Regulation of hepatic transcriptional architecture by Pparα and fatty acid oxidation

Abstract

Hepatic lipid biology is a central regulator of metabolic physiology, requiring tight coordination between the hepatocyte's metabolic state and transcriptional output. Peroxisome proliferator-activated receptor alpha (Pparα) plays a key role in this process as a master regulator of oxidative gene expression. To better resolve Pparα's role in the hepatic response to acutely elevated fatty acids, Pparα-null mice were crossed to mice harboring a liver-specific knockout of carnitine palmitoyltransferase 2 (Cpt2), an obligate enzyme for mitochondrial β-oxidation. The oxidation deficit leads to drastic fatty acid accumulation following a 24hr fast, providing a handle by which to investigate Pparα's response to excess fatty acids. RNA-seq on fasted WT, Cpt2L-/-, Ppar⍺-/-, and Cpt2L-/-;Ppar⍺-/- liver uncovered two distinct classes of Pparα-influenced gene expression: those wholly dependent upon Pparα, such as Fgf21 and Hmgcs2, and those with partial independence, such as Acot2 and Pdk4. The latter implies a secondary regulatory mechanism for a subset of canonical Pparα target genes. Complementing this hypothesis, ATAC-seq demonstrates genes with partial Ppar⍺ independence retain promotor accessibility in Cpt2L-/-;Ppar⍺-/-, but not Ppar⍺-/-, mice, whereas genes wholly dependent on Ppar⍺ display significantly reduced promotor accessibility in both Ppar⍺-null genotypes. Co-analysis of ATAC-seq and ChIP-seq for H3K4me1 and H3K27ac indicates that genes wholly dependent on Pparα are more closely associated with poised distal enhancer elements, and those with partial Pparα independence show active albeit blunted enhancer activity. H3K4me1 occupancy suggests that Pparα target genes are primed regardless of Pparα expression. Taken together, these data provide evidence of a Pparα-independent genomic control mechanism that acts in parallel with Pparα signaling to promote transcription of canonical Pparα target genes.