Cellular responses to environmental stimuli often require rapid transcriptional induction of specific gene subsets, which are somehow “targeted” within minutes despite representing a tiny fraction of the entire DNA sequence within the nucleus. The genome is highly spatially organized within eukaryotic cell nuclei, and a large body of work has correlated gene locations relative to nuclear landmarks, or certain genome configurations, with regulation of DNA metabolism. Active and inactive compartments form topologically separate domains exhibiting signatures of chromatin chemical modifications and factors recruited by them. Within the domains, enhancers can contact promoters specifically or selectively over short or long genomic distances, usually in cis. Enhancers, including super-enhancers, are known to interact stochastically, a feature particularly relevant during cellular differentiation. However it is still unclear whether transcription per se drives spatial reorganization and how we can use this information to gain a better understanding of cell responses in normal and pathological contexts. Moreover, the dynamics of such processes are poorly understood and mainly correlative. By live cell imaging we have recently demonstrated that transcription initiation rapidly confines the transcribed locus and that chromatin dynamics occur in large domains of coordinated movement with abrupt boundaries only in actively transcribing cells. To achieve this, we have developed two complementary new methods, one for particle tracking, the proprietary ANCHOR technology to fluorescently tag up to three specific DNA loci, and one for flow determination of fluorescent proteins and DNA in the entire nucleus. These approaches give us an unprecedented opportunity to assess the mechanism by which chromatin topology evolves and contributes to transcriptional control in living cells. We propose a multiscale approach probing chromatin domain conformation and dynamics of rapidly inducible estrogen target genes in mammary tumor cells. Live cell imaging will be combined with promoter capture Hi-C and polymer modeling to ask how structural reorganization regulates transcriptional output, and how this may be perturbed. Insights into chromosome biology and technological developments will foster new applications for diagnostics and drug discovery.