Identification of thyroid hormone response elements in vivo using mice expressing a tagged thyroid hormone receptor alpha 1

TR alpha 1 (thyroid hormone receptor alpha 1) is well recognized for its importance in brain development. However, due to the difficulties in predicting TREs (thyroid hormone response elements) in silico and the lack of suitable antibodies against TR alpha 1 for ChIP (chromatin immunoprecipitation), only a few direct TR alpha 1 target genes have been identified in the brain. Here we demonstrate that mice expressing a TR alpha 1-GFP (green fluorescent protein) fusion protein from the endogenous TR alpha locus provide a valuable animal model to identify TR alpha 1 target genes. To this end, we analysed DNA-TR alpha 1 interactions in vivo using ChIP with an anti-GFP antibody. We validated our system using established TREs from neurogranin and hairless, and by verifying additional TREs from known TR alpha 1 target genes in brain and heart. Moreover, our model system enabled the identification of novel TR alpha 1 target genes such as RNF166 (ring finger protein 166). Our results demonstrate that transgenic mice expressing a tagged nuclear receptor constitute a feasible approach to study receptor-DNA interactions in vivo, circumventing the need for specific antibodies. Models like the TR alpha 1-GFP mice may thus pave the way for genome-wide mapping of nuclear receptor-binding sites, and advance the identification of novel target genes in vivo.