Pioneer Factor Foxa2 Mediates Chromatin Conformation Changes for Activation of Bile Acid Targets of FXR

Transcription factors regulate gene expression that orchestrates liver physiology. Many bind at distal enhancers and chromatin looping is required to activate their targets. Chromatin architecture has been linked to essential functions of the liver, including metabolism and sexually dimorphic gene expression. We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors farnesoid X receptor (FXR) and liver X receptor-α during acute ligand activation. FXR is activated by bile acids and deletion of Foxa2 in the liver results in intrahepatic cholestasis. We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation and performed genome-wide studies to test this hypothesis.

We performed Foxa2 HiChIP (Hi-C and ChIP) to assess Foxa2-dependent long-range interactions in mouse livers treated with either vehicle control or FXR agonist GW4064.

HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. Ligand-treated livers exhibit extensive redistribution of topological associated domains and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. We demonstrate that chromatin conformation, including genome-wide interactions, topological associated domains, and intrachromosomal and interchromosomal Foxa2-anchored loops, drastically changes on addition of FXR agonist. Additional Foxa2 binding in ligand-activated state leads to formation of Foxa2-anchored loops, leading to distal interactions and activation of gene expression of FXR targets.

Ligand activation of FXR, and likely of related receptors, requires global changes in chromatin architecture. We determine a novel role for Foxa2 in enabling these conformational changes, extending its function in bile acid metabolism.