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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 2, 3, and 4 of Figure 3.An alignment of at least a representative of each involved node is displayed, plus two representatives of node 7 (AluY and AluSx3). Alternative pathways are named A to F. A and B represent recombination events (green), C and D represent events of back mutation (orange) and E and F represent recurrent mutations (blue).
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pone-0064884-g004: Alternative pathways for the origin of Alu subfamilies clustered in nodes 2, 3, and 4 of Figure 3.An alignment of at least a representative of each involved node is displayed, plus two representatives of node 7 (AluY and AluSx3). Alternative pathways are named A to F. A and B represent recombination events (green), C and D represent events of back mutation (orange) and E and F represent recurrent mutations (blue).

Mentions: With the exception of two reticulations that clearly show alternative solutions to mutational events, both networks are well resolved revealing that most active genes originated from pre-existing sequences by mutation. The two reticulations that link nodes 1, 2, 3, 4 and 7, 13, 14, 15, may allude to events of Alu-Alu recombination and this hypothesis was further explored. In one of the cases (Figure 3, left reticulation), the Alu subfamilies represented in nodes 1, 2, 3 and 4 are distinguished by the haplotypic combination of 65–66 and 265.1 polymorphisms (Figure 4). Because positions 65 and 66 are deleted in the youngest AluY subfamily, and present in the old AluJo, the ancestral allele is 65–66 ins (Figure 3, node 1) [36]. Following the same rationale, the 265.1 ins is likely to be the youngest allele. Therefore, several alternative pathways were considered (Figure 4) based on the order of mutational events occurring in each monomer.


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 2, 3, and 4 of Figure 3.An alignment of at least a representative of each involved node is displayed, plus two representatives of node 7 (AluY and AluSx3). Alternative pathways are named A to F. A and B represent recombination events (green), C and D represent events of back mutation (orange) and E and F represent recurrent mutations (blue).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0064884-g004: Alternative pathways for the origin of Alu subfamilies clustered in nodes 2, 3, and 4 of Figure 3.An alignment of at least a representative of each involved node is displayed, plus two representatives of node 7 (AluY and AluSx3). Alternative pathways are named A to F. A and B represent recombination events (green), C and D represent events of back mutation (orange) and E and F represent recurrent mutations (blue).
Mentions: With the exception of two reticulations that clearly show alternative solutions to mutational events, both networks are well resolved revealing that most active genes originated from pre-existing sequences by mutation. The two reticulations that link nodes 1, 2, 3, 4 and 7, 13, 14, 15, may allude to events of Alu-Alu recombination and this hypothesis was further explored. In one of the cases (Figure 3, left reticulation), the Alu subfamilies represented in nodes 1, 2, 3 and 4 are distinguished by the haplotypic combination of 65–66 and 265.1 polymorphisms (Figure 4). Because positions 65 and 66 are deleted in the youngest AluY subfamily, and present in the old AluJo, the ancestral allele is 65–66 ins (Figure 3, node 1) [36]. Following the same rationale, the 265.1 ins is likely to be the youngest allele. Therefore, several alternative pathways were considered (Figure 4) based on the order of mutational events occurring in each monomer.

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