Programmable genome engineering and gene modifications for plant biodesign
Jialin Liu, Ruixiang Zhang, Nan Chai, Su Liu, Zhiye Zheng, Taoli Liu, Ziming Guo, Yuanhao Ma, Yongyao Xie, Xianrong Xie, Qiupeng Lin, L.‐W. Antony Chen, Yao‐Guang Liu, Qinlong Zhu
Abstract
Plant science has entered a transformative era as genome editing enables precise DNA modifications to address global challenges such as climate adaptation and food security. These modifications are primarily driven by the integration of three modular components-DNA-targeting modules, effector modules, and control modules-that can be selectively activated or suppressed. The field has evolved from protein-based systems (e.g., zinc finger nucleases and transcription activator-like effector nucleases) to RNA-guided systems (e.g., CRISPR-Cas) that can control both genetic and epigenetic states. Modular pairing of DNA-targeting and effector domains, with or without inducible control, enables precise transcriptional regulation and chromatin remodeling. The present review examines these three modules and highlights strategies for their optimization. It also outlines innovative tools, such as optogenetic and receptor-integrated systems, that enable spatiotemporal control over genome editor expression. These modular approaches bypass traditional limitations and allow scientists to create plants with desirable traits, decipher complex gene networks, and promote sustainable agriculture.