Date of Award

Spring 1-1-2025

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Physics

First Advisor

Mochrie, Simon

Abstract

The central question in chromatin architecture and dynamics is how meter-long DNA strands are organized within a micrometer-sized nucleus while maintaining regulation of all genomic activities. While some organizational principles have been identified and validated through both theoretical models and experiments, controversies between alternative mechanisms persist,continually refining and enriching our understanding of chromatin architecture and dynamics. At the intermediate length scale, chromatin architecture is characterized by topologically associating domains (TADs), revealed through experimental Hi-C contact maps. This organization can be explained and modeled using loop extrusion factor (LEF) models, which rely on the correlation between TAD boundaries and the genomic positions of boundary elements (BEs). However, although TADs feature prominently in their Hi-C contact maps, non-vertebrate eukaryotes either possess unidentified functional BEs or exhibit few TAD boundaries that correlate with the known BE binding sites, frustrating comparisons between Hi-C data and simulations. To model intermediate-scale chromatin organization across the tree of life, characterized by TADs, the first chapter introduces the conserved-current loop extrusion (CCLE) model that interprets LEFs as a nearly conserved probability current. By design, CCLE eliminates the need to identify BEs and their genomic positions, relying instead on ChIP-seq data of LEFs as its sole input. CCLE provides a modified paradigm for LEF models, shifting from the concept of localized barriers to incorporating position-dependent loop extrusion rates. We show that CCLE accurately predicts the TAD-scale Hi-C contact maps of interphase Schizosaccharomyces pombe, meiotic and mitotic Saccharomyces cerevisiae, and Mus musculus liver cells, demonstrating its utility in eukaryotes both with and without identified functional BEs. More importantly, the success of CCLE in these systems suggests that loop extrusion is indeed the primary mechanism underlying TAD-scale chromatin organization in eukaryotes. Building on the assumption that the loop extrusion mechanism predominantly shapes chromatin organization at the intermediate length scale, the second chapter investigates how loop extrusion affects chromatin dynamics. By incorporating loops and dynamic loop extrusion into the classical nearest-neighbor Rouse model, we enable exact simulations of the resultant looped chromatin polymer. We demonstrate that chromatin loops in a native, dynamic steady state reduce chromatin mobility, as measured by the time- and ensemble-averaged mean square displacements (MSDs), reminiscent of recent experimental results that examine the dynamics of chromatin loci in living cells. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a value near 0.45, which has also been observed in recent experiments. Furthermore, our extended Rouse model approach enables us to investigate chromatin dynamics with any loop configuration. By studying static "rosette" configurations, we demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environments.

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