It is becoming increasingly clear that transcription factors operate in complex 
networks through thousands of genomic binding sites, many of which bind several 
transcription factors. However, the extent and mechanisms of crosstalk between 
transcription factors at these hotspots remain unclear. Using a combination of 
advanced proteomics and genomics approaches, we identify ∼12,000 transcription 
factor hotspots (∼400 bp) in the early phase of adipogenesis, and we find 
evidence of both simultaneous and sequential binding of transcription factors at 
these regions. We demonstrate that hotspots are highly enriched in large 
super-enhancer regions (several kilobases), which drive the early adipogenic 
reprogramming of gene expression. Our results indicate that cooperativity 
between transcription factors at the level of hotspots as well as 
super-enhancers is very important for enhancer activity and transcriptional 
reprogramming. Thus, hotspots and super-enhancers constitute important 
regulatory hubs that serve to integrate external stimuli on chromatin.