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The role of recombination in the origin and evolution of Alu subfamilies.

Teixeira-Silva A, Silva RM, Carneiro J, Amorim A, Azevedo L - PLoS ONE (2013)

Bottom Line: Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes.In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus.From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes.

View Article: PubMed Central - PubMed

Affiliation: IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.

ABSTRACT
Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome.

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Related in: MedlinePlus

Alternative pathways for the origin of Alu subfamilies clustered in nodes 13, 14 and 15 of Figure 3.An alignment of at least one representative of each involved node is displayed. Alternative pathways are named A to C and represent recombination events (green).
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pone-0064884-g005: Alternative pathways for the origin of Alu subfamilies clustered in nodes 13, 14 and 15 of Figure 3.An alignment of at least one representative of each involved node is displayed. Alternative pathways are named A to C and represent recombination events (green).

Mentions: The network reticulation on the right (Figure 3) has an even higher number of possible explanations for the appearance of the observed haplotypes (Figure 5). In this case, the key positions to establish the alternative mutational pathways are the 206.1 and 266–267.


The role of recombination in the origin and evolution of Alu subfamilies.

Teixeira-Silva A, Silva RM, Carneiro J, Amorim A, Azevedo L - PLoS ONE (2013)

Alternative pathways for the origin of Alu subfamilies clustered in nodes 13, 14 and 15 of Figure 3.An alignment of at least one representative of each involved node is displayed. Alternative pathways are named A to C and represent recombination events (green).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3672193&req=5

pone-0064884-g005: Alternative pathways for the origin of Alu subfamilies clustered in nodes 13, 14 and 15 of Figure 3.An alignment of at least one representative of each involved node is displayed. Alternative pathways are named A to C and represent recombination events (green).
Mentions: The network reticulation on the right (Figure 3) has an even higher number of possible explanations for the appearance of the observed haplotypes (Figure 5). In this case, the key positions to establish the alternative mutational pathways are the 206.1 and 266–267.

Bottom Line: Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes.In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus.From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes.

View Article: PubMed Central - PubMed

Affiliation: IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.

ABSTRACT
Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome.

Show MeSH
Related in: MedlinePlus