Limits...
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.

Show MeSH

Related in: MedlinePlus

Evolution of human Alu subfamilies.Blue boxes correspond to indel markers, green boxes correspond to SNPs and purple boxes correspond to putative recombination events and recombinant (chimeric) subfamilies.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3672193&req=5

pone-0064884-g006: Evolution of human Alu subfamilies.Blue boxes correspond to indel markers, green boxes correspond to SNPs and purple boxes correspond to putative recombination events and recombinant (chimeric) subfamilies.

Mentions: A general analysis of the information provided by both indels and SNPs allowed the distinction of Alu subfamilies according to informative positions (Figure 6). Despite the information provided by the combination of both marker types, large clusters incorporating a vast number of subfamilies, mainly in what refers to young AluY elements, are still observed. It is important to mention that although a high number of polymorphic positions were detected among Alu consensus sequences (Dataset S1), only A120T, G194A, T214C, C215G and G219C represent single occurrences in the history of Alu sequences that can be used as diagnostic positions (Figure 6).


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)

Evolution of human Alu subfamilies.Blue boxes correspond to indel markers, green boxes correspond to SNPs and purple boxes correspond to putative recombination events and recombinant (chimeric) subfamilies.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0064884-g006: Evolution of human Alu subfamilies.Blue boxes correspond to indel markers, green boxes correspond to SNPs and purple boxes correspond to putative recombination events and recombinant (chimeric) subfamilies.
Mentions: A general analysis of the information provided by both indels and SNPs allowed the distinction of Alu subfamilies according to informative positions (Figure 6). Despite the information provided by the combination of both marker types, large clusters incorporating a vast number of subfamilies, mainly in what refers to young AluY elements, are still observed. It is important to mention that although a high number of polymorphic positions were detected among Alu consensus sequences (Dataset S1), only A120T, G194A, T214C, C215G and G219C represent single occurrences in the history of Alu sequences that can be used as diagnostic positions (Figure 6).

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