Article
Biochemical Research Methods
Christian Anthon, Giulia Ilaria Corsi, Jan Gorodkin
Summary: The effectiveness of CRISPR/Cas9-mediated genome editing experiments relies on the careful selection of guide RNA (gRNA) for target recognition and cleavage activation. This study presents a user-friendly webserver that incorporates both on- and off-target prediction tools, CRISPRon and CRISPRoff, to facilitate gRNA selection.
Article
Biochemistry & Molecular Biology
Florian Stoertz, Peter Minary
Summary: With the advancement of CRISPR/Cas programmable nuclease system, in vivo therapeutic gene editing applications are becoming more feasible. However, concerns over non-negligible off-target effects remain prominent. crisprSQL is an interactive collection of CRISPR/Cas9 off-target cleavage studies aimed at enriching cleavage profiling, gene editing safety analysis, and transcriptomics.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Daniel M. Sapozhnikov, Moshe Szyf
Summary: PROTECTOR is a novel approach that uses a nuclease-dead Cas protein to bind to off-target sites and interfere with Cas activity, reducing off-target mutation rates without compromising on-target activity. It can be used in combination with high-fidelity Cas enzymes to further decrease off-target editing, offering an ability to protect off-target sites with identical sequences to target sites.
SCIENTIFIC REPORTS
(2023)
Review
Biotechnology & Applied Microbiology
Congting Guo, Xiaoteng Ma, Fei Gao, Yuxuan Guo
Summary: Gene editing involves precise changes to specific nucleic acid sequences. The CRISPR/Cas9 system has revolutionized gene editing, making it efficient, convenient, and programmable. However, off-target effects remain a major concern, leading to unexpected alterations in the genome. Various methods have been developed to detect and mitigate these off-target effects, advancing the precision of CRISPR/Cas9 derivatives. This review summarizes these technological advancements and discusses the challenges in managing off-target effects for future gene therapy.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yanjiao Han, Zhefan Yuan, Sijin Luo Zhong, Haoxian Xu, Shaoyi Jiang
Summary: The CRISPR-Cas9 system is a powerful genome-editing tool used in various applications. However, the high-frequency mutations caused by Cas9 at unintended sites pose a major concern for therapeutic applications. Off-target events primarily result from non-specific mismatch between the guide RNA (sgRNA) and target DNA. This study presents two novel methods, involving chemical conjugation of Cas9 with zwitterionic pCB polymers and genetic fusion of Cas9 with zwitterionic (EK)(n) peptides, to minimize this mismatch issue. The modified CRISPR/Cas9 ribonucleoproteins (RNPs) exhibit reduced off-target DNA editing while maintaining on-target gene editing activity. The off-target efficiency of the modified CRISPR/Cas9 is reduced by an average of 70% and up to 90% compared to the unmodified CRISPR/Cas9 editing. These approaches provide a simple and effective way to enhance the development of CRISPR/Cas9-based genome editing for various biological and therapeutic applications.
Article
Biochemistry & Molecular Biology
Zhixin Lei, Haowei Meng, Yuan Zhuang, Qingguo Zhu, Chengqi Yi
Summary: This article outlines the off-target effects observed for various genome editing tools and discusses the methods for detecting and evaluating off-target editing, along with their advantages and limitations. Additionally, it summarizes current RNA editing tools for RNA therapy and medicine that can potentially serve as alternative approaches to genome editing tools in research and clinical applications.
ACS CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Rodrigo M. Florentino, Kazutoyo Morita, Nils Haep, Takashi Motomura, Ricardo Diaz-Aragon, Lanuza A. P. Faccioli, Alexandra Collin de l'Hortet, Zeliha Cetin, Carla Frau, Lawrence Vernetti, Anna-Klara Amler, Alexander Thomas, Tobias Lam, Lutz Kloke, Kazuki Takeishi, D. Lansing Taylor, Ira J. Fox, Alejandro Soto-Gutierrez
Summary: Advancements in cellular engineering and gene therapy allow for the production of human tissues with programmable genetically enhanced functions to model and treat specific diseases. This study successfully fabricated synthetic human liver tissues with programmable functions using CRISPR-Cas9 to control gene expression. The engineered liver tissues demonstrated enhanced functions compared to primary liver cells.
Article
Plant Sciences
Xiangyu Xiong, Kehui Liu, Zhenxiang Li, Fan-Nv Xia, Xue-Ming Ruan, Xionglei He, Jian-Feng Li
Summary: Researchers have developed a split deaminase system (SAFE) that enables efficient installation of beneficial or corrective point mutations without the need for external regulators. This system reduces unpredictable off-target edits induced by conventional BEs and improves on-target editing.
Article
Biochemical Research Methods
Zengrui Guan, Zhenran Jiang
Summary: The off-target effect is a challenging problem in the practical application of the CRISPR-Cas9 system. Various prediction models have been proposed, but they do not effectively utilize guide RNA and DNA sequence pair information. Additionally, existing methods often ignore noise in off-target datasets. To address these issues, a novel coding scheme and a transformer-based anti-noise model called CrisprDNT were developed. Experimental results showed that including the anti-noise loss functions in the method improved prediction performance compared to state-of-the-art methods. CrisprDNT is available at .
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Zhong-Rui Zhang, Zhen-Ran Jiang
Summary: The study aims to improve the model's performance for predicting off-target activities in the CRISPR/Cas9 system by effectively utilizing sequence pair information. A new coding scheme and a model called CRISPR-IP were proposed. Experimental results show that their coding scheme can effectively represent sequence pair information, and the CRISPR-IP model outperforms others.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Jeonghun Kwon, Minyoung Kim, Seungmin Bae, Anna Jo, Youngho Kim, Jungjoon K. Lee
Summary: Prime editors (PEs) are powerful tools for genome editing, and this study presents a cell-based assay called TAPE-seq that can be used to predict genome-wide off-target candidates for PEs. TAPE-seq shows higher accuracy and reliability compared to other prediction methods.
NATURE COMMUNICATIONS
(2022)
Review
Biochemical Research Methods
Guishan Zhang, Ye Luo, Xianhua Dai, Zhiming Dai
Summary: This review investigates the progress in predicting on- and off-target activity of single guide RNA (sgRNA) in the CRISPR/Cas9 system using deep learning-based methods. The study finds that the methods perform better on large- and medium-scale datasets compared to small-scale datasets for on-target predictions. For off-target predictions, the methods show excellent performance on balanced datasets but have room for improvement on imbalanced datasets.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Vanessa Chenouard, Isabelle Leray, Laurent Tesson, Severine Remy, Alasdair Allan, Daniel Archer, Adam Caulder, Agnes Fortun, Karine Bernardeau, Yacine Cherifi, Lydia Teboul, Laurent David, Ignacio Anegon
Summary: CRISPR-Cas9 cleavage efficacy and accuracy are influenced by the optimal formation of the ribonucleoprotein (RNP) complex. The study shows that an equimolar ratio of Cas9 and guide RNA (gRNA) is optimal for RNP complex formation. Increasing the Cas9/gRNA ratio does not improve knock-in (KI) efficiency, and excess gRNA leads to a decrease in point mutation KI efficiency and an increase in large deletions.
Article
Biotechnology & Applied Microbiology
Jeffrey K. K. Mak, Florian Stortz, Peter Minary
Summary: In this study, the impact of 19 epigenetic features on CRISPR-Cas9 off-target activity was analyzed using an off-target database. The results showed that some computed scores outperformed experimental features and significantly contributed to prediction models. The findings are of great importance for understanding the relationship between epigenetic features and CRISPR-Cas9 off-target activity.
Review
Biochemistry & Molecular Biology
Takuya Tsujino, Kazumasa Komura, Teruo Inamoto, Haruhito Azuma
Summary: In recent years, advances in omics technology and CRISPR/Cas9 technology have improved the identification of genes associated with cancer diseases, providing opportunities for the discovery of new therapeutic targets. This knowledge plays a crucial role in clinicians' decision-making regarding patient treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Mei-Wei Lin, Yen-Wen Tseng, Chih-Che Shen, Mu-Nung Hsu, Jih-Ru Hwu, Chin-Wei Chang, Chung-Ju Yeh, Min-Yuan Chou, Jaw-Ching Wu, Yu-Chen Hu
NUCLEIC ACIDS RESEARCH
(2018)
Article
Chemistry, Medicinal
Jih Ru Hwu, Wen-Chieh Huang, Shu-Yu Lin, Kui-Thong Tan, Yu-Chen Hu, Fa-Kuen Shieh, Sergey O. Bachurin, Alexey Ustyugov, Shwu-Chen Tsay
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
Fang-Hong Lee, Chee Ying Chew, Jih Ru Hwu, Kui-Thong Tan
JOURNAL OF THE CHINESE CHEMICAL SOCIETY
(2019)
Article
Biochemistry & Molecular Biology
Vu Anh Truong, Mu-Nung Hsu, Nuong Thi Kieu Nguyen, Mei-Wei Lin, Chih-Che Shen, Chin-Yu Lin, Yu-Chen Hu
NUCLEIC ACIDS RESEARCH
(2019)
Article
Chemistry, Multidisciplinary
Luca Sorrentino, Federica Cossu, Mario Milani, Bilge Malkoc, Wen-Chieh Huang, Shwu-Chen Tsay, Jih Ru Hwu, Eloise Mastrangelo
Review
Biotechnology & Applied Microbiology
Mu-Nung Hsu, Yu-Han Chang, Vu Anh Truong, Po-Liang Lai, Thi Kieu Nuong Nguyen, Yu-Chen Hu
BIOTECHNOLOGY ADVANCES
(2019)
Article
Biochemical Research Methods
Nam Ngoc Pham, Cho-Yi Chen, Hung Li, Mai Thanh Thi Nguyen, Phung Kim Phi Nguyen, Shen-Long Tsai, June-Yen Chou, Theresia Cecylia Ramli, Yu-Chen Hu
ACS SYNTHETIC BIOLOGY
(2020)
Article
Chemistry, Organic
Jih Ru Hwu, Animesh Roy, Avijit Panja, Wen-Chieh Huang, Yu-Chen Hu, Kui-Thong Tan, Chun-Cheng Lin, Kuo-Chu Hwang, Ming-Hua Hsu, Shwu-Chen Tsay
JOURNAL OF ORGANIC CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Jih Ru Hwu, Avijit Panja, Srinivasan Jayakumar, Shwu-Chen Tsay, Kui-Thong Tan, Wen-Chieh Huang, Yu-Chen Hu, Pieter Leyssen, Johan Neyts
Article
Biochemical Research Methods
Chih-che Shen, Mei-Wei Lin, Bao Khanh Thi Nguyen, Chin-Wei Chang, Jie-Ru Shih, Mai Thanh Thi Nguyen, Yi-Hao Chang, Yu-Chen Hu
ACS SYNTHETIC BIOLOGY
(2020)
Article
Engineering, Biomedical
Nuong Thi Kieu Nguyen, Yu-Han Chang, Vu Anh Truong, Mu-Nung Hsu, Nam Ngoc Pham, Chin-Wei Chang, Yi-Hsiu Wu, Yi-Hao Chang, Hung Li, Yu-Chen Hu
Summary: Healing of large calvarial bone defects in adults is challenging and typically follows the intramembranous pathway. Implanting adipose-derived stem cells (ASC) that differentiate towards chondrogenic lineage can enhance bone repair. Activation of the long non-coding RNA DANCR by SadCas9-VPR-based CRISPRa improves rASC chondrogenesis and promotes calvarial bone healing in rats.
Article
Biotechnology & Applied Microbiology
Nam Ngoc Pham, Chin-Wei Chang, Yi-Hao Chang, Yi Tu, June-Yen Chou, Hsing-Yun Wang, Yu-Chen Hu
Summary: In this study, we developed a CRISPR-based method for genome and metabolic engineering of Candida viswanathii. By optimizing the CRISPR system and protocol, we improved the efficiency of gene integration and increased the production of dodecanedioic acid (DDA) by co-expressing multiple enzymes. Using the split CRISPR system, we successfully integrated four genes into C. viswanathii, resulting in significantly increased DDA production and conversion rate.
METABOLIC ENGINEERING
(2023)
Article
Chemistry, Organic
Anindya Das, Pei-Jhen Li, Avijit K. Adak, Hsin-Ru Wu, Mohammad Tarique Anwar, Pei-Yun Chiang, Chung-Ming Sun, Jih-Ru Hwu, Chun-Cheng Lin
ORGANIC CHEMISTRY FRONTIERS
(2019)