Dynamical phase transition in models that couple chromatin folding with histone modifications

Preserving condensate structure and composition by lowering sequence complexity

Biomolecular condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent interactions, leading to spontaneous aggregation. Theoretical advancements are critical at connecting IDP sequences with condensate emergent properties to establish the so-called molecular grammar. We proposed an extension to the stickers and spacers model, incorporating heterogeneous, nonspecific pairwise interactions between spacers alongside specific interactions among stickers. Our investigation revealed that although spacer interactions contribute to phase separation and co-condensation, their nonspecific nature leads to disorganized condensates. Specific sticker-sticker interactions drive the formation of condensates with well-defined networked structures and molecular composition. We discussed how evolutionary pressures might emerge to affect these interactions, leading to the prevalence of low-complexity domains in IDP sequences. These domains suppress spurious interactions and facilitate the formation of biologically meaningful condensates.

Nonequilibrium switching of segmental states can influence compaction of chromatin

Knowledge about the dynamic nature of chromatin organization is essential to understand the regulation of processes like DNA transcription and repair. The existing models of chromatin assume that protein organization and chemical states along chromatin are static and the 3D organization is purely a result of protein-mediated intra-chromatin interactions. Here we present a new hypothesis that certain nonequilibrium processes, such as switching of chemical and physical states due to nucleosome assembly/disassembly or gene repression/activation, can also simultaneously influence chromatin configurations. To understand the implications of this inherent nonequilibrium switching, we present a block copolymer model of chromatin, with switching of its segmental states between two states, mimicking active/repressed or protein unbound/bound states. We show that competition between switching timescale Tt, polymer relaxation timescale τp, and segmental relaxation timescale τs can lead to non-trivial changes in chromatin organization, leading to changes in local compaction and contact probabilities. As a function of the switching timescale, the radius of gyration of chromatin shows a non-monotonic behavior with a prominent minimum when Tt ≈ τp and a maximum when Tt ≈ τs. We find that polymers with a small segment length exhibit a more compact structure than those with larger segment lengths. We also find that the switching can lead to higher contact probability and better mixing of far-away segments. Our study also shows that the nature of the distribution of chromatin clusters varies widely as we change the switching rate.