Measurement of DNA Mutations Caused by Seconds-period UV-irradiation

Futakami, Masae; Nishigaki, Koichi

doi:10.1246/cl.2007.358

Cited by 8 publications

(7 citation statements)

References 9 publications

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“…This supports the idea of a gradual, additive accumulation of mutations contributing to the genome change observed here. It is important to recognize that the quantities of spiddos appearing here are an ensemble‐average for cells contained in a section, which have been shown to work as if they were taken from a single genome .…”

Section: Resultsmentioning

confidence: 99%

“…Through these processes, each genome sequence can be converted into genome‐intrinsic values ( spiddos : species identification dots) used to calculate the distance between two genomes . The genome distance obtained (symbol d G ) has proven useful and reliable for this purpose . This approach is, in effect, identical to measuring the sequence similarity using representative DNA fragments collected by random PCR.…”

Section: Methodsmentioning

confidence: 99%

“…To the best of our knowledge, this is the only practical approach to obtain the genome distance universally (from virus/bacteria to mammals, ubiquitously). Empirically, the genome distance obtained ( d G ) is proportional to the degree of mutation, given the level of mutation is limited within a small range .…”

Section: Methodsmentioning

confidence: 99%

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Ordered genome change of plant and animal body cells revealed by the genome profiling method

et al. 2016

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In the past, it was widely thought that, although epigenetically different, the genome sequences of cells are basically the same in a single body. In retrospect, the genome-uniformity idea may have been na€ ıve, considering that DNA polymerases cannot be perfect. Here, a systemic, not sporadic, genome change was demonstrated in a single plant (Arabidopsis) and animal (zebrafish) body using genome DNAs taken in an ordered manner using the genome profiling method. This can be explained because mutations accumulate additively in progeny cells, and these results are critically significant for developmental and oncological research.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Ordered genome change of plant and animal body cells revealed by the genome profiling method

et al. 2016

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“…To obtain statistically significant results using conventional high-precision sequencing, high-volume sequencing of the multiple-million base-pair level must be carried out to separate infrequently occurring mutations (e.g., < 10 -6 /mutations/base/replication) from background noise. In this regard, it should be noted that the ability of the GP method to overcome this difficulty has been experimentally demonstrated: GP has been used successfully for species identification and classification [ 24 , 25 , 27 , 28 , 36 ] and in high-sensitivity mutation assays [ 34 , 35 ].…”

Section: Resultsmentioning

confidence: 99%

“…GP has been used as a tool for universal species identification [ 21 , 24 , 27 , 28 , 33 ] and as an accurate detector of mutation [ 34 , 35 ]. In this study, we applied the GP method to a new challenge: detection of extremely small genomic differences between very closely related cells with the aim of examining within-organism sequence variation.…”

Section: Introductionmentioning

confidence: 99%

Systematic genome sequence differences among leaf cells within individual trees

et al. 2014

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BackgroundEven in the age of next-generation sequencing (NGS), it has been unclear whether or not cells within a single organism have systematically distinctive genomes. Resolving this question, one of the most basic biological problems associated with DNA mutation rates, can assist efforts to elucidate essential mechanisms of cancer.ResultsUsing genome profiling (GP), we detected considerable systematic variation in genome sequences among cells in individual woody plants. The degree of genome sequence difference (genomic distance) varied systematically from the bottom to the top of the plant, such that the greatest divergence was observed between leaf genomes from uppermost branches and the remainder of the tree. This systematic variation was observed within both Yoshino cherry and Japanese beech trees.ConclusionsAs measured by GP, the genomic distance between two cells within an individual organism was non-negligible, and was correlated with physical distance (i.e., branch-to-branch distance). This phenomenon was assumed to be the result of accumulation of mutations from each cell division, implying that the degree of divergence is proportional to the number of generations separating the two cells.

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Genome profiling (GP) as an effective tool for monitoring culture collections: A case study with Trichosporon

Hamano

Ueno-Tsuji

Tanaka

et al. 2012

Journal of Microbiological Methods

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Species identification and classification of a large number of microbes are essential and heavy workloads in culture collections and relevant laboratories. The identification of species usually requires different methods depending on species. Therefore, the development of a method which is simple and applicable to any organisms will lessen the burdens, increase the reliability of databases and thus enhance the science on microbes. The genome profiling (GP) method, developed previously, was found effective in monitoring authenticities of all strains/species tested in culture collections and expectedly various species, which was shown by applying the GP and the conventional sequencing methods to identifying and classifying species/strains belonging to the genus Trichosporon (38 strains; 16 species). Small differences between strains (11 strains of Trichosporon asahii and 4 strains of Trichosporon coremiiforme) can be reliably discriminated by GP, which was unsuccessful in the conventional sequencing approach. Importantly, seven possible false-assignments contained in the database were all pointed out by the GP method with near-perfect correctness, showing the power of the GP method.GP was shown to be a potent tool for rapidly and correctly monitoring species and strains of fungi in culture collections owing to its simple and informative natures.

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Measurement of DNA Mutations Caused by Seconds-period UV-irradiation

Cited by 8 publications

References 9 publications

Ordered genome change of plant and animal body cells revealed by the genome profiling method

Ordered genome change of plant and animal body cells revealed by the genome profiling method

Systematic genome sequence differences among leaf cells within individual trees

Genome profiling (GP) as an effective tool for monitoring culture collections: A case study with Trichosporon

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