Recently, the Animal Epigenomics Innovation Team at the Shenzhen Agriculture Genomics Institute of the Chinese Academy of Agricultural Sciences (Shenzhen Branch of Guangdong Laboratory for Lingnan Modern Agriculture Science and Technology) has developed a novel model for predicting the effects of base editing. This model significantly improves the accuracy of predicting the editing effects of base editors at endogenous genomic target sites. The research findings have been published in Cell Discovery.
Base editing technology is an emerging gene editing technique used to modify individual bases at specific locations within DNA molecules, mainly including adenine base editors and cytosine base editors. However, the assessment of base editing efficiency has traditionally relied on experiments, which are time-consuming, labor-intensive, and limited in accuracy, thus hindering the widespread application of base editors.
To identify factors limiting the improvement of prediction accuracy, researchers systematically compared the editing effects of base editors at exogenous integrated target sites and endogenous genomic target sites. The study found that the editing effects of base editors at endogenous target sites are influenced by epigenetic factors such as DNA methylation and histone modifications.
To address this, researchers developed a new model called BE_Endo, based on the integration of guide RNA sequence features and target site epigenetic factors. This model can accurately predict the editing effects of adenine base editors and cytosine base editors at endogenous genomic target sites.
The model also incorporates information from genomic epigenetics to more accurately and efficiently assess the editing effects of base editors at endogenous target sites, which is of significant importance in advancing the application of gene editing tools.
This research was supported by the National Natural Science Foundation of China, the National Key Research and Development Program, and the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences.
Related paper information: https://doi.org/10.1038/s41421-023-00624-1
