Abstract
Organization of the genome into transcriptionally active euchromatin and silenced heterochromatin is essential for eukaryotic cell function. Phase-separation has been implicated in heterochromatin formation, but it is unclear how phase-separated condensates can contribute to stable repression, particularly for heritable epigenetic changes. Polycomb complex PRC1 is key for heterochromatin formation, but the multitude of Polycomb proteins has hindered our understanding of their collective contribution to chromatin repression. Here, we show that PRC1 forms multicomponent condensates through hetero-oligomerization. They preferentially seed at H3K27me3 marks, and subsequently write H2AK119Ub marks. We show that inducing Polycomb phase-separation can cause chromatin compaction, but polycomb condensates are dispensable for maintenance of the compacted state. Our data and simulations are consistent with a model in which the time integral of Polycomb phase-separation is progressively recorded in repressive histone marks, which subsequently drive compaction. These findings link the equilibrium thermodynamics of phase-separation with the fundamentally non-equilibrium concept of epigenetic memory.
Highlights
Organization of the genome into transcriptionally active euchromatin and silenced heterochromatin is essential for eukaryotic cell function
Constitutive heterochromatin is characterized by trimethylation of histone H3 on lysine 9 (H3K9me3) and the presence of heterochromatin protein 1 (HP1), while facultative heterochromatin is characterized by trimethylation of histone H3 on lysine 27 (H3K27me3)[6,7]
We adapted the previously published Corelet system[33] to develop light-activated, multicomponent Polycomb Repressive Complex 1 (PRC1) condensates, which allow mapping of subunit recruitment and collective propensity for phase separation. We note that this approach uses light-dependent optogenetic proteins to oligomerize phase separation-prone proteins and may exhibit differences from the biologically regulated oligomerization important for the formation and function of native condensates. These synthetic PRC1 condensates recapitulate key features of endogenous PRC1, including the ability to directly recognize and write histone marks associated with facultative heterochromatin
Summary
Organization of the genome into transcriptionally active euchromatin and silenced heterochromatin is essential for eukaryotic cell function. Our data and simulations are consistent with a model in which the time integral of Polycomb phaseseparation is progressively recorded in repressive histone marks, which subsequently drive compaction These findings link the equilibrium thermodynamics of phase-separation with the fundamentally non-equilibrium concept of epigenetic memory. Recent studies have provided support for the hypothesis that heterochromatin proteins may induce compaction through phase separation Both HP1 and Polycomb proteins exhibit features characteristic of many proteins that drive phase separation, including oligomerization domains, intrinsically disordered regions, and substrate (chromatin) binding domains[15]. Phase separation could potentially explain the mechanism behind heterochromatin spreading, a poorly understood phenomenon in which histone modifications defining the heterochromatin domain expand[22,23] These chromatin marks are typically inherited by daughter cells after division[24,25,26], while most phase-separated condensates dissolve during mitosis[27]. The potential role of liquid–liquid phase separation in the reading and writing of histone marks, and whether phase separation is necessary for chromatin compaction, remains unclear
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