Comparative Analyses of Human Single- and Multilocus Tandem Repeats

Abstract

Using the compiled human genome sequence, we systematically cataloged all tandem repeats with periods between 20 and 2000 bp and defined two subsets whose consensus sequences were found at either single-locus tandem repeats (slTRs) or multilocus tandem repeats (mlTRs). Parameters compiled for these subsets provide insights into mechanisms underlying the creation and evolution of tandem repeats. Both subsets of tandem repeats are nonrandomly distributed in the genome, being found at higher frequency at many but not all chromosome ends and internal clusters of mlTRs were also observed. Despite the integral role of recombination in the biology of tandem repeats, recombination hotspots colocalized only with shorter microsatellites and not the longer repeats examined here. An increased frequency of slTRs was observed near imprinted genes, consistent with a functional role, while both slTRs and mlTRs were found more frequently near genes implicated in triplet expansion diseases, suggesting a general instability of these regions. Using our collated parameters, we identified 2230 slTRs as candidates for highly informative molecular markers.

Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia

“…Furthermore, hybridization of EPSPS probes at distal ends of homologous chromosomes of K. scoparia (Fig. 1) also suggests that an increase in EPSPS copies in GR K. scoparia may have occurred as a result of unequal crossover, as the gene duplication via unequal crossover most likely occurs at the telomere region of chromosomes (Royle et al, 1988;Amarger et al, 1998;Ames et al, 2008).…”

Coevolution between simple sequence repeats (SSRs) and virus genome size

“…This can be explained by the following statements. Genomes of reptiles are estimated to consist of about 30-50% repeats, birds have been estimated to consist of 15-20% of repeats [40,41], Mus musculus of 26.1% [42,43], and 44.9% of human genome were occupied by repeats [44,45]. While SSR tracts make up 2.4% of the E. coli genome [46], significantly less than vertebrates'.…”

Molecular cytogenetics to characterize mechanisms of gene duplication in pesticide resistance

“…The presence of EPSPS copies at the distal ends of homologous chromosomes 39 suggested that duplication of the EPSPS gene in K. scoparia may have occurred as a result of unequal crossing over, because such events are known to be most likely to occur in the telomeric region of chromosomes. 55 Importantly, a positive correlation between EPSPS gene copies and expression at the transcription and protein levels, 44,45 and continuous variation in EPSPS copies with glyphosate selection, 39 suggest that the EPSPS copy number in K. scoparia increases through an adaptive process because some duplicated genes confer an immediate adaptive advantage. 26 Recently using single-copy FISH, we demonstrated that in A. tuberculatus the EPSPS gene is located in the pericentromeric region of one pair of chromosomes.…”