Abstract Hepatocyte nuclear factor 4α (HNF4α) is an established transcriptional master regulator of differentiation, maintenance, and metabolism. Polymorphisms in HNF4α are linked to several diseases in humans including diabetes and nonalcoholic fatty liver disease (NAFLD). Identifying novel regulation of lipid metabolism by HNF4α would inform on NAFLD development and progression. We directly assessed HNF4α activity through chromatin immunoprecipitation (ChIP)-sequencing and integration of untargeted lipidomics. Direct regulation by HNF4α can be difficult to assess due to the role of HNF4α in liver homeostasis; to rapidly disrupt activity, mice were exposed to cold stress which induces hepatic steatosis in several hours. Cold exposure shifted HNF4α activity with differential genome occupancy of more than 50% of HNF4α binding sites. Focusing on HNF4α binding to promoter with active transcription determined that HNF4α directly regulates fatty acid desaturation, ether lipid synthesis, and peroxisomal biogenesis in response to cold exposure. Integration of lipidomics found that cold exposure increases the very long chain polyunsaturated fatty acid composition of the hepatic lipid pool, including ether lipids, in an HNF4α dependent manner. Because portions of ether lipid synthesis are in the peroxisome and peroxisomal biogenesis is directly HNF4α regulated, we analyzed peroxisomal abundance and found increases with cold exposure that are ablated with loss of HNF4α. This peroxisomal regulation was independent of PPARα— a known regulator of peroxisomes and lipid metabolism—since loss of HNF4α was not rescued by PPARα overexpression. These data determined that regulation of hepatic steatosis by HNF4α is more complex than triglyceride accumulation and includes acyl chain modifications, ether lipid synthesis, and peroxisomal oxidation.

HNF4α regulates acyl chain remodeling and ether lipid accumulation in hepatic steatosis