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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

Clustering of Alu subfamilies using indel markers.The blue slice of node 1 represents the oldest subfamilies (AluJ). AluS elements are represented in pink and members of the young AluY are shown in green. Sites of mutational events are shown in blue boxes in the network’s branches. Networks A and B are the result of size heterogeneity in positions 65 and 66: (A) assuming that the three combinations resulted consecutively (65–66 ins –65 del –66 del) and (B) assuming that they were independent events (65–66 ins –65 del and 65–66 ins - 65–66 del). Networks A and B differ only in the right reticulation (circled) and the branch that connects it to node 7.
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pone-0064884-g003: Clustering of Alu subfamilies using indel markers.The blue slice of node 1 represents the oldest subfamilies (AluJ). AluS elements are represented in pink and members of the young AluY are shown in green. Sites of mutational events are shown in blue boxes in the network’s branches. Networks A and B are the result of size heterogeneity in positions 65 and 66: (A) assuming that the three combinations resulted consecutively (65–66 ins –65 del –66 del) and (B) assuming that they were independent events (65–66 ins –65 del and 65–66 ins - 65–66 del). Networks A and B differ only in the right reticulation (circled) and the branch that connects it to node 7.

Mentions: Once it was established that indel markers are not artifacts of sequence alignment at the time of consensus prediction, we used the haplotypic combination of indels to demonstrate the evolutionary relationships between Alu elements (Figure 3). As a result of size heterogeneity in positions 65 and 66 (65–66 ins, 65–66 del and 65 del), located in the left monomer, two networks were constructed: one assuming that the three combinations resulted consecutively (65–66 ins –65 del –66 del) (Figure 3A) and the other assuming that they were independent events (65–66 ins –65 del and 65–66 ins –65–66 del) (Figure 3B). Both analyses exhibited similar graphs, an indication that the origin of the mutational events does not alter the clustering inference.


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)

Clustering of Alu subfamilies using indel markers.The blue slice of node 1 represents the oldest subfamilies (AluJ). AluS elements are represented in pink and members of the young AluY are shown in green. Sites of mutational events are shown in blue boxes in the network’s branches. Networks A and B are the result of size heterogeneity in positions 65 and 66: (A) assuming that the three combinations resulted consecutively (65–66 ins –65 del –66 del) and (B) assuming that they were independent events (65–66 ins –65 del and 65–66 ins - 65–66 del). Networks A and B differ only in the right reticulation (circled) and the branch that connects it to node 7.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0064884-g003: Clustering of Alu subfamilies using indel markers.The blue slice of node 1 represents the oldest subfamilies (AluJ). AluS elements are represented in pink and members of the young AluY are shown in green. Sites of mutational events are shown in blue boxes in the network’s branches. Networks A and B are the result of size heterogeneity in positions 65 and 66: (A) assuming that the three combinations resulted consecutively (65–66 ins –65 del –66 del) and (B) assuming that they were independent events (65–66 ins –65 del and 65–66 ins - 65–66 del). Networks A and B differ only in the right reticulation (circled) and the branch that connects it to node 7.
Mentions: Once it was established that indel markers are not artifacts of sequence alignment at the time of consensus prediction, we used the haplotypic combination of indels to demonstrate the evolutionary relationships between Alu elements (Figure 3). As a result of size heterogeneity in positions 65 and 66 (65–66 ins, 65–66 del and 65 del), located in the left monomer, two networks were constructed: one assuming that the three combinations resulted consecutively (65–66 ins –65 del –66 del) (Figure 3A) and the other assuming that they were independent events (65–66 ins –65 del and 65–66 ins –65–66 del) (Figure 3B). Both analyses exhibited similar graphs, an indication that the origin of the mutational events does not alter the clustering inference.

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