Polymer model integrates super-resolution imaging and sequencing to elucidate the role of chromatin organization in microenvironment-driven mechanical memory formation

Introduction:: Chromatin, comprised of a complex assembly of DNA and associated proteins, exhibits a highly dynamic and hierarchical organization and is central to all eukaryotic biology. At the mesoscale, chromatin displays clutch domains of characteristic length scales, as evidenced by super-resolution imaging techniques[1]. Meanwhile, at the genomic scale, these domains exhibit selective epigenetic enrichment corresponding to either a genetically active, de-compacted euchromatin state or a genetically repressed, compacted heterochromatin state. Chromatin remodelers, such as HDAC and EZH2, locally perturb this multiscale structure in response to varying chemo-mechanical cues, by reconfiguring the epigenetic marks, ultimately resulting in a global reorganization, and altered genetic regulation[2]. Despite the wealth of information on these associated changes, a unified physics-based approach that explains the phenomenon across multiple length scales and connects various experimental techniques is currently lacking. To address this gap, we present a reaction-based polymer model that integrates sequencing inputs and accurately predicts both local and global configurations observed through imaging, as well as HiC contact patterns. Our model also proposes mechanisms through which chemo-mechanical memory can be stored in chromatin configuration. By utilizing a polymer approach, we aim to provide a more holistic understanding of chromatin structure and function, bridging the gap between various experimental techniques and offering a framework for future investigation into the dynamics of chromatin remodeling.

Materials and Methods:: This study introduces a computational model of chromatin that represents it as a copolymer of beads-on-a-string, with distinct types of beads reflecting euchromatin and heterochromatin epigenetic marks[3]. To capture the interactions between beads of similar and different epigenetic labels, we utilize Lennard-Jones potentials, which are empirically calibrated to match experimental data obtained through FISH[4]. To simulate the temporal evolution of chromatin, we employ a reaction-based Brownian dynamics approach that captures the effect of the microenvironment through epigenetic reactions. This approach enables us to monitor the dynamic changes in epigenetic markers over time, which in turn govern the three-dimensional arrangement of chromatin. To validate our model experimentally, we compare the effects of two treatments - changes in substrate stiffness and exposure to Trichostatin A (TSA) - by analyzing super-resolution (STORM) imaging data to analyze the mesoscale clutch size scaling in response to the changing microenvironment, as well as using Hi-C contact maps to validate changes in local genomic compartments.

Results, Conclusions, and Discussions:: Using the dynamics proposed in our model, we demonstrate the emergence of finite-sized clutch domains observed across various cell lines via super-resolution imaging[1]. These domains exhibit temporal stability in their spatial structure and epigenetic labeling. In response to microenvironment-dependent methylation and acetylation reaction perturbations, chromatin undergoes compaction and expansion, respectively. We re-establish a previously observed analytical relation for the scaling of the heterochromatin domains[1], which is experimentally validated through STORM imaging experiments of stiffness change and Trichostatin A (TSA) exposure. We then use Hi-C contact matrices to relate these mesoscale changes to genomic changes and identify compartment shifts that align with our model's predictions. We find that the major compartment shifts in response to external stimuli occur at domain boundaries, an observation confirmed by experiments. By combining this insight with simulations representing changing microenvironmental conditions, we uncover mechanisms of mechanical memory storage in the nuclear chromatin. The simplicity of our model's dynamics and its successful explanation of the chromatin conformation change at multiple scales introduces a significant stride forward and exemplifies the central role of physical principles in biological understanding. Our nuanced insights not only tie together the multiscale problem but also pave the way for a deeper understanding of eukaryotic genetic regulation.

Acknowledgements (Optional): : We would like to thank the NSF-funded STC, CEMB center, and NIH NCI MetNet center (U54CA261694) for supporting this work.

References (Optional): : [1] Heo, S.J. Nat. Biomed. Eng., 2022, 910.
[2] Alisafaei, F.PNAS. 2019, 116 (27)
[3] Shi G.,Nat. Commun., 2018, 9, 3161
[4] Wang S., Science, 2016, 353, 6299