Alu Repeats: A Source for the Genesis of Primate Microsatellites

Arcot, Santosh S.; Wang, Zhenyuan; Weber, James L.; Deininger, Prescott L.; Batzer, Mark A.

doi:10.1006/geno.1995.1224

Cited by 203 publications

(166 citation statements)

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“…2 Putative Ostrinia nubilalis microsatellite-associated interspersed nuclear element (OnMINE-1) secondary structure elements had homology to Micron superfamily members (Temnykh et al 2001). Primate Alu elements also are located near multiple microsatellite repeat motifs (Arcot et al 1995), with the most ancient AluJ class associated with (GAAA) n repeats (Yandava et al 1997). No prior evidence indicates that MITE or Helitron-like elements are preferentially integrated within microsatellite repeats of insects.…”

Section: Resultsmentioning

confidence: 99%

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

et al. 2010

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Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A + T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA)n microsatellite loci, and was named the microsatellite-associated interspersed nuclear element ( MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA)n microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA)n microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA)n microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains. Abstract Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A ? T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA) n microsatellite loci, and was named the microsatellite-associated interspersed nuclear element (MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA) n microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA) n microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA) n microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains.

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Section: Resultsmentioning

confidence: 99%

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

et al. 2010

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“…Microsatellites often arise from repetitive elements, 52 but usually from the 3 0 end. 53 Comparative primate data 39 show that the …”

Section: Discussionmentioning

confidence: 99%

Haplotypic relationship between SNP and microsatellite markers at the NOS2A locus in two populations

et al. 2003

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The density of genetic markers required for successful association mapping of complex diseases depends on linkage disequilibrium (LD) between non-functional markers and functional variants. The haplotypic relationship between stable markers and potentially unstable but highly informative markers (e.g. microsatellites) indicates that LD might be maintained over considerable genetic distance in non-African populations, supporting the use of such 'mixed marker haplotypes' in LD-based mapping, and allowing inferences to be drawn about human origins. We investigated sequence variation in the proximal 2.6 kb of the inducible nitric oxide synthase (NOS2A) promoter and the relationship between SNP haplotypes and a pentanucleotide microsatellite (the 'NOS2A À2.6 microsatellite') in Gambians and UK Caucasians. UK Caucasians exhibited a subset of sequence diversity observed in Gambians, sharing four of 11 SNPs and a similar haplotypic structure. Five SNPs were found in the sequence of interspersed repetitive DNA elements. In both populations, there was dramatic loss of LD between SNP haplotypes and microsatellite alleles across a very short physical distance, suggesting a high intrinsic mutation rate of the NOS2A À2.6 microsatellite, the SNP haplotypes are relatively ancient, or that this was a region of frequent recombination. Understanding locus-and population-specific LD is essential when designing and interpreting genetic association studies.

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“…Microsatellites-Several studies have demonstrated the ability of some TE sequences to seed the formation of unstable microsatellite repeats [76][77][78]. Because the structure of many TE insertions includes a poly-A rich tail, mutations in the A-tracts can readily create the initial repeats of a microsatellite sequence.…”

Section: Seedingmentioning

confidence: 99%

Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity

Hedges

Deininger

2007

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

279

248

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The ubiquity of mobile elements in mammalian genomes poses considerable challenges for the maintenance of genome integrity. The predisposition of mobile elements towards participation in genomic rearrangements is largely a consequence of their interspersed homologous nature. As tracts of nonallelic sequence homology, they have the potential to interact in a disruptive manner during both meiotic recombination and DNA repair processes, resulting in genomic alterations ranging from deletions and duplications to large-scale chromosomal rearrangements. Although the deleterious effects of transposable element (TE) insertion events have been extensively documented, it is arguably through post-insertion genomic instability that they pose the greatest hazard to their host genomes. Despite the periodic generation of important evolutionary innovations, genomic alterations involving TE sequences are far more frequently neutral or deleterious in nature. The potentially negative consequences of this instability are perhaps best illustrated by the 25 human genetic diseases that are attributable to TE-mediated rearrangements. Some of these rearrangements, such as those involving the MLL locus in leukemia and the LDL receptor in familial hypercholesterolemia, represent recurrent mutations that have independently arisen multiple times in human populations. While TE-instability has been a potent force in shaping eukaryotic genomes and a significant source of genetic disease, much concerning the mechanisms governing the frequency and variety of these events remains to be clarified. Here we survey the current state of knowledge regarding the mechanisms underlying mobile element-based genetic instability in mammals. Compared to simpler eukaryotic systems, mammalian cells appear to have several modifications to their DNA-repair ensemble that allow them to better cope with the large amount of interspersed homology that has been generated by TEs. In addition to the disruptive potential of nonallelic sequence homology, we also consider recent evidence suggesting that the endonuclease products of TEs may also play a key role in instigating mammalian genomic instability.

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Alu Repeats: A Source for the Genesis of Primate Microsatellites

Cited by 203 publications

References 0 publications

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

Haplotypic relationship between SNP and microsatellite markers at the NOS2A locus in two populations

Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity

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