Stochastic dynamics of coupled DNA loci on a compacted chromosome

Chromosomes are highly compacted and organized to fit into the eukaryotic nucleus. For many functional processes, including the initiation of transcription, pair-wise interactions of distal chromosomal elements, such as enhancers and promoters, are essential. Previous theory based on simple polymer models successfully captures the dynamics of single DNA loci in terms of sub-diffusive motion in the viscoelastic nucleoplasm. However, how these approaches extend to the joint motion of pairs of DNA loci remains unclear. Using a live imaging assay to simultaneously measure positions of pairs of enhancers and promoters in thousands of nuclei of the developing fly embryo, we analyze the two-point correlations of these DNA loci. Our analysis reveals long-ranged correlations with striking deviation from simple polymer models. We show how these findings are related to the compaction of the chromosome, highlighting the key role of spatial chromosome organization in determining the coupled dynamics of DNA loci.