The organization of heterochromatin, the part of the genome containing repressed genes, into three-dimensional compartments is essential for the correct functioning of cells. But the mechanisms governing this organization are still not fully understood. In a study published in PNAS, scientists have combined theoretical approaches with measurements on Drosophila embryos and shown that the structural and dynamic properties of these compartments are consistent with an organization pattern based on liquid-liquid phase separation coupled with the intrinsic mechanics of chromosomes.

Abstract

The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid–liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1–chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.

Reference

HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation. Maxime M.C. Tortora, Lucy D. Brennan, Gary Karpen, Daniel Jost. PNAS, August 7, 2023.
DOI : 10.1073/pnas.2211855120

Illustration credits: Maxime Tortora