Article
Biotechnology & Applied Microbiology
Hui Kwon Kim, Goosang Yu, Jinman Park, Seonwoo Min, Sungtae Lee, Sungroh Yoon, Hyongbum Henry Kim
Summary: This study identified factors affecting PE2 efficiency through high-throughput evaluation and developed three computational models to predict pegRNA efficiency, which can be applied to edits of various types and positions. Spearman's correlations between 0.47 and 0.81 were found when testing the accuracy of the predictions using independent test data sets.
NATURE BIOTECHNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Zhangrao Huang, Gang Liu
Summary: Prime editing is a precise genome manipulation technology that utilizes the CRISPR-Cas9 system's search and replace approach, without the need for exogenous donor DNA and DNA double-strand breaks (DSBs). It offers a wider editing scope compared to base editing. Prime editing has shown promise in breeding and genomic functional studies of animals and plants, disease treatment, and modification of microbial strains, as it has been successfully applied in various plant cells, animal cells, and Escherichia coli. This paper provides a brief overview of the basic strategies of prime editing, summarizes its research progress and prospects in multiple species, and outlines various optimization strategies to improve its efficiency and specificity.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Stefan J. Tekel, Nicholas Brookhouser, Kylie Standage-Beier, Xiao Wang, David A. Brafman
Summary: The introduction of transient reporters of editing enrichment (TREE) has enabled highly efficient single-base editing of human cells using a transient episomal fluorescent reporter, allowing for rapid generation of clonal editing efficiencies exceeding 80% in biallelic or multiplexed edited isogenic human pluripotent stem cell lines within approximately 3-4 weeks.
Review
Agriculture, Dairy & Animal Science
Julia Popova, Victoria Bets, Elena Kozhevnikova
Summary: Genome editing has practical applications in farm animals, improving production traits, economic value, and disease resistance. It also has potential in biomedical research and drug production, as well as xenograft donors. Recent advancements in site-specific nucleases and embryological delivery methods have revolutionized transgenesis, providing efficient and reliable tools for genome engineering in agriculture.
Article
Biochemistry & Molecular Biology
Pierre-Francois Perroud, Anouchka Guyon-Debast, Florian Veillet, Marie-Paule Kermarrec, Laura Chauvin, Jean-Eric Chauvin, Jean-Luc Gallois, Fabien Nogue
Summary: The introduction of CRISPR-Cas9 technology has revolutionized plant research and precision crop breeding, while the development of Prime Editing technology has opened up new possibilities for precise genome editing in plants. Successful application of Prime Editing in Physcomitrium patens and potato demonstrated its unique advantage in introducing nucleotide substitutions, with high targeting fidelity observed in P. patens.
Review
Biochemistry & Molecular Biology
Yulin Mu, Chengxiao Zhang, Taihua Li, Feng-Jie Jin, Yun-Ju Sung, Hee-Mock Oh, Hyung-Gwan Lee, Long Jin
Summary: Lactobacillus, important in food production and probiotics, can benefit from CRISPR/Cas9-based genome editing to improve strain efficiency and achieve traceless genome modification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Justin A. Bosch, Gabriel Birchak, Norbert Perrimon
Summary: The study successfully applied prime editing in Drosophila to introduce premature stop codons and achieve efficient germline transmission, demonstrating its potential for studying gene function in Drosophila.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Plant Sciences
Jagesh Kumar Tiwari, Anand Kumar Singh, Tusar Kanti Behera
Summary: The narrow genetic base of tomato presents challenges in breeding, but with the development of CRISPR/Cas9 genome editing, fast and efficient breeding has become possible. CRISPR/Cas9 has been used to edit and characterize various traits in tomato, such as plant architecture, flower characters, fruit quality, disease resistance, and stress tolerance. It has also been used to introduce elite traits from wild relatives to cultivated tomatoes. This mini-review highlights the current research progress in using CRISPR/Cas9 for tomato breeding.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
K. Lakshmi Jayaraj, Nitu Thulasidharan, Aju Antony, Moni John, Rehna Augustine, Navajeet Chakravartty, Smitha Sukumaran, M. Uma Maheswari, Sweety Abraham, George Thomas, V. B. Reddy Lachagari, Somasekar Seshagiri, Subhash Narayanan, Boney Kuriakose
Summary: CRISPR/Cas9 system-induced deletion in the 5' UTR of the carotenoid isomerase gene in tomato resulted in downregulation of the gene and altered plant phenotype. This targeted gene editing technique shows potential significance in improving crop traits.
PLANT CELL REPORTS
(2021)
Article
Biochemical Research Methods
Lijun Hao, Xiangdong Pu, Jingyuan Song
Summary: Prime editing, a new gene editing technology based on CRISPR/Cas, allows for direct and precise editing of specified DNA sites without double strand breaks and donor DNA, offering a wider range of editing types and potential editing capabilities compared to traditional CRISPR/Cas9 and base editing. Successfully developed in mammalian cells and applied in plants, prime editing has the advantage of direct DNA editing without causing double strand breaks, providing a new approach for genetic improvement in plants.
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)
Review
Pharmacology & Pharmacy
Siwei Chen, Deng Chen, Bin Liu, Hidde J. Haisma
Summary: CRISPR/Cas9-mediated genome engineering has extensive applications in basic biology, biotechnology, and medicine. However, the low gene modification efficiency and uncontrollable prolonged Cas9 activity hinder its further use. Researchers have explored small molecules with clinical potential to precisely modulate CRISPR/Cas9 genome editing activity.
DRUG DISCOVERY TODAY
(2022)
Review
Biochemistry & Molecular Biology
Min Ho Lee, Jae Il Shin, Jae Won Yang, Keum Hwa Lee, Do Hyeon Cha, Jun Beom Hong, Yeoeun Park, Eugene Choi, Kalthoum Tizaoui, Ai Koyanagi, Louis Jacob, Seoyeon Park, Ji Hong Kim, Lee Smith
Summary: This review highlights the current and potential use of CRISPR-Cas9 in the management of autoimmune diseases. Several studies have shown that CRISPR-Cas9 can be utilized for immunomodulation, reducing cholesterol, and treating rare diseases. However, there is limited research on the treatment of autoimmune diseases using CRISPR-Cas9.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Kristina J. Tatiossian, Robert D. E. Clark, Chun Huang, Matthew E. Thornton, Brendan H. Grubbs, Paula M. Cannon
Summary: This study found that CRISPR-Cas9 indel signatures can be used to identify gRNAs that maximize HDR outcomes, with the frequency of deletions resulting from MMEJ repair of at least 3 base pairs better predicts HDR frequency. Existing tools can be repurposed to identify gRNAs that promote HDR.
Article
Biochemical Research Methods
Kylie Standage-Beier, Stefan J. Tekel, David A. Brafman, Xiao Wang
Summary: This study introduces a software tool called PINE-CONE which enables high-throughput automated design of pegRNAs and prime editing strategies. By translating edit coordinates and sequences into required designs, PINE-CONE accelerates the application of PE technology in synthetic biology and biomedical research.
ACS SYNTHETIC BIOLOGY
(2021)
Letter
Biochemistry & Molecular Biology
Yuming Lu, Jian-Kang Zhu
Letter
Biochemistry & Molecular Biology
Mugui Wang, Yuming Lu, Jose Ramon Botella, Yanfei Mao, Kai Hua, Jian-kang Zhu
Letter
Biochemistry & Molecular Biology
Mugui Wang, Yanfei Mao, Yuming Lu, Xiaoping Tao, Jian-kang Zhu
Letter
Biochemistry & Molecular Biology
Yuming Lu, Xiao Ye, Renming Guo, Jing Huang, Wei Wang, Jiuyou Tang, Longtao Tan, Jian-kang Zhu, Chengcai Chu, Yangwen Qian
Article
Biochemistry & Molecular Biology
Mugui Wang, Yanfei Mao, Yuming Lu, Zhidan Wang, Xiaoping Tao, Jian-Kang Zhu
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2018)
Review
Plant Sciences
Ashish Kumar Srivastava, Yuming Lu, Gaurav Zinta, Zhaobo Lang, Jian-Kang Zhu
TRENDS IN PLANT SCIENCE
(2018)
Article
Plant Sciences
Yanping Wang, Lin Li, Tiantian Ye, Yuming Lu, Xi Chen, Yan Wu
JOURNAL OF EXPERIMENTAL BOTANY
(2013)
Article
Multidisciplinary Sciences
Yuming Lu, Xi Chen, Yuxuan Wu, Yanping Wang, Yuqing He, Yan Wu
Article
Mathematical & Computational Biology
Jie Xiong, Yuming Lu, Jinmei Feng, Dongxia Yuan, Miao Tian, Yue Chang, Chengjie Fu, Guangying Wang, Honghui Zeng, Wei Miao
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2013)
Letter
Biotechnology & Applied Microbiology
Mugui Wang, Zhidan Wang, Yanfei Mao, Yuming Lu, Ruifang Yang, Xiaoping Tao, Jian-Kang Zhu
PLANT BIOTECHNOLOGY JOURNAL
(2019)
Article
Biochemistry & Molecular Biology
Hai-Jun Liu, Liumei Jian, Jieting Xu, Qinghua Zhang, Maolin Zhang, Minliang Jin, Yong Peng, Jiali Yan, Baozhu Han, Jie Liu, Fan Gao, Xiangguo Liu, Lei Huang, Wenjie Wei, Yunxiu Ding, Xiaofeng Yang, Zhenxian Li, Mingliang Zhang, Jiamin Sun, Minji Bai, Wenhao Song, Hanmo Chen, Xi'ang Sun, Wenqiang Li, Yuming Lu, Ya Liu, Jiuran Zhao, Yangwen Qian, David Jackson, Alisdair R. Fernie, Jianbing Yan
Article
Biotechnology & Applied Microbiology
Yuming Lu, Yifu Tian, Rundong Shen, Qi Yao, Mugui Wang, Mei Chen, Jinsong Dong, Tongen Zhang, Feng Li, Mingguang Lei, Jian-Kang Zhu
NATURE BIOTECHNOLOGY
(2020)
Review
Biochemistry & Molecular Biology
Xiangqiang Zhan, Yuming Lu, Jian-Kang Zhu, Jose Ramon Botella
Summary: The CRISPR technology has significantly impacted plant biology and crop improvement, with developments ranging from gene disruption to precise editing techniques like base editing and gene targeting. Advances have also been made in using different CRISPR systems for gene transcription and epigenome control.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Yuming Lu, Pamela C. Ronald, Bin Han, Jiayang Li, Jian-Kang Zhu
Article
Biotechnology & Applied Microbiology
Xue-Mei Yang, Jing-Hao Zhao, Xiao-Yu Xiong, Zhang-Wei Hu, Ji-Fen Sun, Hao Su, Yan-Jing Liu, Ling Xiang, Yong Zhu, Jin-Lu Li, Sadam Hussain Bhutto, Guo-Bang Li, Shi-Xin Zhou, Chi Li, Mei Pu, He Wang, Zhi-Xue Zhao, Ji-Wei Zhang, Yan-Yan Huang, Jing Fan, Wen-Ming Wang, Yan Li
Summary: The Arabidopsis RPW8.1 gene enhances disease resistance but compromises plant growth. It has been found that RPW8.1 constitutively enhances the expression of WRKY51 transcription factor and activates salicylic acid and ethylene signaling pathways. WRKY51, in turn, suppresses RPW8.1 expression, forming a feedback regulation loop.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Hannes Claeys, Eveline Neyrinck, Lies Dumoulin, Anne Pharazyn, Arne Verstichele, Laurens Pauwels, Michael L. Nuccio, Frederic Van Ex
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Melanie Ormancey, Bruno Guillotin, Camille Ribeyre, Clemence Medina, Nathanael Jariais, Helene San Clemente, Patrice Thuleau, Serge Plaza, Martina Beck, Jean-Philippe Combier
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Edgar Perez-Matas, Diego Hidalgo-Martinez, Elisabeth Moyano, Javier Palazon, Mercedes Bonfill
Summary: In this study, the production of paclitaxel was enhanced by overexpressing the bottleneck genes BAPT and DBTNBT in Taxus baccata cells. The transgenic cells showed significantly higher expression of these genes and improved taxane production compared to the wild type. Transcriptional profiling revealed that the GGPPS, TXS, and DBAT genes were most responsive to DBTNBT overexpression and the dual elicitation treatment.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Biying Dong, Dong Meng, Zhihua Song, Hongyan Cao, Tingting Du, Meng Qi, Shengjie Wang, Jingyi Xue, Qing Yang, Yujie Fu
Summary: This study identified the involvement of the citrate transporter CcMATE35 and the long noncoding RNA CcLTCS in aluminum stress response in pigeon pea. These findings suggest that the modules CcNFYB3-CcMATE35 and CcLTCS-CcCS jointly regulate the efflux and synthesis of citrate to enhance the resistance of pigeon pea under aluminum stress.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Review
Biotechnology & Applied Microbiology
Tien V. Vu, Ngan Thi Nguyen, Jihae Kim, Jong Chan Hong, Jae-Yean Kim
Summary: Prime editing technology uses an extended guide RNA to direct a fusion peptide to a specific location in the genome, enabling precise gene editing. This groundbreaking tool has potential in improving crop varieties, but efficiency limitations exist in certain plants.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Yan Xu, Jinyi Tan, Junxing Lu, Yuelin Zhang, Xin Li
Summary: Sclerotinia sclerotiorum causes white mold in economically important plants, and the discovery of SsGAP1 and SsRAS1/SsRAS2 genes as essential regulators of fungal development and virulence provides potential targets for controlling the disease.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Xiaoyang Chen, Chen Liu, Hailin Wang, Qi Liu, Yaping Yue, Yuhang Duan, Zhaoyun Wang, Lu Zheng, Xiaolin Chen, Yaohui Wang, Junbin Huang, Qiutao Xu, Yuemin Pan
Summary: This study identified a secreted protein, Uv1809, as a key virulence factor in Ustilaginoidea virens-rice interactions. Uv1809 inhibits rice immunity and promotes infection by targeting and enhancing rice histone deacetylase OsSRT2-mediated histone deacetylation. CRISPR-Cas9 edited ossrt2 mutants showed broad-spectrum resistance to rice pathogens, indicating its potential as a genetic resource for breeding disease resistance.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Weishuai Bi, Jing Liu, Yuanyuan Li, Ziwei He, Yongming Chen, Tingting Zhao, Xiangxiu Liang, Xiaodan Wang, Xiangzong Meng, Daolong Dou, Guangyuan Xu
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Shengjie You, Yu Wu, Wen Li, Xiaofeng Liu, Qinlan Tang, Fengkun Huang, Yan Li, Hsihua Wang, Mingchun Liu, Yang Zhang
Summary: In this study, a transcription factor called SlERF.G3-Like in tomato was found to play a role in regulating ethylene synthesis, cell wall degradation, and the flavonoid pathway. The researchers also discovered the interaction between SlERF.G3-Like and the master ripening regulator SlRIN, and increased the production of resveratrol derivatives through genetic manipulation. These findings provide insights into the coordination of fruit maturation and metabolic changes in tomatoes, and have implications for metabolic engineering.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Thomas R. Aalders, Mara de Sain, Fleur Gawehns, Nina Oudejans, Yoran D. Jak, Henk L. Dekker, Martijn Rep, Harrold A. van den Burg, Frank L. W. Takken
Summary: The TPL1 and TPL2 genes in tomato are closely associated with susceptibility to Fusarium wilt disease, and mutating these genes can enhance plant resistance to the disease.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
