Extensive enhancer crosstalk controls PPARG2 activation during adipogenesis

Abstract Peroxisome proliferator-activated receptor γ (PPARγ) is the master regulator of adipogenesis, but the mechanisms underlying its strong induction in response to adipogenic cues are poorly understood. Using human mesenchymal stem cells as a model system, we show that the PPARG locus is primed for activation in the progenitor state by a highly connected enhancer community, which gets further activated and interconnected during adipogenesis. By systematically deleting individual enhancers in the community and interrogating the effect on enhancer function, connectivity and gene expression, we reveal important, non-redundant and cooperative roles of many enhancers. We show that the promoter-proximal enhancers and the downstream super-enhancer constituents cooperate in cis at early time points of differentiation, whereas at later timepoints PPARγ feedback-activates its own expression. Top-scoring non-coding cardiometabolic variants predicted to affect PPARG2 expression map to key enhancers in the community, indicating that regulation via these enhancers is important for human physiology.