| dc.description.abstract | The three-dimensional organization of the genome within the nucleus plays a central role in determining gene regulation and establishing cellular identity, but the mechanisms by which local molecular interactions give rise to global chromatin architecture remain an active area of study. Interactions between nucleosomes—modulated by histone tail post-translational modifications, histone sequence variants, and the DNA sequence itself—are thought to be a major driver of this emergent structure. In this thesis, I address the question of how these intrinsic physicochemical properties of nucleosomes drive the formation of large-scale structures such as chromatin compartments. I develop a theoretical framework based on Flory-Huggins solution theory to derive pairwise internucleosome contact energies from the results of condense-seq, a novel experimental technique that measures the phase separation likelihood of native nucleosomes. I then use these derived energies to parameterize coarse-grained molecular dynamics simulations of chromatin at various resolutions, ranging from 25kb segments to simulate an entire chromosome, down to individual nucleosomes to simulate up to 10Mb genomic regions. These simulations demonstrate that the intrinsic nucleosome properties alone can capture a significant degree of A/B compartment formation observed in Hi-C experiments, despite the deliberate exclusion of all other factors such as loop extrusion and transcriptionfactor-mediated phenomena. This finding establishes that local nucleosome properties play a fundamental role in genome organization. To capture more detailed chromatin physics, I develop an extended chromatin force-field that incorporates anisotropic nucleosome stacking interactions and linker DNA properties using a novel approach for simulating reversible bond formation in molecular dynamics. This model reveals how nucleosome stacking strength, linker DNA geometry, and torsional stress collectively influence higher-order structures. Early results show that the linker-length-dependent DNA torsion contributes to nematic ordering of chromatin, consistent with experimental studies. Future development of this model will enable probing of discrete domain formation observed in imaging studies. Finally, I address a critical consideration for researchers in the chromatin organization field when analyzing Hi-C results. I compare two software tools — cooltools and dcHiC — highlighting the importance of careful parameter selection and analytical choices in designing workflows to ensure reproducible research. Taken together, this work establishes a quantitative, bottom-up modeling framework that directly links the local physicochemical properties of nucleosomes to the global principles governing three-dimensional genome organization. It provides a complementary approach to more data-driven top-down models that have made significant inroads but are challenging to interpret mechanistically. With further development, the work presented in this thesis will contribute towards predicting the structural consequences of specific epigenetic modifications and move us closer to understanding the molecular grammar of chromatin and its role in cellular function and disease. | |
