Phase separation drives heterochromatin domain formation

By Amy R. Strom, A. Emelyanov, Mustafa Mir, D. Fyodorov, X. Darzacq, G. Karpen. Nature, 2017

1,587 citations recorded by the source corpus.

Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: that the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments. We show that Drosophila HP1a protein undergoes liquid–liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/964d715215e8b47fa3e3838564d358c55e870a96

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Citations in the corpus

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome. (2018, positive): “HP1 has been described as a phase separation prone-protein, whose ability to form condensed liquid droplets could facilitate chromatin compaction (Larson et al., 2017; Strom et al., 2017).”
Coactivator condensation at super-enhancers links phase separation and gene control (2018, background): “Why do some proteins, such as HP1a, contribute to phase-separated heterochromatin condensates (59, 60) and others contribute to euchromatic condensates? The rules that govern partitioning into specific types of condensates have begun to be studied (61–65) andwill need to be defined for proteins invo”
Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins (2022, positive): “There is recent interest in phase-separated liquid droplets in heterochromatin organization (Larson et al. 2017; Strom et al. 2017; Sanulli et al. 2019; Wang et al. 2019).”
Chromatin organization by an interplay of loop extrusion and compartmental segregation (2017, methodology): “Conversely, perturbations altering the nuclear volume or the compartmental interaction, e.g. by changing the epigenetic landscape or mediators of compartment interactions, possibly HP1 (44, 45), are expected to affect compartmentalization, while leaving TADs unaffected.”
The multidimensional mechanisms of long noncoding RNA function (2017, background): “Moreover, emerging evidence supports the notion that nuclear compartmentalization could be based on liquid-phase separation dependent on the biophysical properties of the molecules that constitute the distinct chromatin domains [105].”
Ki-67: more than a proliferation marker (2018, background): “Ki-67 may also form a charged surface coating on nucleoli in analogy to its role on mitotic chromosomes (Cuylen et al. 2016) and thereby attract heterochromatin (Larson et al. 2017; Strom et al. 2017).”
Organization of Chromatin by Intrinsic and Regulated Phase Separation (2019, background): “This chromatin phase separation then could act together with the recently demonstrated phase separation of proteins that are unique to different chromatin sub-types (Larson et al., 2017; Plys et al., 2019; Sabari et al., 2018; Strom et al., 2017) to produce the full regulatory capacity and functiona”
Competing protein-RNA interaction networks control multiphase intracellular organization (2020, positive): “Several studies suggest that dimerization of substrate-binding domains might be sufficient for assembly of certain condensates (Larson et al., 2017; Strom et al., 2017).”