1
|
Fu L, Wang S, Liu L, Shibata Y, Okada M, Luu N, Shi YB. Simplifying Genotyping of Mutants from Genome Editing with a Parallel qPCR-Based iGenotype Index. Cells 2024; 13:247. [PMID: 38334640 PMCID: PMC10854663 DOI: 10.3390/cells13030247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Targeted genome editing is a powerful tool in reverse genetic studies of gene function in many aspects of biological and pathological processes. The CRISPR/Cas system or engineered endonucleases such as ZFNs and TALENs are the most widely used genome editing tools that are introduced into cells or fertilized eggs to generate double-strand DNA breaks within the targeted region, triggering cellular DNA repair through either homologous recombination or non-homologous end joining (NHEJ). DNA repair through the NHEJ mechanism is usually error-prone, leading to point mutations or indels (insertions and deletions) within the targeted region. Some of the mutations in embryos are germline transmissible, thus providing an effective way to generate model organisms with targeted gene mutations. However, point mutations and short indels are difficult to be effectively genotyped, often requiring time-consuming and costly DNA sequencing to obtain reliable results. Here, we developed a parallel qPCR assay in combination with an iGenotype index to allow simple and reliable genotyping. The genotype-associated iGenotype indexes converged to three simple genotype-specific constant values (1, 0, -1) regardless of allele-specific primers used in the parallel qPCR assays or gene mutations at wide ranges of PCR template concentrations, thus resulting in clear genotype-specific cutoffs, established through statistical analysis, for genotype identification. While we established such a genotyping assay in the Xenopus tropicalis model, the approach should be applicable to genotyping of any organism or cells and can be potentially used for large-scale, automated genotyping.
Collapse
Affiliation(s)
- Liezhen Fu
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
| | - Shouhong Wang
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Lusha Liu
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuki Shibata
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
- Department of Biology, Nippon Medical School, Tokyo 180-0023, Japan
| | - Morihiro Okada
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
| | - Nga Luu
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
| |
Collapse
|
2
|
Uenosono Y, Kawakami R, Matsumoto S, Yamaguchi Y. Construction of an experimental study and addition of adapter sequences using HiDi DNA polymerase for improving DNA normalization methods relevant to novel gene discovery. J Microbiol Methods 2023; 204:106631. [PMID: 36503828 DOI: 10.1016/j.mimet.2022.106631] [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: 09/14/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022]
Abstract
Microorganisms in the environment can be distinguished into dominant and rare microbial species based on their genes. It is difficult to obtain genetic information derived from rare microbial species (rare genes) because of the differences in relative abundance. DNA normalization is an approach that is used to obtain genetic information derived from rare microbial species from an environmental sample. This method involves the addition of adapter sequences for the amplification, denaturation, and reassociation of the DNA fragments and single-stranded DNA (ssDNA)/double-stranded DNA (dsDNA) separation. In this method, the amount of a high-copy-number of DNA fragments and a low-copy-number of DNA fragments can be equalized. Improvements in this technique are expected to provide novel genetic information or genes in rare microbial species. However, few model experimental systems have been reported to validate the DNA normalization techniques. This study is aimed to improve the DNA normalization technique used to obtain genetic information of rare genes from rare microbial species. An experimental study was constructed with two antibiotic resistance genes, whose copy numbers differed up to a million-fold. Both genes were mixed and the mixture of DNA fragments, of high- and low-copy-number, containing these genes was normalized by separating ssDNA/dsDNA fragments using hydroxyapatite. Normalized DNA fragments were introduced into Escherichia coli and DNA normalization was evaluated by counting colonies. Moreover, we improved the method to amplify a low-copy-number of DNA fragments by the addition of adapter sequences to DNA fragments using HiDi DNA polymerase to increase the efficiency of DNA normalization. This normalization method was achieved with a 100,000-fold difference. These methods allowed for quantitative evaluation of the DNA normalization efficiency. The experimental data and methods obtained in this study are expected to improve the DNA normalization efficiency to obtain novel genetic information or genes.
Collapse
Affiliation(s)
- Yuya Uenosono
- Department of Materials Science and Applied Chemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Chuo-ku, Kumamoto 860-8555, Japan
| | - Ryohei Kawakami
- Department of Materials Science and Applied Chemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Chuo-ku, Kumamoto 860-8555, Japan
| | - Shogo Matsumoto
- Department of Materials Science and Applied Chemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Chuo-ku, Kumamoto 860-8555, Japan
| | - Yoshihiro Yamaguchi
- Department of Materials Science and Applied Chemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Chuo-ku, Kumamoto 860-8555, Japan; Environmental Safety Center, Kumamoto University, 2-40-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.
| |
Collapse
|
3
|
Sakurai T, Shindo T. Production of single- and multiple-gene-modified mice via maternal SpCas9-based gene editing. STAR Protoc 2021; 2:100509. [PMID: 34027476 PMCID: PMC8122177 DOI: 10.1016/j.xpro.2021.100509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Maternally and transiently accumulated SpCas9 (maternal SpCas9) in a zygote derived from a systemically SpCas9-expressing transgenic mouse strain was used to generate single- and multiple-gene-modified mice. Maternal SpCas9-based gene editing allows for high indel and knockin mutation efficiency, low mosaicism, increased pup delivery rate, and simultaneous induction of mutations at multiple loci in contrast to conventional CRISPR/SpCas9-based gene editing. For complete details on the use and execution of this protocol, please refer to Sakurai et al. (2020).
Collapse
Affiliation(s)
- Takayuki Sakurai
- Department of Life Innovation, Institute for Biomedical Sciences, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.,Department of Cardiovascular Research, School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Shindo
- Department of Life Innovation, Institute for Biomedical Sciences, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.,Department of Cardiovascular Research, School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| |
Collapse
|
4
|
Yamasaki R, Goshima T, Oba K, Kanai M, Ohdoi R, Hirata D, Akao T. Development of sake yeast haploid set with diverse brewing properties using sake yeast strain Hiroshima no. 6 exhibiting sexual reproduction. J Biosci Bioeng 2020; 129:706-714. [PMID: 32085973 DOI: 10.1016/j.jbiosc.2020.01.005] [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: 12/18/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 10/25/2022]
Abstract
Among sake yeast strains, Kyokai no. 7 (K7) and its closely related strains (K7 group) are predominantly used because of their excellent brewing properties. In the sake industrial sector, the need for various types of yeast strains is high. Although crossbreeding is an effective method for generating genetic diversity that should result in diverse characteristics, most K7 group strains lack normal sporulation ability, including the ability to undergo meiotic chromosomal recombination, which leads to difficulties in crossbreeding. Accordingly, the improvement of sake yeast strains primarily depends on mutagenesis and suitable selection in a stepwise manner. Our recent study revealed that the long-preserved sake yeast strain Hiroshima no. 6 (H6) does not belong to the K7 group despite genetically being extremely similar. In addition, H6 exhibited normal sporulation. Thus, we isolated haploid cells from H6 and mated them with previously isolated haploid cells of K7 group strains. The crossbred diploid strains had normal sporulation ability; hence, we performed tetrad analysis. The brewing characteristics of the obtained haploid set were extremely diverse. Principal component analysis based on the volatile and organic acid components measured using small-scale sake brewing tests revealed that the haploid strains derived from each diploid strain displayed a characteristic distribution. Thus, we demonstrated the availability of genetic crossbreeding using H6 with sporulation ability to facilitate both the development of novel sake yeast strains with many desirable characteristics and analyses of the function of sake yeast.
Collapse
Affiliation(s)
- Risa Yamasaki
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Tetsuya Goshima
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
| | - Kenji Oba
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
| | - Ritsushi Ohdoi
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Dai Hirata
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; Sakeology Center, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan; Sake Research Center, Asahi Sake Brewing Co., Ltd., 880-1 Asahi, Nagaoka, Niigata 949-5494, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
| |
Collapse
|