The binding of (core) transcription factors critically depends on the recognition of specific DNA sequences, known as DNA motifs. High throughput techniques, such as ChIP-seq and enhanced yeast one-hybrid, which visualizes the interaction of a transcription factor with a bait DNA sequence, are now employed to uncover transcription factor-DNA and DNA-transcription factor interactions, respectively . Such studies show that transcription factor-binding events are abundant and can occur at large genomic distances from genes. Similarly, conserved non-coding sequences can be found throughout the genome. Their conservation implies that they have an important function – they may affect the binding affinity of factors, or encode non-coding RNAs . Interestingly, deletion of these sequences with unknown function can influence gene expression of genes located hundreds of Kb away, implying that long-range looping of DNA brings the sequences into contact with the genes they regulate .