Liquid-liquid phase separation (LLPS) inside the nucleus

This blog sums up the One paper One week LinkedIn series of the past two weeks: check out days 1-4 here.

This one is based on a recent publication (March 2026) by Juan Ausio, from the University of Victoria and Jim Davie from the University of Manitoba, Canada:

"From chromosomal protein disorder to chromatin phase separation."

LLPS is a process where a homogenous ‘one-phase’ liquid of several components spontaneously separates into two distinct phases of different concentrations. LLPS is vital to the compartmentalization of membrane-less biological condensates within the cell. Chromatin adds another layer. In two extreme cases of chromatin compaction, we look into how it can be both liquid-like and solid-like.

Two extremes: somatic vs sperm chromatin

Somatic chromatin

In cells with a nucleus, DNA is packaged with basic, lysine and arginine-rich histones. Together, they act like a viscoelastic polymer: they are dynamic yet can organize into assemblies (Fig.3 B). When the conditions are favourable, nucleosome arrays can undergo LLPS, forming condensates that help regulate gene expression and nuclear organization. However, this separation is highly dynamic and sensitive to changes in pH, histone modifications, which can shift the chromatin from liquid-like to solid-like.

Sperm chromatin (protamine-based)

First connection of chromatin and LLPS was recognized via spinodal decomposition, imaged via transmission electron microscopy (TEM) of late spermatids of the gastropod snail. Spinodal decomposition results in the formation of a liquid-like layered lamella (Figure 3; A-C), which is followed by extreme compaction during the histone to protamine transition.

Despite the compaction, this dense packing of DNA by protamine is reversible.

Vertebrae sperm also shows chromatin condensates during spermiogenesis. In birds and mammals, the condensates can take the form of a rod or a toroid, 40nm thick and 90nm in diameter.

Figure 3 taken directly from the paper; no modifications (Davie and Ausio, 2026) Chromatin phase separation in sperm and somatic cells. (A) During spermiogenesis, chromatin undergoes spinodal decomposition, forming wave-like lamellar structures that reorganize into highly compact sperm chromatin. This process is conserved across species and involves protamine processing and modification. (d) shows protamine-like proteins being processed from protamine-like precursor into the final protamine during spermiogenesis. Blue arrows show the cleavage sites. WHD: winged helix domain. (B) In somatic cells, chromatin can undergo liquid–liquid phase separation (a-b). Reconstituted chromatin forms droplet-like condensates in vitro; c-d show the nucleus from a neuronal cell line with the punctuate pattern of chromatin condensates containing linker histone H1.4.

Polymer perspective

Chromatin is like a polymer. Whether from histones or protamines, chromatin can:

• Self-associate

• Respond to environmental changes

• Phase-separate to form higher-order structures

  
  

This is nothing new. Polymer physics has noticed this behaviour a long ago. Nevertheless, this perspective of chromatin polymer provides a powerful understanding of how genome organization emerges from physical principles.

 

Chromatin, constant communicator

Chromatin does not act alone, and it is in constant communication with:

• linker histone H1

• epigenetic writers (DNMT), readers (MeCP2) and erasers (HDAC)

• other chromatin-associated proteins

  
  

These ‘communications’ drive the formation of localized condensates, which correspond to topologically associated domains (TADs); these are regions within the chromatin that interact more frequently with one another than with other parts of the chromatin.

 

Here, intrinsically disordered proteins (or regions within proteins) come back into the picture. Their ability to mediate weak, multivalent interactions enables these condensates to form, adapt, respond and reorganize.

 

Shifting the understanding of chromatin

Chromatin was originally thought of as a static structure, which could not be further from what we now know it to be: highly dynamic, constantly in flux, and responsive.

Through LLPS, chromatin can:

• Reorganize & compartmentalize

• Respond to cellular stress or other signals

  
  

And at its core are disordered regions and weak multivalent interactions. Intrinsic disorder regions of proteins provide the prerequisite, through their numerous binding partners and interaction types, for chromatin to separate into liquid or solid-like phases.

Full Reference:

Davie, J.R., and J. Ausio. 2026. From chromosomal protein disorder to chromatin phase separation. Epigenetics Chromatin.