Title: Genome Organization from the Ground Up — Deciphering Molecular Mechanisms for Chromatin Organization

Abstract: Chromatin structure tightly regulates gene expression and epigenetic processes. The nuclear environment is complex, featuring tension exerted by force-generating proteins and molecular crowding modulated by different ionic concentrations. Understanding the impact of these factors on chromatin structure is crucial for elucidating the molecular mechanisms of chromatin accessibility and organization. However, it is unclear how chromatin adapts its structure to different nuclear environments in molecular details. Here, we used a residue resolution chromatin model to computationally characterize chromatin structures under tension, crowding, and different ionic environments. Our study of a tetranucleosome revealed multiple irregular chromatin structures that emerged as intermediates of two chromatin folding pathways. Our further study of a dodecameric nucleosomal array showed that chromatin broke into trimeric and tetrameric nucleosome clutches under tension, facilitating the formation of interdigitated chromatin structures via trans interactions among multiple chains in crowded environments. We further incorporated explicit-ion modeling to simulate chromatin conformations and reconciled various experiments on quantifying inter-nucleosome interactions, which can be further modulated by linker DNAs and linker histones. Finally, we showed that Polycomb repressive complex 2 (PRC2), an important epigenetic enzyme, cooperatively looped DNA via allosteric communication and bridged non-adjacent nucleosomes to propagate histone modifications. Our collective work demonstrates the usefulness of this coarse-grained chromatin model in uncovering the structure and regulation of chromatin in nuclear environments, providing mechanistic insights into genome organization.