Optimizing nervous system-specific gene targeting with Cre driver lines: prevalence of germline recombination and influencing factors

The Cre-loxP system is invaluable for spatial and temporal control of gene knockout, knockin, and re- porter expression in the mouse nervous system. However, we report varying probabilities of unex- pected germline recombination in distinct Cre driver lines designed for nervous system-specific recombi- nation. Selective maternal or paternal germline recombination is showcased with sample Cre lines. Collated data reveal germline recombination in over half of 64 commonly used Cre driver lines, in most cases with a parental sex bias related to Cre expres- sion in sperm or oocytes. Slight differences among Cre driver lines utilizing common transcriptional con- trol elements affect germline recombination rates. Specific target loci demonstrated differential recom- bination; thus, reporters are not reliable proxies for another locus of interest. Similar principles apply to other recombinase systems and other genetically targeted organisms. We hereby draw attention to the prevalence of germline recombination and pro- vide guidelines to inform future research for the neuroscience and broader molecular genetics communities