The HSA21 encoded Single-minded 2 (SIM2) transcription factor has key 
neurological functions and is a good candidate to be involved in the cognitive 
impairment of Down syndrome. We aimed to explore the functional capacity of SIM2 
by mapping its DNA binding sites in mouse embryonic stem cells. ChIP-sequencing 
revealed 1229 high-confidence SIM2-binding sites. Analysis of the SIM2 target 
genes confirmed the importance of SIM2 in developmental and neuronal processes 
and indicated that SIM2 may be a master transcription regulator. Indeed, SIM2 
DNA binding sites share sequence specificity and overlapping domains of 
occupancy with master transcription factors such as SOX2, OCT4 (Pou5f1), NANOG 
or KLF4. The association between SIM2 and these pioneer factors is supported by 
co-immunoprecipitation of SIM2 with SOX2, OCT4, NANOG or KLF4. Furthermore, the 
binding of SIM2 marks a particular sub-category of enhancers known as 
super-enhancers. These regions are characterized by typical DNA modifications 
and Mediator co-occupancy (MED1 and MED12). Altogether, we provide evidence that 
SIM2 binds a specific set of enhancer elements thus explaining how SIM2 can 
regulate its gene network in neuronal features.