The Farnesoid-X-Receptor activates transcription independently of RXR at non-canonical response elements

The Farnesoid-X-Receptor (FXR) is a nuclear receptor (NR) known to obligately heterodimerize with Retinoid-X-Receptor (RXR). FXR is expressed as four isoforms (α1-α4) that drive transcription from IR-1 (inverted repeat-1) DNA motifs. More recently, FXR isoforms α2/α4 were found to activate transcription predominantly from non-canonical ER-2 (everted repeat-2) DNA motifs, mediating most metabolic effects of general FXR activation. Here, we explored molecular determinants of FXRα2 regulation from ER-2 elements through quantitative interaction proteomics, site-directed mutagenesis, and transcriptomics. We discovered that FXRα2 binds to and activates ER-2 elements in vitro and in reporter assays independently of RXR. Genome-wide analysis in mouse liver revealed higher ER-2 motif enrichment in RXR-lacking FXR binding sites. Abrogation of FXRα2:RXR heterodimerization abolished IR-1, but preserved ER-2 transactivation. Transcriptome-wide, RXR overexpression inhibited 25% of FXRα2 targets in HepG2. These genes were specifically activated by the heterodimerization-deficient mutant FXRα2-L434R, were enriched for ER-2 motifs at their promoters and were involved in lipid metabolism and ammonia detoxification. In conclusion, RXR acts as a molecular switch, promoting FXRα2 activation from IR-1 instead of ER-2 motifs. Our results showcase FXR as the first NR with RXR-dependent and independent modes of activation, highlighting a potential new layer of complexity for other RXR-heterodimerizing NRs. To investigate the transcriptome-wide effect of RXRA on FXRa2 target genes in liver cells, we generated HepG2 cell lines overexpressing FXRa2 in the presence or absence of ectopic RXRA. In addition, we also analysed the RXR heterodimerization-deficient mutant FXRa2-L434R. We performed gene expression profiling analysis using data obtained from RNA-seq of 5 cell lines after treatment with an FXR agonist or vehicle. Comparative gene expression profiling analysis of RNA-seq data to determine (1) the effect of agonist treatment for each line generated and (2) the consequences of FXRa2/RXRA overexpression