Expansion of GAA trinucleotide repeats in mammals

Clark, Rhonda M.; Bhaskar, Sanjeev S.; Miyahara, Masaki; Dalgliesh, Gillian L.; Bidichandani, Sanjay I.

doi:10.1016/j.ygeno.2005.09.006

Cited by 39 publications

(38 citation statements)

References 35 publications

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“…in barn swallows, (46) in honey bees, (128) or some trinucleotide repeats in mammals. (10,129) Kruglyak et al (91) proposed that microsatellite growth reaches a finite upper limit since expansion by slippage is hindered by the introduction of imperfections in the repeat array, as shown earlier (Fig. 1A,D).…”

Section: Midlife Crisismentioning

confidence: 71%

The rise, fall and renaissance of microsatellites in eukaryotic genomes

2006

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Microsatellites are among the most versatile of genetic markers, being used in an impressive number of biological applications. However, the evolutionary dynamics of these markers remain a source of contention. Almost 20 years after the discovery of these ubiquitous simple sequences, new genomic data are clarifying our understanding of the structure, distribution and variability of microsatellites in genomes, especially for the eukaryotes. While these new data provide a great deal of descriptive information about the nature and abundance of microsatellite sequences within eukaryotic genomes, there have been few attempts to synthesise this information to develop a global concept of evolution. This review provides an up-to-date account of the mutational processes, biases and constraints believed to be involved in the evolution of microsatellites, particularly with respect to the creation and degeneration of microsatellites, which we assert may be broadly viewed as a life cycle. In addition, we identify areas of contention that require further research and propose some possible directions for future investigation.

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Section: Midlife Crisismentioning

confidence: 71%

The rise, fall and renaissance of microsatellites in eukaryotic genomes

2006

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“…8A, 9) and triNR (Supplemental Fig. 8B; Clark et al 2006) sequences that formed the longest distributions in the primate lineage (human and chimpanzee) reveals their R:Y-rich nature, suggestive of a role for R:Y asymmetry in supporting extended repeat lengths over evolutionary time.…”

Section: Repeat Length Distributions and Base-stackingmentioning

confidence: 96%

“…Another characteristic of simple repeats is the lengths attained genome-wide by specific sequences such as AAG repeats, which are consistently the longest by quite a margin within the triNR family (Clark et al 2006). This behavior is also enigmatic.…”

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confidence: 99%

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

Bacolla¹,

Larson²,

Collins³

et al. 2008

Genome Res.

105

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Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies of 82 synthetic single-stranded oligonucleotides comprising all tetra-and trinucleotide repeats revealed an inverse correlation between the stability of folded-back hairpin and quadruplex structures and the sequence representation for repeats Ն30 bp in length in nine vertebrate genomes. Alternatively, the predicted energies of base-stacking interactions correlated directly with the longest length distributions in vertebrate genomes. Genome-wide analyses indicated that unstable sequences, such as CAG:CTG and CCG:CGG, were over-represented in coding regions and that micro/minisatellites were recruited in genes involved in transcription and signaling pathways, particularly in the nervous system. Microsatellite instability (MSI) is a hallmark of cancer, and length polymorphism within genes can confer susceptibility to inherited disease. Sequences that manifest the highest MSI values also displayed the strongest base-stacking interactions; analyses of 62 tri-and tetranucleotide repeat-containing genes associated with human genetic disease revealed enrichments similar to those noted for micro/minisatellite-containing genes. We conclude that DNA structure and base-stacking determined the number and length distributions of microsatellite repeats in vertebrate genomes over evolutionary time and that micro/minisatellites have been recruited to participate in both gene and protein function.

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“…[50][51][52][53][54][55] A special class of polypurine stretches that have the characteristics of mirror repeats are enriched in the yeast as well as the human genome and common in many other genomes. 55,56 Mirror repeats are especially interesting because they can engage in inter-and The zinc-dependent protein present in nuclear extracts from different cell types was found to bind to DNA sequence prone to adopt triplehelical structure and to recognise structure-specific rather than sequence-specific features.…”

confidence: 99%