Hi-C Contacts Encode Heterogeneity in Sub-diffusive Motion of E. coli Chromosomal Loci

Abstract

Underneath its apparently simple architecture, the circular chromosome of E. coli is known for displaying complex dynamics in its cytoplasm. Recent experiments have hinted at an inherently heterogeneous dynamics of chromosomal loci, the origin of which has largely been elusive. In this regard, here we investigate the loci dynamics of E. coli chromosome in a minimally growing condition at 30°C by integrating the experimentally derived Hi-C interaction matrix within a computer model. Our quantitative analysis demonstrates that, while the dynamics of the chromosome is sub-diffusive in a viscoelastic media in general, the diffusion constants and the diffusive exponents are strongly dependent on the spatial coordinates of chromosomal loci. In particular, the loci in Ter Macro-domain display slower mobility compared to the others. The result is found to be robust even in the presence of active noise. Interestingly, a series of control investigations reveal that the absence of Hi-C interactions in the model would have abolished the heterogeneity in loci diffusion, indicating that the observed coordinate-dependent chromosome dynamics is heavily dictated via Hi-C-guided long-range inter-loci communications. Overall, the study underscores the key role of Hi-C interactions in guiding the inter-loci encounter and in modulating the underlying heterogeneity of the loci diffusion.