Journal of Genetics and Genomics

2019 Vol. 46, No. 11

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Off-target effects of cytidine base editor and adenine base editor: What can we do?

Puping Liang, Jinkun Wen, Junjiu Huang

2019, 46(11): 509-512. doi: 10.1016/j.jgg.2019.09.004

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Review

Advances in detecting and reducing off-target effects generated by CRISPR-mediated genome editing

Jinjing Li, Shunyan Hong, Wanjin Chen, Erwei Zuo, Hui Yang

2019, 46(11): 513-521. doi: 10.1016/j.jgg.2019.11.002

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CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors. Currently, poor efficiency and off-target problems have impeded the application of CRISPR systems. The on-target efficiency has been improved in several advanced versions of CRISPR systems, whereas the off-target detection still remains a key challenge. Here, we outline the different versions of CRISPR systems and off-target detection strategies, discuss the merits and limitations of off-target detection methods, and provide potential implications for further gene editing research.

Engineering guide RNA to reduce the off-target effects of CRISPR

Jing Wu, Hao Yin

2019, 46(11): 523-529. doi: 10.1016/j.jgg.2019.11.003

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Abstract:
As versatile and robust genome editing tools, clustered regularly interspaced short palindromic repeats (CRISPR) technologies have been broadly used in basic research, biotechnology, and therapeutic development. Off-target mutagenesis by CRISPR systems has been demonstrated, and various methods have been developed to markedly increase their specificity. In this review, we highlight the efforts of producing and modifying guide RNA (gRNA) to minimize off-target activities, including sequence and structure design, tuning expression and chemical modification. The modalities of gRNA engineering can be applied across CRISPR systems. In conjunction with CRISPR protein effectors, the engineered gRNA enables efficient and precise genome editing.

Site-directed RNA editing (SDRE): Off-target effects and their countermeasures

Shaoshuai Mao, Yajing Liu, Shisheng Huang, Xingxu Huang, Tian Chi

2019, 46(11): 531-535. doi: 10.1016/j.jgg.2019.11.005

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Abstract:
Site-directed RNA editing (SDRE) is invaluable to basic research and clinical applications and has emerged as a new frontier in genome editing. The past few years have witnessed a surge of interest in SDRE, with SDRE tools emerging at a breathtaking pace. However, off-target effects of SDRE remain a tough problem, which constitutes a major hurdle to their clinical applications. Here we discuss the diverse strategies for combating off-target editing, drawing lessons from the published studies as well as our ongoing research. Overall, SDRE is still at its infancy, with significant challenges and exciting opportunities ahead.

Original research

Drosophila CTP synthase can form distinct substrate- and product-bound filaments

Xian Zhou, Chen-Jun Guo, Huan-Huan Hu, Jiale Zhong, Qianqian Sun, Dandan Liu, Shuang Zhou, Chia Chun Chang, Ji-Long Liu

2019, 46(11): 537-545. doi: 10.1016/j.jgg.2019.11.006

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Abstract:
Intracellular compartmentation is a key strategy for the functioning of a cell. In 2010, several studies revealed that the metabolic enzyme CTP synthase (CTPS) can form filamentous structures termed cytoophidia in prokaryotic and eukaryotic cells. However, recent structural studies showed that CTPS only forms inactive product-bound filaments in bacteria while forming active substrate-bound filaments in eukaryotic cells. In this study, using negative staining and cryo-electron microscopy, we demonstrate that Drosophila CTPS, whether in substrate-bound or product-bound form, can form filaments. Our results challenge the previous model and indicate that substrate-bound and product-bound filaments can coexist in the same species. We speculate that the ability to switch between active and inactive cytoophidia in the same cells provides an additional layer of metabolic regulation.

Letter to the editor

Establishment and characterization of a complete set of Triticum durum-Thinopyrum elongatum monosomic addition lines with resistance to Fusarium head blight in wheat

Jing Wang, Qinghua Shi, Xianrui Guo, Fangpu Han

2019, 46(11): 547-549. doi: 10.1016/j.jgg.2019.09.006

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Abstract:

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