A qPCR Method to Distinguish between Expression of Transgenic and Endogenous Copies of Genes

Study of gene function in eukaryotes frequently requires data on the impact of the gene when it is expressed as a transgene, such as in ectopic or overexpression studies. Currently, the use of transgenic constructs designed to achieve these aims is often hampered by the difficulty in distinguishing between the expression levels of the endogenous gene and its transgene equivalent, which may involve either laborious microdissection to isolate specific cell types or harvesting tissue at narrow timepoints. To address this challenge, we have exploited a feature of the Golden Gate cloning method to develop a simple, restriction digest-based protocol to differentiate between expression levels of transgenic and endogenous gene copies. This method is straightforward to implement when the endogenous gene contains a Bpi1 restriction site but, importantly, can be adapted for most genes and most other cloning strategies. Key features This protocol was developed to determine the expression level of an ectopically expressed transcription factor with broad native expression in all surrounding tissues. The method described is most directly compatible with Golden Gate cloning but is, in principle, compatible with any cloning method. The protocol has been developed and validated in the model plant Arabidopsis thaliana but is applicable to most eukaryotes. Graphical overview.