Integrating experiment, theory and simulation to determine the structure and dynamics of mammalian chromosomes

Abstract

Eukaryotic chromosomes are complex polymers, which largely exceed in size most biomolecules that are usually modelled in computational studies and whose molecular interactions are to a large extent unknown. Since the folding of the chromatin fiber in the cell nucleus is tightly linked to biological function and gene expression in particular, characterizing the conformational and dynamical properties of chromosomes has become crucial in order to better understand how genes are regulated. In parallel with the development of experimental techniques allowing to measure physical contacts within chromosomes inside the cell nucleus, a large variety of physical models to study the structure and mechanisms of chromosome folding have recently emerged. Such models can be roughly divided into two classes, based on whether they adopt specific hypotheses on the interaction mechanism within chromosomes, or learn those interactions on the available experimental data using the principle of maximum entropy. All of them have played a key role in interpreting experimental data and advancing our understanding the folding principles of the chromatin fiber.