thousands of copies (TBLASTN hits), revealing the repetitive nature of these sequences and suggesting a TE origin.Fig. 2.


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

Abascal F, Tress ML, Valencia A - Bioinformatics (2015)

(A) A multiple sequence alignment including the LAP2alpha domains of mammalian LAP2α and ZNF451-L2a and homologous sequences from non-mammalian DIRS1-like elements. The phylogenetic tree in (B) was built with Phyml for the LAP2alpha domains of LAP2α and ZNF451-L2a. Overall dN/dS ratios were calculated with the SLAC method in DataMonkey (see Supplementary Appendix). (C) A schematic structure of the DIRS1-like element from which the LAP2alpha domain originated
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495291&req=5

btv132-F2: (A) A multiple sequence alignment including the LAP2alpha domains of mammalian LAP2α and ZNF451-L2a and homologous sequences from non-mammalian DIRS1-like elements. The phylogenetic tree in (B) was built with Phyml for the LAP2alpha domains of LAP2α and ZNF451-L2a. Overall dN/dS ratios were calculated with the SLAC method in DataMonkey (see Supplementary Appendix). (C) A schematic structure of the DIRS1-like element from which the LAP2alpha domain originated
Mentions: In contrast, we found numerous significant similarity hits (TBLASTN e value < 1e-05) within the genomes of anole lizard (6), Chinese soft-shell turtle (9) and coelacanth (11; Fig 2A). With further sequence searches, we found that these genomes in fact contained hundreds or thousands of copies (TBLASTN hits), revealing the repetitive nature of these sequences and suggesting a TE origin.Fig. 2.

Bottom Line: 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 LAP2alpha-specific isoform of TMPO (LAP2α) has been co-opted for important roles in the cell, whereas the ZNF451 LAP2alpha isoform is evolving under strong purifying selection but remains uncharacterized.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid 28029, Spain.

No MeSH data available.