• 농업과학연구
• /
• 제46권4호
• /
• pp.885-895
• /
• 2019

Plant biotechnologists have long dreamed of technologies to manipulate genes in plants at will. This dream has come true partly through the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, which now has been used to edit genes in several important crops. However, there are many restrictions in editing a gene precisely using the CRISPR/Cas9 technology because CRISPR/Cas9 may cause deletions or additions in some regions of the target gene. Several other technologies have been developed for gene targeting and precision editing. Among these, base editors might be the most practically and efficiently used compared to others. Base editors are tools which are able to cause a transition from cytosine into thymine, or from adenine into guanine very precisely on specific sequences. Cytosine base editors basically consist of nCas9, cytosine deaminase, and uracil DNA glycosylase inhibitor (UGI). Adenine base editors consist of nCas9 and adenine deaminase. These were first developed for human cells and have since also been applied successfully to crops. Base editors have been successfully applied for productivity improvement, fortification and herbicide resistance of crops. Thus, base editor technologies start to open a new era for precision gene editing or breeding in crops and might result in revolutionary changes in crop breeding and biotechnology.

• International Journal of Stem Cells
• /
• 제16권2호
• /
• pp.234-243
• /
• 2023

The recent advances in human pluripotent stem cells (hPSCs) enable to precisely edit the desired bases in hPSCs to be used for the establishment of isogenic disease models and autologous ex vivo cell therapy. The knock-in approach based on the homologous directed repair with Cas9 endonuclease, causing DNA double-strand breaks (DSBs), produces not only insertion and deletion (indel) mutations but also deleterious large deletions. On the contrary, due to the lack of Cas9 endonuclease activity, base editors (BEs) such as adenine base editor (ABE) and cytosine base editor (CBE) allow precise base substitution by conjugated deaminase activity, free from DSB formation. Despite the limitation of BEs in transition substitution, precise base editing by BEs with no massive off-targets is suggested to be a prospective alternative in hPSCs for clinical applications. Considering the unique cellular characteristics of hPSCs, a few points should be considered. Herein, we describe an updated and optimized protocol for base editing in hPSCs. We also describe an improved methodology for CBE-based C to T substitutions, which are generally lower than A to G substitutions in hPSCs.

• 산업기술연구
• /
• 제42권1호
• /
• pp.29-36
• /
• 2022

The CRISPR system has revolutionized gene editing field. Cas9-mediated gene editing such as Indel induction or HDR enable targeted gene disruption or precise correction of mutation. Moreover, CRISPR-based new editing tools have been developed such as base editors. In this review, we focus on gene editing in human pluripotent stem cells, which is principal technique for gene correction therapy and disease modeling. Pluripotent stem cell-specific drug YM155 enabled selection of target gene-edited pluripotent stem cells. Also, we discussed base editing for treatment of congenital retina disease. Adenine base editor delivery as RNP form provide an approach for genetic disease treatment with safe and precise in vivo gene correction.

• BMB Reports
• /
• 제57권1호
• /
• pp.30-39
• /
• 2024

Directed evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates have been developed to facilitate DE in native genetic environments of multicellular organisms. Notably, deaminase-based base editing-TRM (BE-TRM) tools have greatly expanded the scope and efficiency of DE schemes by enabling base substitutions and randomization of targeted DNA sequences. BE-TRM tools provide a robust platform for the continuous molecular evolution of desired proteins, metabolic pathway engineering, creation of a mutant library of desired locus to evolve novel functions, and other applications, such as predicting mutants conferring antibiotic resistance. This review provides timely updates on the recent advances in BE-TRM tools for DE, their applications in biology, and future directions for further improvements.

• BMB Reports
• /
• 제52권8호
• /
• pp.475-481
• /
• 2019

The evolution of genome editing technology based on CRISPR (clustered regularly interspaced short palindromic repeats) system has led to a paradigm shift in biological research. CRISPR/Cas9-guide RNA complexes enable rapid and efficient genome editing in mammalian cells. This system induces double-stranded DNA breaks (DSBs) at target sites and most DNA breakages induce mutations as small insertions or deletions (indels) by non-homologous end joining (NHEJ) repair pathway. However, for more precise correction as knock-in or replacement of DNA base pairs, using the homology-directed repair (HDR) pathway is essential. Until now, many trials have greatly enhanced knock-in or substitution efficiency by increasing HDR efficiency, or newly developed methods such as Base Editors (BEs). However, accuracy remains unsatisfactory. In this review, we summarize studies to overcome the limitations of HDR using the CRISPR system and discuss future direction.

• BMB Reports
• /
• 제57권1호
• /
• pp.19-29
• /
• 2024

Mitochondrial DNA (mtDNA), a multicopy genome found in mitochondria, is crucial for oxidative phosphorylation. Mutations in mtDNA can lead to severe mitochondrial dysfunction in tissues and organs with high energy demand. MtDNA mutations are closely associated with mitochondrial and age-related disease. To better understand the functional role of mtDNA and work toward developing therapeutics, it is essential to advance technology that is capable of manipulating the mitochondrial genome. This review discusses ongoing efforts in mitochondrial genome editing with mtDNA nucleases and base editors, including the tools, delivery strategies, and applications. Future advances in mitochondrial genome editing to address challenges regarding their efficiency and specificity can achieve the promise of therapeutic genome editing.

• Molecules and Cells
• /
• 제40권11호
• /
• pp.823-827
• /
• 2017

Genome editing using programmable nucleases such as CRISPR/Cas9 or Cpf1 has emerged as powerful tools for gene knock-out or knock-in in various organisms. While most genetic diseases are caused by point mutations, these genome-editing approaches are inefficient in inducing single-nucleotide substitutions. Recently, Cas9-linked cytidine deaminases, named base editors (BEs), have been shown to convert cytidine to uridine efficiently, leading to targeted single-base pair substitutions in human cells and organisms. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. Injection of base editor 3 (BE3) ribonucleoprotein targeting the tyrosinase (tyr) gene in early embryos can induce site-specific base conversions with the rates of up to 20.5%, resulting in oculocutaneous albinism phenotypes without off-target mutations. We further test this base-editing system by targeting the tp53 gene with the result that the expected single-base pair substitutions are observed at the target site. Collectively, these data establish that the programmable deaminases are efficient tools for creating targeted point mutations for human disease modeling in Xenopus.

• 한국미생물·생명공학회지
• /
• 제51권4호
• /
• pp.374-389
• /
• 2023

Organophosphorus (OP) pesticides, particularly malathion, parathion, diazinon, and chlorpyrifos, are widely used in both agricultural and residential contexts. This refractory quality is shared by certain organ phosphorus insecticides, and it may have unintended consequences for certain non-target soil species. Bioremediation cleans organic and inorganic contaminants using microbes and plants. Organophosphate-hydrolyzing enzymes can transform pesticide residues into non-hazardous byproducts and are increasingly being considered viable solutions to the problem of decontamination. When coupled with system analysis, the multi-omics technique produces important data for functional validation and genetic manipulation, both of which may be used to boost the efficiency of bioremediation systems. RNA-guided nucleases and RNA-guided base editors include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR), which are used to alter genes and edit genomes. The review sheds light on key knowledge gaps and suggests approaches to pesticide cleanup using a variety of microbe-assisted methods. Researches, ecologists, and decision-makers can all benefit from having a better understanding of the usefulness and application of systems biology and gene editing in bioremediation evaluations.

• Asian Pacific Journal of Cancer Prevention
• /
• 제14권6호
• /
• pp.3377-3378
• /
• 2013

The APJCP Impact Factor for 2012 is 1.271, returning from 0.659 for 2011 (1.240 for 2010 and 1.108 for 2009). For an Asian Pacific journal publishing over 100 papers a month from countries with very varied resources it is heartening and we thank all those who continued to submit papers and cite references in the APJCP through our difficult period. However, we still have very much room for improvement. As Chief Editors it is our shared responsibility to act for the benefit of the cancer control research community who utilize the journal in our region of over four billion people and provide a prestigious forum for publication of research findings which can be freely shared by all. The motivation for the APOCP/APJCP has never been financial profit but a firm financial base is nevertheless essential. Although we have kind support from the Korean National Cancer Center for our Managing Editor and the website, our ability to maintain our Chinese and Thai offices is totally dependent on the processing charges paid by the authors. In order to expand our staff to cope with increased submissions and provide greater assistance in ensuring comprehensive reference coverage and dissemination of findings published in the APJCP to the worldwide research community, a joint decision has been made to increase formatting charges by 50% from July. We ask for author understanding. In addition, we appeal to scientists to positively consider our requests to make their reference lists as comprehensive as possible, including papers from the APJCP where appropriate. The future of the journal and the APOCP is largely in your own hands.

• 한국IT서비스학회지
• /
• 제22권5호
• /
• pp.71-86
• /
• 2023

Recently, various geographic information systems have been used based on spatial information of geographic information systems. Accordingly, it is essential to produce a large-scale map as a small-scale map for various uses of spatial information. However, maps currently being produced have inconsistencies between data due to production timing and limitations in expression, and productivity efficiency is greatly reduced due to errors in products or overlapping processes. In order to improve this, various efforts are being made, such as publishing research and reports for automating domestic mapping, but because there is no specific result, it relies on editors to make maps. This is mainly done by hand, so the time required for mapping is excessive, and quality control for each producer is different. In order to solve these problems, technology that can be automatically produced through computer programs is needed. Research has been conducted to apply the rule base to geometric generalization. The algorithm tolerance setting applied to rule-based modeling is a factor that greatly affects the result, and the level of the result changes accordingly. In this paper, we tried to study the effectiveness of mapping according to tolerance setting. To this end, the utility was verified by comparing it with a manually produced map. In addition, the original data and reduction rate were analyzed by applying generalization algorithms and tolerance values. Although there are some differences by region, it was confirmed that the complexity decreased on average. Through this, it is expected to contribute to the use of spatial information-based services by improving tolerances suitable for small-scale mapping regulations in order to secure spatial information data that guarantees consistency and accuracy.