• Research in Plant Disease
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• v.25 no.2
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• pp.49-61
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• 2019

Plant viruses are among the important pathogens that cause severe crop losses. The most efficient method to control viral diseases is currently to use virus resistant crops. In order to develop the virus resistant crops, a detailed understanding of the molecular interactions between viral and host proteins is necessary. Recessive resistance to a pathogen can be conferred when plant genes essential in the life cycle of a pathogens are deficient, while dominant resistance is mediated by host resistance (R) genes specifically interacting with effector proteins of pathogens. Thus, recessive resistance usually works more stably and broadly than dominant resistance. While most of the recessive resistance genes have so far been identified by forward genetic approaches, recent advances in genome editing technologies including CRISPR/Cas9 have increased interest in using these technologies as reverse genetic tools to engineer plant genes to confer recessive resistance. This review summarizes currently identified recessive resistance genes and introduces reverse genetic approaches to identify host interacting partner proteins of viral proteins and to evaluate the identified genes as genetic resources of recessive resistance. We further discuss recent advances in various precise genome editing technologies and how to apply these technologies to engineer plant immunity.

• Microbiology and Biotechnology Letters
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• v.49 no.4
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• pp.534-542
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• 2021

Single-molecular guide RNA (sgRNA) plays a role in recognizing the DNA target sequence in CRISPR technology for genome editing and gene expression control. In this study, we systematically compared the length of the target recognition sequence in sgRNAs required for genome editing using Cas9-NG (an engineered Cas9 recognizing 5'-NG as PAM sequence) and gene expression control using deactivated Cas9-NG (dCas9-NG) by targeting the gal promoter in E. coli. In the case of genome editing, the truncation of three nucleotides in the target recognition sequence (TRS) of sgRNA was allowed. In gene expression regulation, we observed that target recognition and binding were possible even if eleven nucleotides were deleted from twenty nucleotides of the TRS. When 4 or more nucleotides are truncated in the TRS of the sgRNA, it is thought that the sgRNA/Cas9-NG complex can specifically bind to the target DNA sequence, but lacks endonuclease activity to perform genome editing. Our study will be helpful in the development of artificial transcription factors and various CRISPR technologies in the field of synthetic biology.

• Genomics & Informatics
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• v.17 no.3
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• pp.23.1-23.6
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• 2019

The acquisition of somatic mutations is the most common event in cancer. Neoantigens expressed from genes with mutations acquired during carcinogenesis can be tumor-specific. Since the immune system recognizes tumor-specific peptides, they are potential targets for personalized neoantigen-based immunotherapy. However, the discovery of druggable neoantigens remains challenging, suggesting that a deeper understanding of the mechanism of neoantigen generation and better strategies to identify them will be required to realize the promise of neoantigen-based immunotherapy. Alternative splicing and RNA editing events are emerging mechanisms leading to neoantigen production. In this review, we outline recent work involving the large-scale screening of neoantigens produced by alternative splicing and RNA editing. We also describe strategies to predict and validate neoantigens from RNA sequencing data.

• BMB Reports
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• v.48 no.1
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• pp.6-12
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• 2015

Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future.

• Journal of Animal Reproduction and Biotechnology
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• v.34 no.2
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• pp.65-69
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• 2019

Since the development of the first genetically-modified mouse, transgenic animals have been utilized for a wide range of industrial applications as well as basic research. To date, these transgenic animals have been used in functional genomics studies, disease models, and therapeutic protein production. Recent advances in genome modification techniques such zinc finger nuclease (ZFN), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRIPSR)-Cas9, have led to rapid advancement in the generation of genome-tailored livestock, as well as experimental animals; however, the development of genome-edited poultry has shown considerably slower progress compared to that seen in mammals. Here, we will focus primarily on the technical strategies for production of transgenic and gene-edited chickens, and their potential for future applications.

• Genomics & Informatics
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• v.7 no.1
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• pp.46-48
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• 2009

Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.

• Genomics & Informatics
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• v.4 no.4
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• pp.170-172
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• 2006

ESTin is an easy-to-use tool that allows EST researchers to build a dbEST submission file with EST sequences and related data. The advantages of ESTin are its user-friendly interface, various editing functions, and rigorous validation function.

• Proceedings of the Korean Society of Crop Science Conference
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• 2020.11a
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• pp.109-109
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• 2020

• Proceedings of the Korean Society of Crop Science Conference
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• 2023.04a
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• pp.165-165
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• 2023

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.04a
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• pp.112-112
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• 2022