Figure 1. Optimizing Cre-Lox recombination: factors affecting efficiency and reliability.

(a) The Cre-Lox system, consisting of the enzyme Cre and its specific DNA sequence lox, enables spatial-temporal control over gene expression in mice. It is widely used in research, allowing researchers to study the function of specific genes with precise control over expression time and location, deepening our understanding of biological processes. Cre-Lox technology has a notable limitation—the unpredictability of efficiency of Cre-mediated recombination and mosaicism (i.e., incomplete recombination—the targeted genetic changes do not occur uniformly across the targeted tissue). Although a high recombination efficiency is in most cases the desired outcome, for some biological questions, genetic mosaicism is of physiological relevance. Our lack of understanding of how various considerations affect recombination efficiency, especially when using tissue-specific Cre drivers, undermines the reliability of the Cre-Lox system, leading to variable experimental outcomes that may not align optimally with the investigator’s intention. (b) We systematically examined the role of various factors, including the Cre-driver strain, inter-loxP distance, Cre breeder age at the time of mating, zygosity of the floxed allele (heterozygous versus homozygous floxed allele), wildtype versus mutant loxP sites, and the various genetic loci of floxed alleles across the genome on Cre-recombination efficiency and mosaicism.