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Nishigaki K. Short lifetime structures appearing in RNA and DNA. Brief Funct Genomics 2018; 18:174-181. [PMID: 30445594 DOI: 10.1093/bfgp/ely035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 09/24/2018] [Accepted: 10/02/2018] [Indexed: 11/12/2022] Open
Abstract
The structure and function of unstable single-stranded DNA (ssDNA) have not been widely examined. While numerous studies have investigated DNA as an information molecule, the different potentials of DNA, particularly those of ssDNA, remain unclear. For polypeptides, the significance of denatured structures has been established in the past two decades. Polynucleotides have chemically distinct properties from polypeptides, but their behaviours have not been thoroughly studied. In this review, three different phenomena related to unstable ssDNA are discussed: i) ssDNA cleavage of restriction enzymes; ii) single-stranded conformation polymorphism, which can be theoretically explained by single-stranded conformation dynamics; and iii) random PCR (Polymerase Chain Reaction). These features can be utilized for scientific or technical applications. Previous studies showed that the phenomena exhibited by ssDNA were correctly understood only when unstable and transient structures were taken into account. Transient structures of ssDNA may have undiscovered functions governed by very rapid processes and/or multi-diversity states because of their intrinsic natures.
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Affiliation(s)
- Koichi Nishigaki
- Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan.,Graduate School of Science and Technology, Saitama University, Shimo-okubo, Saitama City, Saitama, Japan
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Diwan D, Masubuchi Y, Furukawa T, Nishigaki K. Ordered genome change of plant and animal body cells revealed by the genome profiling method. FEBS Lett 2016; 590:2119-26. [PMID: 27277546 DOI: 10.1002/1873-3468.12248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/14/2016] [Accepted: 05/20/2016] [Indexed: 01/30/2023]
Abstract
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 naïve, 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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Affiliation(s)
- Deepti Diwan
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Yuki Masubuchi
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Tatsuya Furukawa
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
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Diwan D, Komazaki S, Suzuki M, Nemoto N, Aita T, Satake A, Nishigaki K. Systematic genome sequence differences among leaf cells within individual trees. BMC Genomics 2014; 15:142. [PMID: 24548431 PMCID: PMC3937000 DOI: 10.1186/1471-2164-15-142] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 02/10/2014] [Indexed: 01/09/2023] Open
Abstract
Background Even 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. Results Using 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. Conclusions As 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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Affiliation(s)
| | | | | | | | | | | | - Koichi Nishigaki
- Graduate School of Science and Engineering, Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan.
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Hamano K, Ueno-Tsuji S, Tanaka R, Suzuki M, Nishimura K, Nishigaki K. Genome profiling (GP) as an effective tool for monitoring culture collections: a case study with Trichosporon. J Microbiol Methods 2012; 89:119-28. [PMID: 22401825 DOI: 10.1016/j.mimet.2012.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 02/08/2012] [Accepted: 02/10/2012] [Indexed: 11/28/2022]
Abstract
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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Affiliation(s)
- Keiichi Hamano
- Rational Evolutionary Design of Advanced Biomolecules, Saitama Small Enterprise Promotion Corporation, SKIP city, 3-12-18 Kamiaoki, Kawaguchi, Saitama 333-0844, Japan.
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Ahmed S, Komori M, Tsuji-Ueno S, Suzuki M, Kosaku A, Miyamoto K, Nishigaki K. Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one. PLoS One 2011; 6:e23963. [PMID: 21912611 PMCID: PMC3166070 DOI: 10.1371/journal.pone.0023963] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 08/02/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Ribosomal RNAs have been widely used for identification and classification of species, and have produced data giving new insights into phylogenetic relationships. Recently, multilocus genotyping and even whole genome sequencing-based technologies have been adopted in ambitious comparative biology studies. However, such technologies are still far from routine-use in species classification studies due to their high costs in terms of labor, equipment and consumables. METHODOLOGY/PRINCIPAL FINDINGS Here, we describe a simple and powerful approach for species classification called genome profiling (GP). The GP method composed of random PCR, temperature gradient gel electrophoresis (TGGE) and computer-aided gel image processing is highly informative and less laborious. For demonstration, we classified 26 species of insects using GP and 18S rDNA-sequencing approaches. The GP method was found to give a better correspondence to the classical phenotype-based approach than did 18S rDNA sequencing employing a congruence value. To our surprise, use of a single probe in GP was sufficient to identify the relationships between the insect species, making this approach more straightforward. CONCLUSION/SIGNIFICANCE The data gathered here, together with those of previous studies show that GP is a simple and powerful method that can be applied for actually universally identifying and classifying species. The current success supported our previous proposal that GP-based web database can be constructible and effective for the global identification/classification of species.
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Affiliation(s)
- Shamim Ahmed
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Manabu Komori
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Sachika Tsuji-Ueno
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Miho Suzuki
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Akinori Kosaku
- Laboratory of Clinical Sciences, Dokkyo Medical University, Tochigi, Japan
| | - Kiyoshi Miyamoto
- Laboratory of Medical Sciences, Dokkyo Medical University, Tochigi, Japan
| | - Koichi Nishigaki
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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Identification of forensically important blowfly species (Diptera: Calliphoridae) by high-resolution melting PCR analysis. Int J Legal Med 2010; 124:277-85. [DOI: 10.1007/s00414-009-0396-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 11/18/2009] [Indexed: 10/20/2022]
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Futakami M, Nishigaki K. Measurement of DNA Mutations Caused by Seconds-period UV-irradiation. CHEM LETT 2007. [DOI: 10.1246/cl.2007.358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kouduka M, Sato D, Komori M, Kikuchi M, Miyamoto K, Kosaku A, Naimuddin M, Matsuoka A, Nishigaki K. A solution for universal classification of species based on genomic DNA. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2007; 2007:27894. [PMID: 18253463 PMCID: PMC1893011 DOI: 10.1155/2007/27894] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2006] [Revised: 10/08/2006] [Accepted: 10/08/2006] [Indexed: 05/25/2023]
Abstract
Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems comprising various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. Furthermore, a single probe was sufficient for the genome profiling, thereby demonstrating that this methodology is universal and compact.
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Affiliation(s)
- Mariko Kouduka
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| | - Daisuke Sato
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| | - Manabu Komori
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| | - Motohiro Kikuchi
- Chitose Salmon Aquarium Chitose, Youth Educational Foundation, Chitose, Hokkaido, Japan
| | - Kiyoshi Miyamoto
- Institute of Medical Science, Dokkyo Medical University, Tochigi, Japan
| | - Akinori Kosaku
- Institute of Medical Science, Dokkyo Medical University, Tochigi, Japan
| | - Mohammed Naimuddin
- Department of Functional Materials Science, Saitama University, Saitama, Japan
- Biol. Res. and Functions, National Inst. AIST, Tsukuba, Ibaraki, Japan
| | | | - Koichi Nishigaki
- Department of Functional Materials Science, Saitama University, Saitama, Japan
- Rational Evolutionary Design of Advanced Biomolecules, Saitama Small Enterprise Promotion Corporation, SKIP City, Saitama, Japan
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Kouduka M, Matuoka A, Nishigaki K. Acquisition of genome information from single-celled unculturable organisms (radiolaria) by exploiting genome profiling (GP). BMC Genomics 2006; 7:135. [PMID: 16740170 PMCID: PMC1523345 DOI: 10.1186/1471-2164-7-135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 06/02/2006] [Indexed: 11/21/2022] Open
Abstract
Background There is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians. Even worse, such organisms are often very difficult to collect. Sequence analysis of 18S rDNA has been carried out, but obtaining the data has been difficult and it has provided a rather limited amount of genome information. In this paper, we have developed a method which provides a sufficient amount of data from an unculturable organism. The effectiveness of this method was demonstrated by applying it to the provisional classification of a set of unculturable organisms (radiolarians). Results Dendrogram was drawn regarding the single-celled unculturable species based on the similarity score termed PaSS, offering a consistent result with the conventional taxonomy of them built up based on phenotypes. This fact has shown that genome profiling-based technology developed here can obtain genome information being sufficient for identifying and classifying species from a single-celled organism. Conclusion Since this method is so simple, general, and yet powerful, it can be applied to various organisms and cells, especially single-celled, uncluturable ones, for their genome analysis.
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Affiliation(s)
- Mariko Kouduka
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| | - Atsushi Matuoka
- Department of Geology Historical Geology, Niigata University, Niigata, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Saitama University, Saitama, Japan
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