Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization

Abstract

The heterochromatin protein 1 (HP1) family is a crucial component of heterochromatin with diverse functions in gene regulation, cell cycle control, and cell differentiation. In humans, there are three paralogs, HP1α, HP1β, and HP1γ, which exhibit remarkable similarities in their domain architecture and sequence properties. Nevertheless, these paralogs display distinct behaviors in liquid-liquid phase separation (LLPS), a process linked to heterochromatin formation. Here, we employ a coarse-grained simulation framework to uncover the sequence features responsible for the observed differences in LLPS. We highlight the significance of the net charge and charge patterning along the sequence in governing paralog LLPS propensities. We also show that both highly conserved folded and less-conserved disordered domains contribute to the observed differences. Furthermore, we explore the potential co-localization of different HP1 paralogs in multicomponent assemblies and the impact of DNA on this process. Importantly, our study reveals that DNA can significantly reshape the stability of a minimal condensate formed by HP1 paralogs due to competitive interactions of HP1α with HP1β and HP1γ versus DNA. In conclusion, our work highlights the physicochemical nature of interactions that govern the distinct phase-separation behaviors of HP1 paralogs and provides a molecular framework for understanding their role in chromatin organization. Distinct interaction patterns of HP1 paralogs, in concert with DNA modulation, induce the organization of chromatin via liquid-liquid phase separation.

Conformational diversity of human HP1α

“…Consistent with these studies, AlphaFold2 predicts less contacts between the CD and CSD of HP1β where the NMR analysis shows that the two domains reorient largely independent from each other in solution. AlphaFold2 also predicts less CD‐CSD interactions in HP1γ when compared to HP1α (Figure 2a), which supports coarse‐grained simulations predicting a large radius of gyration of HP1γ (3.48 ± 0.69 nm) relative to HP1α (3.20 ± 0.31 nm) (Phan et al, 2023). The combined data suggest that interactions between the CD and CSD are evolutionary favored in HP1α when compared to HP1β and HP1γ.…”

Fundamental Aspects of Phase-Separated Biomolecular Condensates

“…The foregoing methods can all work with a coarse-grained representation of solute molecules with solvent treated implicitly. Many slab-geometry simulations at the coarse-grained level have been carried out for biomolecular condensates. ,,,,,− FMAP has been used to calculate binodals for proteins represented at the all-atom level, albeit with the proteins treated as rigid and the solvent treated implicitly. , Zhang et al . have developed a hybrid model for proteins, where the backbone is represented at the all-atom level whereas side chains are at the coarse-grained level, and the solvent is treated implicitly.…”