3D chromatin contacts via HiChIP - Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of beige adipocytes

Epigenetic regulation is a key determinant of adipocyte fate and function, conferring phenotypic plasticity to adipose tissue in response to metabolic and thermal challenges. To understand the spatiotemporal regulation of chromatin during the establishment of a beige thermogenic adipocyte phenotype, we analyzed the transcriptomic, epigenetic, and enhancer connectome dynamics during white and beige adipogenesis. Using a machine learning approach, we find that the white-specific transcriptional program is associated with promoter modulations of H3K2ac levels and chromatin accessibility. In contrast, beige-specific mitochondrial gene expression correlates with promoter changes in H3K4me3 levels. Adipocyte beiging is also mediated by a remodeling of the 3D genome involving the recruitment of short range enhancers targeting fatty acid oxidation and thermogenic genes. These increased promoter-enhancer contacts correlate with increased chromatin opening at sites enriched for C/EBP transcription factor motifs. We notably identify the C/EBP transcription factor NFIL3 as differentially bound between white and beige adipocytes at enhancers regulating PDK4, a key metabolic switch promoting fatty acid oxidation. Our results highlight a multimodal, pathway-specific regulation of the transcriptional program underlying the beige adipocyte phenotype. Overall design: Primary human adipocyte stem cells from a single subject were differentiated for 15 days into both beige and white adipocytes in the presence or absence of rosiglitazone, respectively, and short range chromatin contacts at loci with H3K27ac were assessed using Hi- Chromatin Immunoprecipation and sequencing (Hi-ChIP-Seq). Two differentiations were seqeuenced as a bioloigcal duplicate.