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

Alu consensus alignment and position numbering.Sequence Alignment of at least one representative of each haplotype defined by the 11 indel markers; node 1 is represented by two sequences: AluJo and AluSx. Position numbering was performed according to the reference AluJo. The first base of each indel is also indicated (red). Poly-A linker polymorphisms were disregarded. Dots represent identical bases and hyphens represent gaps (absent or deleted bases). R represents bases A or G according to the IUPAC code for nucleotide ambiguities.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3672193&req=5

pone-0064884-g001: Alu consensus alignment and position numbering.Sequence Alignment of at least one representative of each haplotype defined by the 11 indel markers; node 1 is represented by two sequences: AluJo and AluSx. Position numbering was performed according to the reference AluJo. The first base of each indel is also indicated (red). Poly-A linker polymorphisms were disregarded. Dots represent identical bases and hyphens represent gaps (absent or deleted bases). R represents bases A or G according to the IUPAC code for nucleotide ambiguities.

Mentions: The collection of consensus Alus was aligned in Geneious v5.4 [31] and poly-A tails were not considered (Text S2). The ancestral AluJo was set up as the reference sequence in our analyses and, consequently, position numbering was performed according to AluJo consensus sequence (Figure 1). Insertion and deletion polymorphisms (indels) were named as in the following example: a single-base deletion in position 65 is indicated as “65 del” and an insertion of an adenine after position 177 is indicated as “177.1 ins” (AluJo). Consensus Alus and polymorphic sites were then inputted into a database that provides all the information regarding the position and the distinct allelic forms of each polymorphism present in human consensus sequences. The database of Alu variability is accessible in Dataset S1.


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)

Alu consensus alignment and position numbering.Sequence Alignment of at least one representative of each haplotype defined by the 11 indel markers; node 1 is represented by two sequences: AluJo and AluSx. Position numbering was performed according to the reference AluJo. The first base of each indel is also indicated (red). Poly-A linker polymorphisms were disregarded. Dots represent identical bases and hyphens represent gaps (absent or deleted bases). R represents bases A or G according to the IUPAC code for nucleotide ambiguities.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0064884-g001: Alu consensus alignment and position numbering.Sequence Alignment of at least one representative of each haplotype defined by the 11 indel markers; node 1 is represented by two sequences: AluJo and AluSx. Position numbering was performed according to the reference AluJo. The first base of each indel is also indicated (red). Poly-A linker polymorphisms were disregarded. Dots represent identical bases and hyphens represent gaps (absent or deleted bases). R represents bases A or G according to the IUPAC code for nucleotide ambiguities.
Mentions: The collection of consensus Alus was aligned in Geneious v5.4 [31] and poly-A tails were not considered (Text S2). The ancestral AluJo was set up as the reference sequence in our analyses and, consequently, position numbering was performed according to AluJo consensus sequence (Figure 1). Insertion and deletion polymorphisms (indels) were named as in the following example: a single-base deletion in position 65 is indicated as “65 del” and an insertion of an adenine after position 177 is indicated as “177.1 ins” (AluJo). Consensus Alus and polymorphic sites were then inputted into a database that provides all the information regarding the position and the distinct allelic forms of each polymorphism present in human consensus sequences. The database of Alu variability is accessible in Dataset S1.

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