FRAP calibrated polymer model of chromatin with HP1a predicts heterochromatin domain sizes, 3D organization, and dynamics.

Phase-separated heterochromatin domains are enriched for H3K9me2/3 with an abundance of heterochromatin protein 1 (HP1a). In vitro, HP1a exhibits liquid-liquid phase separation (LLPS), however, in vivo, its effects on dynamics and structure of heterochromatin domains remain unclear. We develop a simple model containing spherical particles to mimic HP1a protein and a single-chain polymer representing the chromatin. We account for HP1a self-interaction and its attraction to methylation markers and analyze the thermodynamic behavior of the system. We show that the heterochromatin domains are stabilized by the interplay of HP1a self-interactions and HP1-H3k9me2/3 interactions. We reveal that HP1a concentrations inside heterochromatin domains and nucleoplasm depend on the total concentration of HP1a in the nucleus which is consistent with the thermodynamics of multicomponent LLPS. Unlike other polymer models which mostly are tuned on structural experimental data (e.g. Hi-C contact map), we calibrate our model parameters to reproduce the dynamics of HP1a consistent with the in-vivo fluorescence recovery after photobleaching experiment (FRAP) of HP1a. The tuned model predicts the 3D genome organization and heterochromatin domain size verifiable through Hi-C and super-resolution imaging experimental data. Furthermore, our model shows that the transition from compact heterochromatin domains to coil-state euchromatin domains is accompanied by hysteresis, suggesting metastability of both phases. Therefore, our model predicts that substantial perturbation of heterochromatin domains by obliteration of methylation marks (as during replication) does not result in the system leaving that epigenetic state; in other words, cells have a memory of epigenetic states during reorganization.