Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRa

Type II nuclear hormone receptors, such as FXR, LXR, and PPAR, which function in glucose and lipid metabolism and serve as drug targets for metabolic diseases, are permanently positioned in the nucleus regardless of the ligand status. Ligand activation of these receptors is thought to occur by co-repressor/co-activator exchange, followed by initiation of transcription. However, recent genome-wide location analysis showed that LXRa and PPARa binding in the liver is largely ligand-dependent. We hypothesized that pioneer factor Foxa2 evicts nucleosomes to enable ligand-dependent receptor binding. We show that chromatin accessibility, FXR binding and LXRa occupancy, and ligand-responsive activation of gene expression by FXR and LXRa require Foxa2. Unexpectedly, Foxa2 occupancy is drastically increased when either receptor, FXR or LXRa, is bound by an agonist. In addition, co-immunoprecipitation experiments demonstrate that Foxa2 interacts with either receptor in a ligand-dependent manner, suggesting that Foxa2 and the receptor bind DNA as an interdependent complex during ligand activation. Furthermore, PPARa binding is induced in Foxa2 mutants treated with FXR and LXR ligands, leading to activation of PPARa targets. Overall design: Chromatin accessibility, binding, and transcriptional analysis (ATAC-Seq, ChIP-Seq, and RNA-seq) of WT and Foxa2 mutant mouse livers after 4 hours after injection of a ligand (FXR agonist GW4064, LXR agonist GW3965, or GW agonist T09) or vehicle control ATAC-Seq was performed on WT and Foxa2 KO mouse livers in replicates of 2. For ATAC-Seq analysis, PeakSeq was used to call peaks in the WT ligand conditions against vehicle control . Foxa2 ChIP-Seq was performed on WT mouse livers in replicates of 3. FXR ChIP-Seq was performed on WT and Foxa2 KO mouse livers in replicates of 2. LXRa ChIP-Seq was performed on WT and Foxa2 KO mouse livers in replicates of 4. PPARa ChIP-Seq was performed on WT and Foxa2 KO mouse livers in replicates of 2. For ChIP-Seq analysis, PeakSeq was used to call peaks in the all conditions against input control. RNA-Seq was performed on WT and Foxa2 mutant mouse livers in replicates of 3 or 4. For RNA-Seq analysis, EdgeR was used for differential expression.