DNA length tunes the fluidity of DNA-based condensates

Abstract

Living organisms typically store their genomic DNA in a condensed form. Mechanistically, DNA condensation can be driven by macromolecular crowding, multivalent cations, or positively charged proteins. At low DNA concentration, condensation triggers the conformational change of individual DNA molecules into a compacted state, with distinct morphologies. Above a critical DNA concentration, condensation goes along with phase separation into a DNA-dilute and a DNA-dense phase. The latter DNA-dense phase can have different material properties and has been reported to be rather liquid-like or solid-like depending on the characteristics of the DNA and the solvent composition. Here, we systematically assess the influence of DNA length on the properties of the resulting condensates. We show that short DNA molecules with sizes below 1 kb can form dynamic liquid-like assemblies when condensation is triggered by polyethylene glycol and magnesium ions, binding of linker histone H1, or nucleosome reconstitution in combination with linker histone H1. With increasing DNA length, molecules preferentially condense into less dynamic more solid-like assemblies, with phage l-DNA with 48.5 kb forming mostly solid-like assemblies under the conditions assessed here. The transition from liquid-like to solid-like condensates appears to be gradual, with DNA molecules of roughly 1-10 kb forming condensates with intermediate properties. Titration experiments with linker histone H1 suggest that the fluidity of condensates depends on the net number of attractive interactions established by each DNA molecule. We conclude that DNA molecules that are much shorter than a typical human gene are able to undergo liquid-liquid phase separation, whereas longer DNA molecules phase separate by default into rather solid-like condensates. We speculate that the local distribution of condensing factors can modulate the effective length of chromosomal domains in the cell. We anticipate that the link between DNA length and fluidity established here will improve our understanding of biomolecular condensates involving DNA.

Shelterin components modulate nucleic acids condensation and phase separation in the context of telomeric DNA

“…Similar results can be recapitulated using coarse-grained simulations that capture the overall trends of DNA compaction and phase separation propensity in the presence of a ligand. Taken all together, our observations support the original interpretation proposed by Post and Zimm (18) and are consistent with the idea that protein-dependent collapse of a single nucleic acid chain and the phase separation of mixtures of protein and nucleic acids are two distinct outcomes driven by the same set of molecular interactions (68, 82, 83).…”

“…One interpretation of these results reflects a model in which HP1a drives heterochromatin territories through bona fide liquid-liquid phase separation (7, 8, 21). Another is that the intrinsically multivalent nature HP1a and many other DNA binding proteins (such as TRF2) drives DNA compaction through distributed multivalent interactions which will inevitably also drive phase separation with sufficiently short nucleic acid molecules in vitro (68, 82, 88). Altering the degree of DNA compaction by modulating the same interactions that would also drive phase separation could allow for the rheostatic control of access to genomic loci.…”

In Diverse Conditions Intrinsic Chromatin Condensates Have Liquid-like Material Properties

“…To demonstrate how introducing one of these additional constraints, the very long length of chromosomes, would affect FRAP behavior we formed condensates composed of nucleosomal arrays with increasing length and found that photobleach recovery lessens at longer chromatin sizes (Figures 6A-6D). This length-dependent effect on condensate dynamics is general, as recently demonstrated with other biomolecular condensates in vitro (Keenen et al, 2021;Muzzopappa et al, 2021) or by fragmenting mitotic chromatin in cells (Schneider et al, 2021). This slowing of dynamics is driven by length-dependent steric occlusion of movement by neighboring molecules and increases in intermolecular contacts (Rubinstein and Colby, 2003).…”

The solid and liquid states of chromatin

“…It should be noted that the liquid chromatin droplets have high internal viscosity and are not particularly fluid [ 33 ]. Of note, it has recently been demonstrated that the material state of DNA-based condensates is sensitive to the DNA fragment length [ 65 ]. For both H1–DNA condensates and nucleosomal arrays, shorter (< 1 kb) DNAs formed liquid condensates while longer fragments formed more solid condensates.…”