The Farnesoid X Receptor (FXR) is a nuclear receptor activated by bile acids, which acts as a metabolic homeostat for lipids, glucose and amino acids. FXR is expressed as four isoforms (FXRα1-4), and canonically activates transcription from IR-1 (inverted repeat-1) response elements, upon heterodimerization with Retinoid X Receptor (RXR). We recently showed that FXRα/4 bind to non-canonical response elements ER-2 (everted repeat-2), representing 89% of FXR binding sites, selectively blocking de novo lipogenesis and increasing mitochondrial respiratory capacity. Here, we questioned whether protein complex formation at both DNA binding motifs is different.

Using DNA pulldown followed by mass-spectrometry, we found RXR enriched on IR-1 but not on ER-2 response elements. In agreement, RXR-lacking FXR binding sites in the mouse liver genome were enriched for ER-2 motifs. To our surprise, RXR inhibited FXR-driven transactivation from ER-2 in luciferase reporters. Moreover, pharmacological and mutational abrogation of the FXR-RXR heterodimerization specifically retained ER-2-transactivation capacities, while downregulating IR-1.

In HepG2 cells, we found 25% of FXR targets reduced upon RXR overexpression, but specifically activated by RXR-heterodimerization-deficient mutant FXRα2^L434R. These included genes involved in xenobiotic metabolism and ammonia detoxification. In conclusion, we discovered that RXR is not required and even inhibits the binding of FXRα2 to ER-2. Boosting this non-canonical ER-2 mediated FXRα2 feature will likely improve liver metabolism.