Characteristic enrichment of DNA repeats in different genomes

Cox, Randal; Mirkin, Sergei M.

doi:10.1073/pnas.94.10.5237

Cited by 114 publications

(79 citation statements)

References 39 publications

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“…With the steadily increasing number of genomic sequences, an alternative approach to study microsatellite evolution has become feasible (Jurka and Pethiyagoda 1995;Bell and Jurka 1997;Cox and Mirkin 1997;Field and Wills 1998). Assuming that the distribution of microsatellites in the genome reflects an equilibrium state between the operating evolutionary forces, information about the underlying mutation processes could be extracted from the analysis of genomic sequences.…”

Section: Institut Für Tierzucht Und Genetik 1210 Wien Austriamentioning

confidence: 99%

Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species

Dieringer¹,

2003

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We surveyed microsatellite distribution in 10 completely sequenced genomes. Using a permutation-based statistic, we assessed for all 10 genomes whether the microsatellite distribution significantly differed from expectations. Consistent with previous reports, we observed a highly significant excess of long microsatellites. Focusing on short microsatellites containing onlya few repeat units, we demonstrate that this repeat class is significantly underrepresented in most genomes. This pattern was observed across different repeat types. Computer simulations indicated that neither base substitutions nor a combination of length-dependent slippage and base substitutions could explain the observed pattern of microsatellite distribution. When we introduced one additional mutation process, a length-independent slippage (indel slippage) operating at repeats with few repetitions, our computer simulations captured the observed pattern of microsatellite distribution

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Section: Institut Für Tierzucht Und Genetik 1210 Wien Austriamentioning

confidence: 99%

Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species

Dieringer¹,

2003

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“…These sequences are found in great excess throughout the genomes of all studied eukaryotes (Hancock 1995;Cox and Mirkin 1997). Tandem repeats experience replication slippage, a unique mutational process that leads to insertions and deletions of one or a few repeat units.…”

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confidence: 99%

Domain-Level Differences in Microsatellite Distribution and Content Result from Different Relative Rates of Insertion and Deletion Mutations

Metzgar¹,

Liu²,

Hansen³

et al. 2002

Genome Res.

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Microsatellites (short tandem polynucleotide repeats) are found throughout eukaryotic genomes at frequencies many orders of magnitude higher than the frequencies predicted to occur by chance. Most of these microsatellites appear to have evolved in a generally neutral manner. In contrast, microsatellites are generally absent from bacterial genomes except in locations where they provide adaptive functional variability, and these appear to have evolved under selection. We demonstrate a mutational bias towards deletion (repeat contraction) in a native chromosomal microsatellite of the bacterium Mycoplasma gallisepticum, through the collection and analysis of independent mutations in the absence of natural selection. Using this and similar existing data from two other bacterial species and four eukaryotic species, we find strong evidence that deletion biases resulting in repeat contraction are common in bacteria, while eukaryotic microsatellites generally experience unbiased mutation or a bias towards insertion (repeat expansion). This difference in mutational bias suggests that eukaryotic microsatellites should generally expand wherever selection does not exclude them, whereas bacterial microsatellites should be driven to extinction by mutational pressure wherever they are not maintained by selection. This is consistent with observed bacterial and eukaryotic microsatellite distributions. Hence, mutational biases that differ between eukaryotes and bacteria can account for many of the observed differences in microsatellite DNA content and distribution found in these two groups of organisms.

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“…The non-B DNA structure forming sequences are found to be rich in genomes from divergent organisms (Table 1) (Cox & Mirkin, 1997;Svozil et al, 2008;Cerz et al, 2011). For example, nearly half of the human genome consists of repetitive sequences, which can be arranged as inverted, direct tandem, and homopurine-homopyrimidine mirror repeats.…”

Section: Dna Sequences Which Are Susceptible To Abnormal Foldingmentioning

confidence: 99%