In the last 20 years, genomics has revolutionised our understanding of genome organisation and its regulation. It led to near complete annotation of the genome and the factors regulating expression of our genes. Yet, almost all of this knowledge arises from experiments that sample millions of regulatory events to create an average static picture that fails to capture the mechanistic steps and the dynamics that underlie these complex processes. The last decade has seen the independent emergence in the field of microscopy and genomics of technologies able to study gene regulatory processes at the resolution of individual DNA molecules. Joining the power of these orthogonal approaches promise to bring us towards a molecular understanding of gene regulation mechanisms in vivo.