The Mediator complex regulates transcription by connecting enhancers to 
promoters. High Mediator binding density defines super enhancers, which regulate 
cell-identity genes and oncogenes. Protein interactions of Mediator may explain 
its role in these processes but have not been identified comprehensively. Here, 
we purify Mediator from neural stem cells (NSCs) and identify 75 protein-protein 
interaction partners. We identify super enhancers in NSCs and show that 
Mediator-interacting chromatin modifiers colocalize with Mediator at enhancers 
and super enhancers. Transcription factor families with high affinity for 
Mediator dominate enhancers and super enhancers and can explain genome-wide 
Mediator localization. We identify E-box transcription factor Tcf4 as a key 
regulator of NSCs. Tcf4 interacts with Mediator, colocalizes with Mediator at 
super enhancers and regulates neurogenic transcription factor genes with super 
enhancers and broad H3K4me3 domains. Our data suggest that high binding-affinity 
for Mediator is an important organizing feature in the transcriptional network 
that determines NSC identity.