Multiple transgenic mice expressing Cre. Raw sequence reads

Cre/LoxP technology is widely used in the field of mouse genetics for spatial and/or temporal regulation of gene function. For Cre lines generated via pronuclear microinjection of a Cre transgene construct, the integration site is random and in most cases not known. Integration of a transgene can disrupt an endogenous gene, potentially interfering with interpretation of the phenotype. In addition, knowledge of where the transgene is integrated is important for planning of crosses between animals carrying a conditional allele and a given Cre allele in case the alleles are on the same chromosome. We have used Targeted Locus Amplification (TLA) to efficiently map the transgene location in seven previously published Cre and CreERT2 transgenic strains. In all seven lines, transgene insertion was associated with structural changes of variable complexity, illustrating the importance of testing for rearrangements around the integration site. In all seven animals the exact integration site breakpoint sequences were identified. In three out of seven a duplication in the integration locus prevented the design of a genotyping assay that efficiently distinguish wildtype, hemizygous and homozygous animals. Our methods, data and genotyping assays can be used as a resource for the mouse community and our results illustrate the power of the Targeted Locus Amplification method to not only efficiently map the integration site of any transgene, but also provide additional information regarding the transgene integration events.