A Brief Review of Short Tandem Repeat Mutation

Fan, Hao; Chu, Jiayou

doi:10.1016/s1672-0229(07)60009-6

Cited by 233 publications

(166 citation statements)

References 59 publications

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“…Another peculiarity of C-left is the excess of microsatellites, i.e., tandem repeats of short DNA sequences, scattered throughout eukaryote and prokaryote genomes (for review, see Richard et al 2008) and known to present a mutation rate higher than that of unique DNA sequences (for review, see Fan and Chu 2007). We screened for the presence of di-, tri-, and tetranucleotide repeats in the L. kluyveri genome and found a significant enrichment in C-left compared with the rest of the genome (up to twice; Supplemental Table S2).…”

Section: Resultsmentioning

confidence: 99%

Unusual composition of a yeast chromosome arm is associated with its delayed replication

Payen¹,

Fischer²,

Marck³

et al. 2009

Genome Res.

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The 11.3-Mb genome of the yeast Lachancea (Saccharomyces) kluyveri displays an intriguing compositional heterogeneity: a region of ;1 Mb, covering almost the whole left arm of chromosome C (C-left), has an average GC content of 52.9%, which is significantly higher than the 40.4% global GC content of the rest of the genome. This region contains the MAT locus, which remains normal in composition. The excess of GC base pairs affects both coding and noncoding sequences, and thus is not due to selective pressure acting on protein sequences. It leads to a strong codon usage bias and alters the amino acid composition of the 457 proteins encoded on C-left that do not show obvious bias for functional categories, or the presence of paralogs or orthologs of essential genes of Saccharomyces cerevisiae. They share significant synteny conservation with other species of the Saccharomycetaceae, and phylogenetic analysis indicates that C-left originates from a Lachancea species. In contrast, there is a complete absence of transposable elements in C-left, whereas 18 elements per megabase are distributed across the rest of the genome. Comparative hybridization of synchronized cells using high-density genome arrays reveals that C-left is replicated later during S phase than the rest of the genome. Two possible primary causes of this major compositional heterogeneity are discussed: an ancient hybridization of two related species with very distinct GC composition, or an intrinsic mechanism, possibly associated with the loss of the silent cassettes from C-left that progressively increased the GC content and generated the delayed replication of this chromosomal arm.

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Section: Resultsmentioning

confidence: 99%

Unusual composition of a yeast chromosome arm is associated with its delayed replication

Payen¹,

Fischer²,

Marck³

et al. 2009

Genome Res.

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“…Microsatellites or short tandem repeats (STRs) consist of tandemly repeated DNA units with lengths ranging from two to six nucleotides (Edwards et al 1991(Edwards et al , 1992Fan and Chu 2007). STRs are named according to the number of repeats; different STR alleles can occur in a single STR locus, thereby resulting in STR polymorphism.…”

Section: Introductionmentioning

confidence: 99%

Variations in short tandem repeats deduced on the basis of the number of repeats and the relationship of these variations with longevity

Liu

Wang

Xuelian

et al. 2010

AGE

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The objective of this study was to investigate the quantitative characteristics of short tandem repeat (STR) variations deduced on the basis of the number of STRs that are beneficial for human survival. The longevity group included 60 nonagenarian subjects, and the control group included 250 reference adults (age, 20-50 years). Alleles of 15 Combined DNA Index System STR loci were determined using a commercial polymerase chain reaction kit. An STR with the highest frequency distribution in a population (control group) was considered as a conservative STR, and the number of core unit repeats of this STR allele was considered as the median repeat number in the STR locus (STRm). The absolute difference between the STRm and the number of core unit repeats of other STR alleles can be considered as the quantitative marker of variation for that particular STR allele (M value). The mean M values of CSF1TPO in the longevity group were significantly higher than those in the control group (P<0.05). These findings appear to suggest that at least one of the STR loci may be associated with longevity. The M value of STR may be a new and high-efficacy genetic marker.

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“…In many disease-causing bacteria, some -contingency genes‖ reside in STR sequences that allow frame-shift mutations for promoting adaptation and better ability to survive host defence (Fan and Chu 2007). A polymorphic dinucleotide repeat in intron 1 has been shown to modulate transcription of epidermal growth factor receptor gene in vitro (Gebhardt et al, 1999).…”

Section: Pcr Amplification Of Selected Microsatellitementioning

confidence: 99%

In Silico Characterization of Selected Microsatellite Loci Reported in Zebrafish Genome

Pathan¹,

Nesnas²,

Acharya³

et al. 2017

Int.J.Curr.Microbiol.App.Sci

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A Brief Review of Short Tandem Repeat Mutation

Cited by 233 publications

References 59 publications

Unusual composition of a yeast chromosome arm is associated with its delayed replication

Unusual composition of a yeast chromosome arm is associated with its delayed replication

Variations in short tandem repeats deduced on the basis of the number of repeats and the relationship of these variations with longevity

In Silico Characterization of Selected Microsatellite Loci Reported in Zebrafish Genome

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