Article
Biochemistry & Molecular Biology
Wataru Aiba, Takamitsu Amai, Mitsuyoshi Ueda, Kouichi Kuroda
Summary: This study successfully increased the efficiency of precise genome editing by creating a donor DNA/guide RNA hybrid duplex. Compared to editing with separately introduced gRNA and donor DNA, the HDR-mediated editing efficiency using this hybrid duplex technique was improved by 1.8-fold.
Review
Biochemistry & Molecular Biology
Chenyu Lu, Jingyu Kuang, Tong Shao, Sisi Xie, Ming Li, Lingyun Zhu, Lvyun Zhu
Summary: Prime editing technology has shown attractive potential for versatile genome editing ability, but improvements are needed in terms of editing efficiency, off-target effects, and delivery systems. Recent optimizations have resulted in promising prospects for its application in various fields. This review provides a concise insight into the development, barriers, optimization efforts, and application directions of prime editing, offering clues for future advancements in this emerging field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Dan Liang, Aleksei Mikhalchenko, Hong Ma, Nuria Marti Gutierrez, Tailai Chen, Yeonmi Lee, Sang-Wook Park, Rebecca Tippner-Hedges, Amy Koski, Hayley Darby, Ying Li, Crystal Van Dyken, Han Zhao, Keliang Wu, Jingye Zhang, Zhenzhen Hou, Seongjun So, Jongsuk Han, Jumi Park, Chong-Jai Kim, Kai Zong, Jianhui Gong, Yilin Yuan, Ying Gu, Yue Shen, Susan B. Olson, Hui Yang, David Battaglia, Thomas O'Leary, Sacha A. Krieg, David M. Lee, Diana H. Wu, P. Barton Duell, Sanjiv Kaul, Jin-Soo Kim, Stephen B. Heitner, Eunju Kang, Zi-Jiang Chen, Paula Amato, Shoukhrat Mitalipov
Summary: The range of DNA repair in response to double-strand breaks induced in human preimplantation embryos is uncertain due to the complexity of analyzing single- or few-cell samples. Whole genome amplification, which is necessary for sequencing such minute DNA input, can introduce artifacts that restrict genotyping accuracy. This study shows that allelic dropouts occur in over 25% of pre-existing heterozygous loci in control single blastomere samples after whole genome amplification. To overcome these limitations, the authors validate gene editing seen in human embryos by studying embryonic stem cells.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Yang Ni, Xinyi Zhang, Jingling Li, Qianqi Lu, Haimei Chen, Binxin Ma, Chang Liu
Summary: In this study, the mitochondrial genome of Coffea arabica L. was sequenced and characterized. The genome is composed of two circular chromosomes encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. Simple Sequence Repeats and tandem repeats were also detected in the genome. Recombination events and RNA editing events were identified, providing insights into the genetic characteristics and gene regulation of C. arabica mitochondria. These findings have important implications for coffee breeding, evolution, and the development of molecular markers.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Xueli Zhang, Chaohui Zhang, Caijiao Liang, Bizhou Li, Fanmei Meng, Yuncan Ai
Summary: Bacteriophages, the most abundant organisms in the biosphere, have been sequenced extensively. However, the study of bacteriophage functional genomics has been hindered by a lack of effective research methods. This study designed a phage genome editing platform based on the CRISPR-Cas9 system, and successfully achieved gene editing in Vibrio natriegens phage TT4P2. This platform has the potential to advance research on phage gene diversity and accelerate the development of phage synthetic biology and nanotechnology.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Takuya Abe, Yuya Suzuki, Teppei Ikeya, Kouji Hirota
Summary: Research suggests that manipulation of trisomic chromosomes can create unique artificial chromosomes. Trisomic chromosome 2 has minimal impact on the proliferative capacity of DT40 cells, and truncation of chromosome 2 by introducing telomere repeat sequences can create a mini-chromosome whose stability can be influenced by reducing the cohesin regulatory protein DDX11.
SCIENTIFIC REPORTS
(2021)
Editorial Material
Cell & Tissue Engineering
Daniel E. Bauer
Summary: In this study, Ferrari et al. identified issues with commonly used AAV donors in gene editing, including weakened hematopoietic repopulation and frequent genomic integrations.
Editorial Material
Genetics & Heredity
Kevin Davies
Summary: Thirty years ago, Nature Genetics was launched as the first spin-off journal bearing the famous Nature logo. With the Human Genome Project as a driving force, there were high expectations for the new journal and the future of human genetics. Over the past 30 years, significant progress has been made in the field of genetics.
Article
Multidisciplinary Sciences
Susie Suh, Elliot H. Choi, Aditya Raguram, David R. Liu, Krzysztof Palczewski
Summary: CRISPR-Cas genome editing technologies have the potential to treat a wide range of inherited diseases, including genetic disorders of vision. Recent advancements in precision genome editing agents and delivery technologies allow for precise gene correction and improved safety in therapeutic settings. These improvements could revolutionize the treatment of genetic disorders of vision.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
I. F. Schene, I. P. Joore, J. H. L. Baijens, R. Stevelink, G. Kok, S. Shehata, E. F. Ilcken, E. C. M. Nieuwenhuis, D. P. Bolhuis, R. C. M. van Rees, S. A. Spelier, H. P. J. van der Doef, J. M. Beekman, R. H. J. Houwen, E. E. S. Nieuwenhuis, S. A. Fuchs
Summary: This study presents a fluorescent prime editing and enrichment reporter (fluoPEER) system to evaluate the efficiency of pegRNAs and prime editor variants. The results show that stalling cells in the G1/S boundary can increase prime editing efficiency, and plasmid editing enriches for genomic editing. The findings demonstrate that fluoPEER can be used for rapid and efficient correction of patient cells, selection of gene-edited cells, and elucidation of cellular mechanisms needed for successful prime editing.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Daoheng Hu, Yiming Yu, Chun Wang, Yanping Long, Yue Liu, Li Feng, Dongdong Lu, Bo Liu, Jinbu Jia, Rui Xia, Jiamu Du, Xuehua Zhong, Lei Gong, Kejian Wang, Jixian Zhai
Summary: This study utilized CRISPR-Cas9 technology to edit all nine DNA methyltransferases in rice, revealing the significant roles of certain methyltransferases in maintaining non-CG methylation in rice.
Review
Biotechnology & Applied Microbiology
Tara Murty, Crystal L. Mackall
Summary: Gene editing platforms are being explored to enhance the potency of adoptive T cell therapies by knocking out molecules that inhibit immune responses and improving gene expression profiles. These approaches also aim to create off-the-shelf therapies that can prevent immune rejection, thus increasing the effectiveness and ease of use of these treatments.
Article
Multidisciplinary Sciences
Issei Nakazato, Miki Okuno, Chang Zhou, Takehiko Itoh, Nobuhiro Tsutsumi, Mizuki Takenaka, Shin-Ichi Arimura
Summary: In addition to their role in respiration, mitochondria in land plants contain important genes whose functions and regulations are not fully understood. Until recently, it has been challenging to analyze and improve these genes due to the lack of methods for stably modifying plant mitochondrial genomes. However, the use of mitochondria-targeting transcription activator-like effector nucleases (mitoTALENs) has provided a breakthrough in gene disruption without causing major changes in genome structure. This study demonstrates the successful use of mitochondria-targeting TALEN-based cytidine deaminase to substitute targeted base pairs in plant mitochondrial genomes, highlighting the potential for precise genetic modifications in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Mauro Mandrioli
Summary: In the last decade, genome editing technologies have become highly effective and are being used in clinical trials for treating genetic diseases. However, the debate about the bioethical and regulatory practices of genome editing still lacks satisfactory answers, despite over 50 years of discussions on the frontiers of genetics in human health and evolution. The delay in finding answers is due to an excessive focus on the effectiveness of the technologies in regulatory practices, rather than considering other factors such as accessibility and acceptability at a bioethical level.
Review
Biochemistry & Molecular Biology
Hyun-Min Kim, Yebin Hong, Jiani Chen
Summary: CRISPR-Cas enables highly efficient genome editing, allowing the introduction of desired modifications such as mutations and deletions. C. elegans has emerged as a significant model organism for CRISPR-Cas, with numerous strategies established. However, the abundance of methods makes it challenging to choose the correct approach, highlighting the importance of selecting appropriate screening methods for genome modification planning.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Tetsuya Suzuki, Yusuke Wakao, Takuya Goda, Hiroyuki Kamiya
JOURNAL OF GENE MEDICINE
(2020)
Article
Genetics & Heredity
Tetsuya Suzuki, Yuri Katayama, Yasuo Komatsu, Hiroyuki Kamiya
Article
Biochemistry & Molecular Biology
Hidehiko Kawai, Kento Sato, Wataru Shirahama, Tetsuya Suzuki, Hiroyuki Kamiya
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS
(2020)
Article
Multidisciplinary Sciences
Ayuna Takeishi, Hiroyuki Kogashi, Mizuki Odagiri, Hiroyuki Sasanuma, Shunichi Takeda, Manabu Yasui, Masamitsu Honma, Tetsuya Suzuki, Hiroyuki Kamiya, Kaoru Sugasawa, Kiyoe Ura, Akira Sassa
Article
Cell Biology
Takashi Imada, Takeshi Shimi, Ai Kaiho, Yasushi Saeki, Hiroshi Kimura
Summary: In eukaryotic nuclei, various phase-separated nuclear bodies (NBs) coexist, with Pol II playing a critical role in transcription and interacting with CBs and HLBs. PCs increase during S phase, coinciding with the activation of histone genes, and form ternary associations with CBs and HLBs.
Article
Biotechnology & Applied Microbiology
Hidehiko Kawai, Kentaro Yazama, Yuri Yanai, Ryotaro Kamitsubo, Hiroyuki Kamiya
Summary: The study found that 5'-TDs with 100-base ss editor DNAs were as effective in gene correction as those with longer editor DNAs. Additionally, the antisense strand was more effective as the editor than the sense strand. These results suggest that 5'-TD fragments with shorter editor strands are useful for gene correction.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2021)
Article
Genetics & Heredity
Tetsuya Suzuki, Hiroshi Masuda, Madoka Mori, Rikako Ito, Hiroyuki Kamiya
Summary: In human cells, G:C sites distant from 8-oxo-7,8-dihydroguanine are frequently mutated when the Werner syndrome (WRN) protein is reduced. The study suggests the involvement of APOBEC3-family cytosine deaminases in untargeted mutations at G:C sites induced by G degrees and in cancer initiation by oxidative stress.
Article
Genetics & Heredity
Tetsuya Suzuki, Yudai Zaima, Yoshihiro Fujikawa, Ruriko Fukushima, Hiroyuki Kamiya
Summary: Oxidatively damaged bases can induce mutations, and 8-hydroxyguanine is a common oxidized base that can cause targeted and untargeted base substitution mutations. The frequency of untargeted mutations increases when the Werner syndrome protein is decreased. In this study, knocking down both OGG1 and WRN resulted in fewer untargeted mutations compared to knocking down WRN alone, suggesting the paradoxical role of OGG1 in accelerating untargeted mutations caused by oxidized guanine base.
Article
Biotechnology & Applied Microbiology
Hidehiko Kawai, Ryotaro Kamitsubo, Hiroyuki Kamiya
Summary: Mutations of important genes can cause various disorders, including cancer. Recent research has shown that a new version of a double-stranded structure can correct base substitution mutations in target genes in human cells. The experiments demonstrated the effective gene editing capabilities of this structure.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2022)
Article
Biology
Hidehiko Kawai, Ren Iwata, Shungo Ebi, Ryusei Sugihara, Shogo Masuda, Chiho Fujiwara, Shingo Kimura, Hiroyuki Kamiya
Summary: This study presents an advanced method for mutation analysis using the supF gene. The method is simple, versatile, and cost-effective, and provides valuable insights into mutation frequencies and spectra. The results reveal previously undetected mutations and offer a novel perspective on the mechanisms of mutagenesis.
Article
Genetics & Heredity
Tetsuya Suzuki, Hiroyuki Kamiya
Summary: In this report, a new arabinose-inducible ss phagemid production method without helper phage infection was described. This method allows for consistent production of large quantities of phagemid ss DNA of interest, with reduced contamination from VCSM13 DNA.
GENES AND ENVIRONMENT
(2022)
Article
Biotechnology & Applied Microbiology
Ruriko Fukushima, Tetsuya Suzuki, Yasuo Komatsu, Hiroyuki Kamiya
Summary: 8-Oxo-7,8-dihydroguanine (8-hydroxyguanine, G?) is a major oxidized base that plays pivotal roles in various diseases. The study found that oxidized bases located downstream of genes and on the lagging strand template are more likely to induce action-at-a-distance mutations.
MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS
(2022)
Article
Toxicology
Tetsuya Suzuki, Yuri Katayama, Yasuo Komatsu, Hiroyuki Kamiya
Summary: Studies have shown that abasic sites formed in cells may be involved in cancer, but mutations caused by certain abasic site analogs may not necessarily be affected by human apurinic/apyrimidinic endonuclease 1.
JOURNAL OF TOXICOLOGICAL SCIENCES
(2021)
Editorial Material
Genetics & Heredity
Hiroyuki Kamiya
GENES AND ENVIRONMENT
(2020)
Article
Genetics & Heredity
Ruriko Fukushima, Tetsuya Suzuki, Hiroyuki Kamiya
GENES AND ENVIRONMENT
(2020)
