  While bacterial chromosomes were long thought to be amorphous, recent
experiments reveal pronounced organizational features. However, the extent of
bacterial chromosome organization remains unclear. Here, we develop a fully
data-driven maximum entropy approach to extract the distribution of single-cell
chromosome conformations from experimental normalized Hi-C data. We apply this
inference to the model organism Caulobacter crescentus. On small genomic scales
of 104-105 basepairs, our model reveals a pattern of local chromosome
extensions that correlates with transcriptional and DNA loop extrusion
activity. On larger genomic scales, we find that chromosome structure is
predominantly present along the long cell axis: chromosomal loci not only have
well-defined axial positions, they also exhibit long-ranged correlations due
interacting large emergent genomic clusters, termed Super Domains. Finally, our
model reveals information contained in chromosome structure that can guide
cellular processes. Our approach can be generalized to other species, providing
a principled way of analyzing spatial chromosome organization.
