Yuqiang Qian#, Fengjiao Hui#, Wenchao Niu, Di Wang, Yang Hao, Qingying Meng, Siyu Ren, Deqiang Kong, Heng Gong, Jiayu Wu, Kexin Chen, Muna Alariqi, Junping Gao*, Zhanjun Li*, Shuangxia Jin*

Genome Biology volume 26, Article number: 391 (2025), Published: 17 November 2025

Abstract

Background

Cytidine base editors (CBEs) consist of a single-strand specific cytidine deaminase fused to Cas9 nickase, enabling efficient C-to-T conversion across diverse organisms. Enhancing editing range and efficiency of these tools is essential for expanding their applications.

Results

In this study, we report that fusing a double-stranded DNA-specific cytosine deaminase DddAE1347A to CBEs significantly improves editing activity and broadens the editing window in cell lines, embryos, tobacco, and cotton. Compared to BE4max, the optimized DddAE1347A-BE4max exhibits up to a 93- fold increase in editing efficiency, achieving up to 52% efficiency at C14 and C15 in cell lines. Further investigation reveals that DddAE1347A is compatible with various Cas9 variants (SpCas9, SpaCas9, and Nme2Cas9) and deaminase variants (rA1, A3G, and A3A). Additionally, we demonstrate that cytosine deaminases with single-stranded DNA activity fail to enhance the CBE system. In contrast, various DddA variants can improve CBE editing activity at PAM-proximal cytosine positions, highlighting the modularity of fusion between DddAs and CBEs.

Conclusions

These findings suggest that the double-stranded DNA-specific cytosine deaminase protein can act as an engineered fusion module in the CBE system, altering the performance (window/efficiency) of CBEs.

论文链接：https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03849-3