Liquid-like interactions in heterochromatin: Implications for mechanism and regulation

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Abstract

A large portion of the eukaryotic genome is packed into heterochromatin, a versatile platform that is essential to maintain genome stability. Often associated with a compact and transcriptionally repressed chromatin state, heterochromatin was earlier considered a static and locked compartment. However, cumulative findings over the last 17 years have suggested that heterochromatin displays dynamics at different timescales and size scales. These dynamics are thought to be essential for the regulation of heterochromatin. This review illustrates how the key principles underlying heterochromatin structure and function have evolved along the years and summarizes the discoveries that have led to the continuous revision of these principles. Using heterochromatin protein 1–mediated heterochromatin as a context, we discuss a novel paradigm for heterochromatin organization based on two emerging concepts, phase separation and nucleosome structural plasticity. We also examine the broader implications of this paradigm for chromatin organization and regulation beyond heterochromatin.

Section snippets

Heterochromatin organization and function

Heterochromatin is a highly conserved, structurally poorly defined type of chromatin that is essential for the functional organization of eukaryotic genomes. It was first described by Heitz [1] in 1928 as a chromatin region that remained visible and condensed throughout the cell cycle. Since its first observation, extensive research has identified many molecular features and mechanisms of action of heterochromatin. The two major types of heterochromatin are constitutive and facultative, defined

HP1-mediated heterochromatin as a model system for chromatin compaction

HP1 molecules are structural proteins that are at the core of constitutive heterochromatin organization and function [22]. Initially identified in Drosophila melanogaster, they are also highly conserved between yeast and humans. HP1 proteins consist of three conserved domains: the N-terminal chromodomain, which binds the H3K9me3 tail; the hinge region, which is flexible and binds nucleic acid; and the chromo shadow domain, which mediates HP1 dimerization and interacts with other proteins (

Nucleosome conformational dynamics can regulate chromatin phase separation

An extra level of complexity has been added by recent work showing that Swi6, the major Schizosaccharomyces pombe HP1 protein, induces conformational dynamics within the core of individual nucleosomes to drive heterochromatin phase separation [32] (Figure 2c). Such dynamics reshape nucleosomes and transiently expose buried regions of the folded core of the histone proteins. It is proposed that the exposed core residues participate in weak and dynamic between nucleosomes, thereby coupling phase

A liquid-like model for heterochromatin

Overall, these recent data reinforce the concept of a highly dynamic heterochromatin and provide the following new conceptualizations. First, chromatin is a fluid polymer whose compaction is coupled to its phase separation. Second, chromatin phase separation relies on internucleosomal interactions that can be regulated by chromatin-binding factors, such as HP1, and by chromatin properties, such as histone tail PTMs and nucleosome conformational dynamics. Third, these internucleosomal

Implications of nucleosome conformational dynamics

HP1-mediated nucleosome conformational dynamics on the atomic scale appear to be tightly coupled with the three-dimensional folding of chromatin and compaction into liquid droplets [32]. In this framework, we can imagine that changes in nucleosome structural flexibility will directly impact chromatin organization. Nucleosomes have been shown to adopt conformations distinct from the one seen in the crystal structure, and recent work suggests that nucleosomes in mitotic chromatin may adopt

Implications of phase separation by chromatin

Phase separation has not only been observed in the context of HP1-mediated heterochromatin. It has also been reported that phase separation of the Polycomb complex PRC1 is important for Polycomb-mediated chromatin compaction and gene regulation [50]. Furthermore, phase separation of many other chromatin-binding factors such as BRD4 has been linked to their functions on chromatin [51∗∗, 52, 53, 54, 55, 56]. The discovery of an increasing number of chromatin factors bearing phase separation

Challenges for the future

Despite having identified some of the key interactions that drive formation of HP1-mediated heterochromatin condensates, it remains unclear how HP1 and chromatin are structurally organized within droplets and how heterogeneous and diverse any such organization may be. For example, HP1 can phase separate upon phosphorylation, in the presence of DNA, or upon interaction with both unmethylated and H3K9me chromatin [25,32]. In these different contexts, the critical concentration required for phase

Conflict of interest statement

Nothing declared.

Acknowledgements

We thank JD Gross, N Gamarra, R Tibble for helpful comments on the manuscript and members of the Gross and Narlikar laboratories for stimulating discussion. We thank Draw In Science for the artwork. This work was supported by grant NIH NIH R01GM108455 and R35 GM127020 to GJN.

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      An alternative model for chromatin organization has been proposed recently based on the intrinsic property of chromatin to form liquid-like droplets by liquid-liquid phase separation (LLPS), both in vitro and in vivo (Gibson et al., 2019; Maeshima et al., 2016; Sanulli et al., 2019; Strom et al., 2017). LLPS is a physical process that generates spatially separated membrane-less domains inside the cell (Banani et al., 2017; Boeynaems et al., 2018; Brangwynne et al., 2009; Erdel and Rippe, 2018; Hubstenberger et al., 2017; Hyman et al., 2014; Sanulli and Narlikar, 2020); optically, they appear as liquid droplets that coexist with a dilute phase (Boeynaems et al., 2018). In this recent LLPS model, the phase transition of chromatin into droplets drives compartmentalization and organization of long-lasting multiphase systems (Palikyras and Papantonis, 2019; Shakya et al., 2020), which has been posited to control chromatin accessibility by the cellular machinery (Palikyras and Papantonis, 2019; Shin et al., 2018; Wright et al., 2019).

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      In this work, we simulated LLPS and the organization of multi-component systems with a near-atomistic model. We focused on the phase behavior of chromatin regulators that play crucial roles in heterochromatin formation and gene silencing, including heterochromatin protein 1 (HP1) and histone H1 (2,42). A recently developed force field, MOFF (43,44), which is well suited for simulating both ordered and disordered proteins, was combined with a chemically accurate DNA model (45) to study protein-DNA condensates.

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      Replication compartments may also represent distinct phases as the replication machinery, including origin recognition complex components, Cdc6 and Cdt1, contains evolutionarily conserved IDRs and forms liquid-like foci on DNA origins [54]. It is important to note that phase separation of chromatin into liquid-like bodies may not be a universal nor the exclusive physical mechanism of genome organization [55,56]. For example, mouse heterochromatin does not appear to exhibit canonical features of phase separation in vivo, as the heterochromatin compaction state is not influenced by HP1 levels as would be expected in a phase separation model [57].

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