Gene expression regulation in eukaryotes includes interactions between promoters and enhancers, but our understanding of the mechanisms that drive these interactions, or that determine their specificity, is far from complete. At the basis of transcription lies the DNA code that directly determines the composition and location of DNA elements and provides specific recognition sites for DNA binding proteins. The binding of transcription factors and recruitment of complexes that modify histones create an environment that allows for element interaction and initiation of gene transcription. However, predicting the location of promoters and enhancers based solely on histone modifications and transcription factor binding relies on complicated models that are still suboptimal . Moreover, recent findings on the involvement of non-coding RNA in transcriptional regulation further imply a more complicated reality.