Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2018 May 22;114(10):2262-2270.
doi: 10.1016/j.bpj.2018.03.011. Epub 2018 Apr 6.

Formation of Chromatin Subcompartments by Phase Separation

Affiliations
Review

Formation of Chromatin Subcompartments by Phase Separation

Fabian Erdel et al. Biophys J. .

Abstract

Chromatin is partitioned on multiple length scales into subcompartments that differ from each other with respect to their molecular composition and biological function. It is a key question how these compartments can form even though diffusion constantly mixes the nuclear interior and rapidly balances concentration gradients of soluble nuclear components. Different biophysical concepts are currently used to explain the formation of "chromatin bodies" in a self-organizing manner and without consuming energy. They rationalize how soluble protein factors that are dissolved in the liquid nuclear phase, the nucleoplasm, bind and organize transcriptionally active or silenced chromatin domains. In addition to cooperative binding of proteins to a preformed chromatin structure, two different mechanisms for the formation of phase-separated chromatin subcompartments have been proposed. One is based on bridging proteins that cross-link polymer segments with particular properties. Bridging can induce a collapse of the nucleosome chain and associated factors into an ordered globular phase. The other mechanism is based on multivalent interactions among soluble molecules that bind to chromatin. These interactions can induce liquid-liquid phase separation, which drives the assembly of liquid-like nuclear bodies around the respective binding sites on chromatin. Both phase separation mechanisms can explain that chromatin bodies are dynamic spherical structures, which can coalesce and are in constant and rapid exchange with the surrounding nucleoplasm. However, they make distinct predictions about how the size, density, and stability of chromatin bodies depends on the concentration and interaction behavior of the molecules involved. Here, we compare the different biophysical mechanisms for the assembly of chromatin bodies and discuss experimental strategies to distinguish them from each other. Furthermore, we outline the implications for the establishment and memory of functional chromatin state patterns.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Models for the formation of chromatin subcompartments. (A) Chromatin regions containing nucleosomes with specific binding sites (gray) can form subcompartments by conceptually different mechanisms as shown in the following panels. Intermediate cases are also possible depending on the properties of the proteins involved. (B) Protein binding without phase separation is shown. The interacting protein (dark brown) will follow the preexisting 3D chromatin conformation. It can yield localized enrichment because of clustering of binding sites, cooperative binding, and/or allostery. (C) Polymer-polymer phase separation (PPPS). The formation of an ordered globule is induced via proteins (blue) that bridge nucleosomes residing in close spatial proximity to each other. (D) Liquid-liquid phase separation (LLPS). A chromatin-associated liquid-like droplet is formed, which is stabilized by proteins (light green) that exhibit multivalent interactions among each other. (E) Upon removal of the chromatin scaffold, the body will fall apart for simple chromatin binding and PPPS. In case of LLPS, the liquid-like protein droplet is predicted to persist. To see this figure in color, go online.
Figure 2
Figure 2
Response of chromatin bodies to concentration changes in the nucleoplasm. The axis label “Body + or –” denotes the position of the respective genomic region inside or outside of the chromatin body. The gray dots in the plots represent binding sites corresponding to gray nucleosomes in the cartoon. (A) For PPPS, the chromatin region that contains binding sites (gray) for bridging factors organizes into a collapsed/ordered chromatin globule when bridging factors are added. The genomic extension of the globule remains invariant if the concentration of bridging proteins is further increased. At very high concentrations, binding sites might become saturated and the size of the body might increase (not depicted in the figure). (B) For LLPS, the initial formation of chromatin bodies can occur with or without compaction of the incorporated chromatin (depending on the ability of multivalent binders to bridge chromatin segments). The bodies become larger if the concentration of multivalent binders is increased. This should lead either to the incorporation of adjacent chromatin regions into the chromatin body (top) or to decondensation of the chromatin region that is “dissolved” in the chromatin body (bottom). At very high concentrations, the dense liquid phase might become a gel or an aggregate (not depicted in the figure). To see this figure in color, go online.
Figure 3
Figure 3
Properties of chromatin bodies that are informative about the underlying assembly mechanism. Chromatin bodies formed by PPPS and LLPS are shown in blue and beige colors, respectively. (A) PPPS predicts strict colocalization of bridging proteins and chromatin, whereas LLPS establishes a homogeneous liquid-like phase around the chromatin fiber. (B) Both models are compatible with dynamic exchange of constituents. Transport across the phase boundaries is regulated by their different molecular properties. (C) Once nucleated, phase-separated droplets formed via LLPS should be stable independently of the chromatin scaffold. (D) Increasing the concentration of the constituting factors in the nucleus can have different effects on phase-separated chromatin bodies. For PPPS, the size of collapsed chromatin bodies remains constant, whereas the concentration of chromatin binders in the body increases. Chromatin bodies formed by LLPS show the opposite behavior, i.e., their size increases but the concentration of chromatin binders in the body is not changed. (E) Coalescence upon contact between two chromatin bodies is shown. The geometry of the intermediate state and the coalescence rate should differ in PPPS and LLPS because of the surface tension at the liquid-liquid interface in LLPS. To see this figure in color, go online.

Similar articles

Cited by

References

    1. Meldi L., Brickner J.H. Compartmentalization of the nucleus. Trends Cell Biol. 2011;21:701–708. - PMC - PubMed
    1. Rippe K. Dynamic organization of the cell nucleus. Curr. Opin. Genet. Dev. 2007;17:373–380. - PubMed
    1. Mao Y.S., Zhang B., Spector D.L. Biogenesis and function of nuclear bodies. Trends Genet. 2011;27:295–306. - PMC - PubMed
    1. Cremer T., Cremer M., Cremer C. The 4D nucleome: evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments. FEBS Lett. 2015;589:2931–2943. - PubMed
    1. Boisvert F.M., van Koningsbruggen S., Lamond A.I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 2007;8:574–585. - PubMed

Publication types