Current epigenomics approaches have facilitated the genome-wide identification 
of regulatory elements based on chromatin features and transcriptional regulator 
binding and have begun to map long-range interactions between regulatory 
elements and their targets. Here, we focus on the emerging roles of CTCF and the 
cohesin in coordinating long-range interactions between regulatory elements. We 
discuss how species-specific transposable elements may influence such 
interactions by remodeling the CTCF binding repertoire and suggest that 
cohesin's association with enhancers, promoters, and sites defined by CTCF 
binding has the potential to form developmentally regulated networks of 
long-range interactions that reflect and promote cell-type-specific 
transcriptional programs.