Population Properties of Self-Avoiding Polymer Chain Models of Chromosomes in a Confined Space of Nucleus

Abstract

Global architecture of cell nucleus and the spatial organization of chromatin play important roles in gene expression and nuclear function. Single-cell imaging and chromosome conformation capture-based techniques provide information on chromosome conformations and their spatial organizations. Here we propose a polymer model to study the higher order chromatin organization in the nucleus. This model is based on generating self-avoiding chains with appropriate diameters of chromatin fiber in a confined space where the excluded volume effect is taken into consideration. using a sequential importance sampling technique, we are able to generate 10,000 independent conformations explicitly and study their statistical properties, such as spatial distance vs. genomic length relationship and loop forming probability. This model can capture many scaling properties of chromatin folding reported experimentally and can also explain many biological properties of chromatin fibers.