van der Veen Suzanne W, Dijkstra Jelmer J, Willemsen Ellen C L, Houtman René, Milona Alexandra, Marchet Nikolas, Spit Maureen, Hollman Danielle, Zwartkruis Fried J T, Vermeulen Michiel, Ramos Pittol Jose M, van Mil Saskia W C
Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Stratenum Building, Universiteitsweg 100, 3584CG Utrecht, The Netherlands.
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26-28, 6525GA Nijmegen, The Netherlands.
Nucleic Acids Res. 2025 Feb 8;53(4). doi: 10.1093/nar/gkae1214.
The farnesoid X receptor (FXR) is a nuclear receptor (NR) known to obligately heterodimerize with the retinoid X receptor (RXR). FXR is expressed as four isoforms (α1-α4) that drive transcription from IR-1 (inverted repeat-1) response elements (REs). Recently, we found that FXR isoforms α2/α4 also activate transcription from non-canonical ER-2 (everted repeat-2) REs, mediating most metabolic effects of general FXR activation. Here, we explored molecular determinants of regulation by FXRα2 from ER-2 REs through quantitative interaction proteomics, site-directed mutagenesis and transcriptomics. We discovered FXRα2 binds to and activates ER-2 elements in vitro and in reporter assays independently of RXR. Genome-wide binding analysis in mouse liver revealed higher ER-2 motif enrichment in FXR sites lacking RXR. 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 FXRα2L434R, enriched for ER-2 motifs at their promoters, and involved in lipid metabolism and ammonia detoxification. In conclusion, RXR acts as a molecular switch, inhibiting FXRα2 activation from ER-2 while enhancing it from canonical IR-1 REs. Our results showcase FXR as the first NR with isoform-specific RXR-independent REs, highlighting a new layer of regulation and complexity for RXR-heterodimerizing NRs.
法尼酯X受体（FXR）是一种核受体（NR），已知它会与视黄酸X受体（RXR）形成 obligately 异二聚体。FXR 以四种异构体（α1-α4）的形式表达，这些异构体驱动来自 IR-1（反向重复-1）反应元件（REs）的转录。最近，我们发现 FXR 异构体α2/α4 还能从非经典的 ER-2（正向重复-2）REs 激活转录，介导一般 FXR 激活的大多数代谢效应。在这里，我们通过定量相互作用蛋白质组学、定点诱变和转录组学探索了 FXRα2 对 ER-2 REs 的调控分子决定因素。我们发现 FXRα2 在体外和报告基因分析中独立于 RXR 结合并激活 ER-2 元件。在小鼠肝脏中的全基因组结合分析显示，在缺乏 RXR 的 FXR 位点中 ER-2 基序富集更高。FXRα2:RXR 异二聚体化的消除消除了 IR-1，但保留了 ER-2 的反式激活。在全转录组范围内，RXR 的过表达抑制了 HepG2 中 25%的 FXRα2 靶标。这些基因被异二聚体化缺陷型突变体 FXRα2L434R 特异性激活，在其启动子处富含 ER-2 基序，并参与脂质代谢和氨解毒。总之，RXR 作为一个分子开关，抑制 FXRα2 从 ER-2 的激活，同时增强其从经典 IR-1 REs 的激活。我们的结果表明 FXR 是第一个具有异构体特异性的独立于 RXR 的 REs 的核受体，突出了 RXR 异二聚化核受体调控的新层面和复杂性。
