NR5A2 controls gene expression and chromatin contacts of essential circadian metabolic genes in the liver

Circadian regulation of gene expression relies on the coordinated action of core clock components, tissue-specific transcription factors, and epigenetic mechanisms, including dynamic enhancer–promoter interactions. Although rhythmic chromatin looping has been described in the liver, the transcription factors that mediate these temporal interactions remain poorly defined. Here, we identify the nuclear receptor NR5A2 as a key regulator of circadian enhancer–promoter communication in the mouse liver. We show that NR5A2 protein levels fluctuate over the 24-h cycle, peaking around Zeitgeber time 0 (ZT0). Genome-wide analysis reveals that NR5A2 preferentially binds H3K27ac-enriched enhancer regions, many of which engage in chromatin looping with promoters of metabolic genes. High-resolution 4C-seq analyses demonstrate that promoters of Elovl5 and Ppp1r3c dynamically interact with NR5A2- and H3K27ac-enriched enhancers in a time-dependent manner, with maximal interactions at ZT0 and reduced contacts at ZT12. Pharmacological inhibition of NR5A2 in vivo leads to alterations in hepatic glycogen and cholesterol accumulation, attenuates the rhythmic expression of circadian metabolic genes, including Ppp1r3c, Cyp8b1, and Elovl5, and disrupts enhancer–promoter contact frequencies at the Elovl5 locus. Together, our findings provide in vivo evidence that NR5A2 integrates circadian and metabolic regulation by modulating enhancer–promoter chromatin interactions, thereby shaping rhythmic liver gene expression.