Extracting the degree of order in the bacterial chromosome using statistical physics

Elucidating the three-dimensional spatial organization of the bacterial chromosome is essential to understand how genomic processes are spatially regulated inside the cell. Recent Hi-C chromosome conformation capture experiments provide contact frequency maps of the chromosome. These experiments reveal structural organization beyond that of an amorphous polymer. However, despite such experimental advances, the degree of spatial organization of the bacterial chromosome remains unclear. To investigate this, we develop a maximum entropy approach to extract the three-dimensional structure of the bacterial chromosome from such data. Using this approach, we obtain a coarse-grained model for the full distribution of chromosome configurations for the bacterium C. crescentus. We validate the predictive power of our model by experiments on the localization of chromosomal loci in the cell. Our model reveals novel features of spatial chromosome organization on various length scales. Our approach is not organism-specific, and opens up a new way of analyzing spatial chromosome organization.