Transcriptional enhancer elements are noncoding stretches of DNA that have a central role in controlling gene expression programs in cells. Rather than on-off switches, enhancers are hypothesized to function as transcriptional rheostats to fine-tune target transcript levels. Higher-order three-dimensional organization of chromatin facilitates physical interactions between enhancers and their target promoters. Interactions between enhancers and their targets may occur on the same chromosome (in cis) or on different chromosomes (in trans) (Figure 1) [1-3]. In any given mammalian cell type, the number of putative enhancer elements ranges from 50,000 to 100,000, and therefore far exceeds the number of protein-coding genes.
