Summary The cyclic recombinase (Cre)/ loxP recombination system is a powerful technique for in vivo cell labeling and tracking. However, achieving high spatiotemporal precision in cell tracking using this system is challenging due to the requirement for reliable tissue-specific promoters. In contrast, light-inducible systems offer superior regional confinement, tunability and non-invasiveness compared to conventional lineage tracing methods. Here, we took advantage of the unique strengths of the zebrafish to develop an easy-to-use highly efficient, genetically encoded, Magnets-based, light-inducible transgenic Cre/ loxP system. Our system relies on the reassembly of split Cre fragments driven by the affinity of the Magnets and is controlled by the zebrafish ubiquitin promoter. We demonstrate that our system does not exhibit phototoxicity or leakiness in the dark, and it enables efficient and robust Cre/ loxP recombination in various tissues and cell types at different developmental stages through noninvasive illumination with blue light. Our newly developed tool is expected to open novel opportunities for light-controlled tracking of cell fate and migration in vivo . Highlights zPA-Cre is a novel zebrafish transgenic optogenetic split-Cre tool zPA-Cre allows loxP-mediated DNA recombination in various tissues and cell types It enables light-induced DNA recombination at different developmental stages. It allows spatio-temporal DNA recombination in a specific tissue region with high resolution

A non-invasive photoactivatable split-Cre recombinase system for genome engineering in zebrafish