Polymer Model Integrates Imaging and Epigenomics to Elucidate the Role of the Cell's Microenvironment in Shaping 4D Chromatin Organization [RNA-Seq]
Chromatin epigenetic markers have been recognized to colocalize with phase-separated genomic compartments. While the correlation between 3D organization and epigenetic changes in response to extracellular stimuli has been observed, the causal physical underpinnings of 4D chromatin reorganization with changes in the cell microenvironment remain elusive. To tackle this, we introduce a dynamic, histone epigenetic remodeler-driven polymer model that incorporates next-generation sequencing data to identify active and repressed chromatin regions. The proposed chromatin-chromatin interaction energetics and diffusion-epigenetic reaction driven dynamics predict the formation and maintenance of characteristic heterochromatin-rich domains.  We establish a scaling relation for the sizes of these chromatin domains with modulation of epigenetic reaction rates. Additionally, our model predicts that the epigenetic and accessibility changes occur predominantly at the domain boundaries resulting from the diffusion-reaction balance. These predictions are verified using super-resolution imaging and Hi-C sequencing of hyperacetylated melanoma cells. Subsequent RNA-seq analysis suggests a pivotal role of these epigenetic shifts in driving the cell's phenotype. Extending our model's universality, we validate our mesoscale findings against chromatin rearrangement resulting from changes in the microenvironmental substrate stiffness.  Lastly, we evaluate the effect of altering the epigenetic reaction rates in silico and uncover a domain boundary driven cell-type invariant mechanism by which chromatin organization can drive epigenetic memory formation. These findings significantly advance our comprehension of how chromatin dynamics impact both short-term (immediate response) and long-term (memory) cellular behavior. Overall design: We use Tricostatin A (TSA) as an HDAC inhibitor (Fisher Scientific 14-061). For TSA treatment, the cells were grown to >70% confluence for more than 24 hours before addition of 500 nM TSA along with basal media. These were put back into the incubator and cultured for another 2 hours.  These cells are then used for Hi-C and RNA-seq analyses