Assessing leaky expression of Cre-dependent DNA constructs in the mouse genome using sensitive bioluminescent reporters

Leaky expression of genes in Cre-dependent DNA constructs in the absence of Cre recombinase has the potential to undermine precision of conditional gene manipulation. Here, we reliably detected and quantified this phenomenon in mice using highly sensitive bioluminescence imaging (BLI). By generating a series of knockin mice carrying Cre-dependent DNA constructs incorporating AkaBLI system, we found that a transcriptional STOP cassette alone was insufficient, producing significant Cre-independent leaky expression. This leaky expression can be suppressed by a combination of transcriptional and translational controls, facilitating precise detection and quantification of Cre-mediated recombination. Furthermore, application of leak-suppressed AkaBLI reporter mice to Cre-driver mice led to unambiguous identification of Cre-mediated recombination at intended and unintended sites throughout the mouse body. Thus, our data provide a generalizable solution to the leaky expression associated with Cre-loxP system, thereby enabling generation of diverse model organisms that require tight gene expression control.