A study of bacterial chromosome organization using bead-spring polymer models

Abstract

The chromosome, a long polymer ($\sim 2$m in the human cell and $\sim 1$mm in a bacterial cell), consists of all the genetic information and is packed $\sim 1000$ fold inside the nucleus (in a human cell) or in the bacterial cell. The chromosome is involved in various cellular processes, e.g., DNA replication, transcription and is not like a random-walk polymer but shows a unique spatial organization at $\mu$ length-scales, as is evident from the recent experimental studies. The contact map generated from the experimental technique Hi-C gives the frequency of two chromosome segments of $1$ kilo base-pair- $1$ mega base-pair) each, to be in proximity to each other. The Hi-C contact maps which give essential insights about the chromosome organization but do not provide the overall 3D structure of the chromosome. Also, despite several theoretical and experimental efforts, the mechanism leading to the $\mu$ length-scale organization of the chromosome remains elusive. Currently, the primary challenge in the field is to build a physical model of the chromosome that can predict the 3D organization and shed light on the mechanism in the chromosome organization obtained in the Hi-C contact map. Developing such a model requires statistically significant high-throughput data from individual cells, with close dialogue between modeling and experiment.

Here in this thesis, we use bead-spring model of the ring polymer to understand the role of different physical mechanisms, e.g., DNA binding proteins, the crowding environment due to various proteins, enzymes inside the cell, release of topological constraints and the confinement of the cell wall in the chromosome organization of bacteria E. coli and C. crescentus. We also predict the overall 3D organization of the chromosome and validate our prediction with the available experimental data. In particular, we use the data from the Hi-C contact map of E. coli and C. crescentus to introduce the cross-links at particular positions in the bead-spring polymer where one coarse-grained bead represents $1000$ base pairs (BP) of the DNA. The cross-links at specific positions mimic DNA-binding proteins. Via suitable Monte Carlo simulations, we show that the presence of $<2\%$ cross-links leads to a particular organization of the chain at large (micron) length scales. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain. We find that though the polymer does get organized at the large length scales, the nature of the organization is quite different from the organization observed with cross-links at specific biologically determined positions. We next individually study the effect of chain crossing, crowding-environment of the cell, or the confinement due to the cell wall on the organization of the cross-linked polymer and then combined all the effects and predict the 3D organization of the chromosomes of bacteria E. coli and C. crescentus.