CRISPR-LRS for mapping transgenes in mouse genome

Microinjected transgenes, including bacterial artificial chromosomes (BACs), insert randomly in the mouse genome. Traditional methods of mapping a transgene are challenging, thus complicating breeding strategies and the accurate interpretation of phenotypes, especially when a transgene disrupts critical coding or non-coding sequences. Here, we introduce CRISPR-Cas9 long-read sequencing (CRISPR-LRS) to ascertain transgene site of integration and estimated copy number. This method determined estimated copy numbers for two BAC mouse strains and the integration site for another BAC and a Cre driver strain. CRISPR-LRS offers a facile approach to establish robust breeding practices and accurate phenotyping of most any transgenic mouse line.