Progress in Transposable Element-Assisted Targeted Insertion of Large DNA Fragments

The rapidly evolving genome editing technologies have demonstrated strong application potential in animal and plant breeding, microbial engineering, and basic scientific research. Current genome editing techniques allow for the insertion, deletion, and substitution of single or multiple nucleotides at specific genomic targets across a wide range of species. However, editing types involving large DNA fragment insertion or replacement still face technical bottlenecks, such as low efficiency and fidelity, as well as difficulties in donor delivery. These limitations restrict the application of gene editing in important scenarios, including multigene stacking with genetic linkage, precise replacement of favorable alleles, and targeted integration of DNA fragments at genomic safe harbors. Transposable elements, as mobile genetic elements widely present in biological genomes, offer a novel approach to overcoming these challenges due to their inherent mobility and large DNA cargo capacity. They hold promise for being engineered into key molecular tools for precise large DNA fragment editing. This review summarizes recent advances in targeted large DNA fragment insertion technologies based on transposable elements, focusing on the application status and prospects of prokaryotic-derived CRISPR-associated transposons (CAST) and certain DNA transposons and retrotransposons in eukaryotes. Prokaryotic-derived CAST systems have shown outstanding performance, enabling efficient large fragment integration in prokaryotes and, after optimization, also achieving large fragment insertion in eukaryotic cells. In eukaryotes, engineered DNA transposons such as mPing/Pong and retrotransposon-related tools like R2 and L1 have been utilized for large DNA fragment insertion in animals and plants. At the same time, the field of transposon-based large DNA fragment insertion faces challenges. On the one hand, the cross-species adaptability of transposable elements is limited, making it difficult for some elements to function when transferred to other species. On the other hand, the large size or multiplicity of protein components involved leads to low delivery efficiency in certain types of eukaryotic cells. Additionally, some systems carry safety risks, such as stimulating the mammalian immune system and triggering inflammatory responses. Future research may focus on the discovery of novel transposable elements, engineering of transposases, development of new delivery vectors, and in-depth elucidation of transposition mechanisms, in order to provide key technical support for establishing efficient and safe large fragment editing technologies. This will contribute to foundational innovations in crop genetic improvement, gene therapy, and microbial genome editing.