Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes and Neighboring Endogenous Genes

Abstract

Transgenic mouse lines are routinely employed to label and manipulate distinct cell types. The transgene generally comprises cell-type specific regulatory elements linked to a cDNA encoding a reporter or other protein. However, off-target expression seemingly unrelated to the regulatory elements in the transgene is often observed, it is sometimes suspected to reflect influences related to the site of transgene integration in the genome. To test this hypothesis, we used a proximity ligation-based method, Targeted Locus Amplification (TLA), to map the insertion sites of three well-characterized transgenes that appeared to exhibit insertion site-dependent expression in retina. The nearest endogenous genes to transgenes HB9-GFP, Mito-P, and TYW3 are Cdh6, Fat4 and Khdrbs2, respectively. For two lines, we demonstrate that expression reflects that of the closest endogenous gene (Fat4 and Cdh6), even though the distance between transgene and endogenous gene is 550 and 680 kb, respectively. In all three lines, the transgenes decrease expression of the neighboring endogenous genes. In each case, the affected endogenous gene was expressed in at least some of the cell types that the transgenic line has been used to mark and study. These results provide insights into the effects of transgenes and endogenous genes on each other’s expression, demonstrate that mapping insertion site is valuable for interpreting results obtained with transgenic lines, and indicate that TLA is a reliable method for integration site discovery.

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“…To generate probes, RNA was extracted from P19 C57BL/6J mouse retina and reverse transcribed as described in Laboulaye et al (2018). Probes were generated from cDNA by PCR using Q5 Polymerase and the following sets of primers.…”

Genome Engineering for Xenotransplantation

“…Despite the speed and ease of generation, random integration of TGs has several drawbacks. Variabilities in genome structure can affect the expression level of genes inserted at distinct chromosomal regions, such that identical TGs may express at very different levels depending upon their specific location [63]. Furthermore, multiple copies of a given TG may be inserted into the genome at a single site, creating concatenated repeats which can be unstable and yield variable expression levels [64].…”