Explanipedia

Large-scale single-cell long-read genomics enables high-resolution microbiome profiling Open

Yifan Liu, Mengzhen Li, Shiyan Li, Hengxin Liu, Xuanpei Zhai , et al. · 2025

Microbial communities are extraordinarily diverse and play crucial roles in health and disease, yet current methods lack the resolution and scalability needed to dissect their genomic and ecological complexity at the single-cell level. Her…

Mechanisms and engineering of a miniature type V-N CRISPR-Cas12 effector enzyme Open

Wenhan Fu, Jiacheng Ma, Zhipeng Wang, Na Tang, Deng Pan , et al. · 2025

Type V CRISPR-Cas12 systems are highly diverse in their functionality and molecular compositions, including miniature Cas12f1 and Cas12n genome editors that provide advantages for efficient in vivo therapeutic delivery due to their small s…

Systematic trans‐Activity Comparison of Several Reported Cas12f Nucleases† Open

Yannan Wang, Na Tang, Quanjiang Ji · 2025

Comprehensive Summary Cas12f possesses both cis ‐ and trans ‐cleavage activities, with the former being extensively studied for its application in genome editing, while the latter remains less explored, particularly for diagnostic purposes…

CRISPR-AsCas12f1 couples out-of-protospacer DNA unwinding with exonuclease activity in the sequential target cleavage Open

Xiaoxuan Song, Ziting Chen, Wenjun Sun, Hao Yang, Lijuan Guo , et al. · 2024

Type V-F CRISPR-Cas12f is a group of hypercompact RNA-guided nucleases that present a versatile in vivo delivery platform for gene therapy. Upon target recognition, Acidibacillus sulfuroxidans Cas12f (AsCas12f1) distinctively engenders thr…

VirBR, a transcription regulator, promotes IncX3 plasmid transmission, and persistence of blaNDM-5 in zoonotic bacteria Open

Tengfei Ma, Ning Xie, Yuan Gao, Jiani Fu, Chun E. Tan , et al. · 2024

BacPE: a versatile prime-editing platform in bacteria by inhibiting DNA exonucleases Open

Hongyuan Zhang, Jiacheng Ma, Zhaowei Wu, Xiaoyang Chen, Yangyang Qian , et al. · 2024

A KDPG sensor RccR governsPseudomonas aeruginosacarbon metabolism and aminoglycoside antibiotic tolerance Open

Y. Wang, Zhipeng Wang, Weizhong Chen, Ze-Hui Ren, Hui Gao , et al. · 2023

Pseudomonas aeruginosa harbors sophisticated transcription factor (TF) networks to coordinately regulate cellular metabolic states for rapidly adapting to changing environments. The extraordinary capacity in fine-tuning the metabolic state…

Structure and engineering of miniatureAcidibacillus sulfuroxidansCas12f1 Open

Zhaowei Wu, Dongliang Liu, Deng Pan, Haopeng Yu, Jin Shi , et al. · 2023

The miniature CRISPR-Cas12f nucleases allow for efficient delivery via cargo-size-limited adeno-associated virus delivery vehicles, thereby showing promising potential for in vivo therapeutic applications. Acidibacillus sulfuroxidans Cas12…

Using CRISPR–Cas9-Based Methods for Genome Editing inStaphylococcus aureus Open

Angelika Gründling, Quanjiang Ji, Stephen J. Salipante · 2023

Chromosomal mutations and targeted gene deletions and inactivations in Staphylococcus aureus are typically generated using the allelic exchange method. In recent years, however, more rapid methods have been developed, often using CRISPR–Ca…

Frontispiece: Mapping the Complete Photocycle that Powers a Large Stokes Shift Red Fluorescent Protein Open

Ziyu Wang, Ya Zhang, Cheng Chen, Ruixue Zhu, Jiaming Jiang , et al. · 2023

Photochemistry. In their Research Article (e202212209), Quanjiang Ji, Yifan Huang, Chong Fang, Weimin Liu et al. present a toolset for the mapping of the complete photocycle that powers a large Stokes shift red fluorescent protein.

Frontispiz: Mapping the Complete Photocycle that Powers a Large Stokes Shift Red Fluorescent Protein Open

Ziyu Wang, Ya Zhang, Cheng Chen, Ruixue Zhu, Jiaming Jiang , et al. · 2023

Photochemistry. In their Research Article (e202212209), Quanjiang Ji, Yifan Huang, Chong Fang, Weimin Liu et al. present a toolset for the mapping of the complete photocycle that powers a large Stokes shift red fluorescent protein.

Development of a versatile nuclease prime editor with upgraded precision Open

Xiangyang Li, Guiquan Zhang, Shisheng Huang, Yao Liu, Jin Tang , et al. · 2023

The applicability of nuclease-based form of prime editor (PEn) has been hindered by its complexed editing outcomes. A chemical inhibitor against DNA-PK, which mediates the nonhomologous end joining (NHEJ) pathway, was recently shown to pro…

Mapping the Complete Photocycle that Powers a Large Stokes Shift Red Fluorescent Protein Open

Ziyu Wang, Ya Zhang, Cheng Chen, Ruixue Zhu, Jiaming Jiang , et al. · 2022

Large Stokes shift (LSS) red fluorescent proteins (RFPs) are highly desirable for bioimaging advances. The RFP mKeima, with coexisting cis‐ and trans ‐isomers, holds significance as an archetypal system for LSS emission due to excited‐stat…

Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP Open

Bingyan Wei, Tao Zhang, Pengyu Wang, Yihui Pan, Jiahui Li , et al. · 2022

Guide RNA engineering enables efficient CRISPR editing with a miniature Syntrophomonas palmitatica Cas12f1 nuclease Open

Yujue Wang, Yannan Wang, Deng Pan, Haopeng Yu, Yifei Zhang , et al. · 2022

Gene therapy is limited by inefficient delivery of large clustered regularly interspaced short palindromic repeat (CRISPR) effectors, such as Cas9 and Cas12a nucleases. Cas12f nucleases are currently one of the most compact CRISPR genome e…

Capsule type defines the capability of Klebsiella pneumoniae in evading Kupffer cell capture in the liver Open

Xueting Huang, Xiuyuan Li, Haoran An, Juanjuan Wang, Ming Ding , et al. · 2022

Polysaccharide capsule is the main virulence factor of K . pneumoniae , a major pathogen of bloodstream infections in humans. While more than 80 capsular serotypes have been identified in K . pneumoniae , only several serotypes are frequen…

Molecular basis for cell-wall recycling regulation by transcriptional repressor MurR in Escherichia coli Open

Ya Zhang, Weizhong Chen, Di Wu, Yushi Liu, Zhaowei Wu , et al. · 2022

The cell-wall recycling process is important for bacterial survival in nutrient-limited conditions and, in certain cases, is directly involved in antibiotic resistance. In the sophisticated cell-wall recycling process in Escherichia coli, …

PAM-Expanded Streptococcus thermophilus Cas9 C-to-T and C-to-G Base Editors for Programmable Base Editing in Mycobacteria Open

Hongyuan Zhang, Yifei Zhang, Weixiao Wang, Weizhong Chen, Xia Zhang , et al. · 2022

Enhancement of prime editing via xrRNA motif-joined pegRNA Open

Guiquan Zhang, Yao Liu, Shisheng Huang, Shiyuan Qu, Daolin Cheng , et al. · 2022

The prime editors (PEs) have shown great promise for precise genome modification. However, their suboptimal efficiencies present a significant technical challenge. Here, by appending a viral exoribonuclease-resistant RNA motif ( xr RNA) to…

Enhancing prime editing efficiency by modified pegRNA with RNA G-quadruplexes Open

Xiangyang Li, Xin Wang, Wenjun Sun, Shisheng Huang, Mingtian Zhong , et al. · 2022

Live-cell RNA imaging using the CRISPR-dCas13 system with modified sgRNAs appended with fluorescent RNA aptamers Open

Heng Tang, Junran Peng, Shuang Peng, Qi Wang, Xin Jiang , et al. · 2022

The development of RNA imaging strategies in live cells is essential to improve our understanding of their role in various cellular functions.

Virulence-related regulatory network of Pseudomonas syringae Open

Jiadai Huang, Chunyan Yao, Yue Sun, Quanjiang Ji, Xin Deng · 2022

EasyCatch, a convenient, sensitive and specific CRISPR detection system for cancer gene mutations Open

Yin Liu, Yanling Chen, Lu Dang, Yixin Liu, Shisheng Huang , et al. · 2021

PAM-expanded Streptococcus thermophilus Cas9 C-to-T and C-to-G base editors for programmable base editing in mycobacteria Open

Quanjiang Ji, Hongyuan Zhang, Yifei Zhang, Weixiao Wang, Weizhong Chen , et al. · 2021

New therapeutic strategies for rapid and effective treatment of tuberculosis are highly desirable, and their development can be drastically accelerated by facile genetic manipulation methods in Mycobacterium tuberculosis. CRISPR base edito…

PAM-expanded Streptococcus thermophilus Cas9 C-to-T and C-to-G base editors for programmable base editing in mycobacteria Open

Quanjiang Ji, Hongyuan Zhang, Yifei Zhang, Weixiao Wang, Weizhong Chen , et al. · 2021

New therapeutic strategies for rapid and effective treatment of tuberculosis are highly desirable, and their development can be drastically accelerated by facile genetic manipulation methods in Mycobacterium tuberculosis. CRISPR base edito…

Targeted genetic screening in bacteria with a Cas12k-guided transposase Open

Weizhong Chen, Ze-Hui Ren, Na Tang, Guoshi Chai, Hongyuan Zhang , et al. · 2021

Microbes employ sophisticated cellular networks encoded by complex genomes to rapidly adapt to changing environments. High-throughput genome engineering methods are valuable tools for functionally profiling genotype-phenotype relationships…

CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation Open

Haopeng Yu, Zhaowei Wu, Xiangdan Chen, Quanjiang Ji, Shiheng Tao · 2020

Life science has been in pursuit of precise and efficient genome editing in living cells since the very beginning of the first restriction cloning attempt. The introduction of RNA-guided CRISPR-associated (Cas) nucleases contributed to thi…

A novel copper-sensing two-component system for activating Dsb genes in bacteria Open

Liang Yu, Qiao Cao, Weizhong Chen, Nana Yang, Cai‐Guang Yang , et al. · 2020

Copper is an essential element for biological systems but becomes toxic when present in excess. In Pseudomonas aeruginosa , an important human pathogen, the resistance to copper requires the induction of dsbDEG operon encoding proteins inv…

CRISPR-Cas9-Based Genome Editing and Cytidine Base Editing in Acinetobacter baumannii Open

Yu Wang, Zhipeng Wang, Quanjiang Ji · 2020

Programmable adenine deamination in bacteria using a Cas9–adenine-deaminase fusion Open

Ya Zhang, Hongyuan Zhang, Zhipeng Wang, Zhaowei Wu, Yu Wang , et al. · 2020

We report a pABE system which enables highly efficient adenine to guanine conversion in bacteria. Key residues of a staphylopine/metal complex transportercntBCwere systematically screenedviathe pABE system.

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