Force generation by protein-DNA co-condensation

Abstract

SummaryCapillary forces are driven by interactions between liquids and surfaces1. These forces are crucial for many processes ranging from biology and physics to engineering, such as the motion of aquatic insects on the surface of water2, modulation of the material properties of spider silk3,4, and self-assembly of small objects and microstructures5. Recent studies have shown that cells assemble biomolecular condensates in a manner similar to phase separation6. In the nucleus, these condensates are thought to drive transcription7–10, heterochromatin formation11,12, nucleolus assembly13,14, and DNA repair15,16. Here, we test if the interaction between liquid-like condensates and chromatin generates capillary forces, which might play a role in bringing distant regulatory elements of DNA together, a key step in transcriptional regulation. We combine quantitative microscopy, in vitro reconstitution, and theory to show that the pioneer transcription factor FoxA1 mediates the condensation of a DNA-protein phase via a mesoscopic first-order phase transition. Surprisingly, after nucleation, capillary forces drive growth of this phase by pulling non-condensed DNA. Altering the tension on the DNA strand enlarges or dissolves the condensates, revealing their mechanosensitive nature. These findings show that DNA condensation mediated by transcription factors could bring distant regions of DNA in close proximity using capillary forces. Our work suggests that the physics of DNA and protein condensation driven by capillary forces provides a general regulatory principle for chromatin organization.

RNA polymerase II clusters form in line with liquid phase wetting of chromatin

“…The causal relevance of Pol II phosphorylation is supported by the application of chemical inhibitors of Pol II phosphorylation, which induces changes in cluster morphology and cluster number that are in line with predictions from our lattice simulations. In combination with previous work on Pol II liquid phase behavior 13,14 and studies showing condensation of transcription factors by wetting of DNA in vitro 23,24 , our findings in zebrafish, an embryonic model system, suggest that similar liquid phase wetting of chromatin might also occur in vivo.…”

“…Formation of macromolecular clusters at genomic target regions has recently been described using a model of liquid phase condensation on polymers as microscopic surfaces 13,14,23,24 . To test whether such a model can reproduce the different cluster morphologies seen in our experiments, we implemented corresponding lattice kinetic Monte Carlo (LKMC) simulations 31,32 (for details see Supplementary Material).…”

“…In other cases, formation of clusters requires transcriptional activity at specific genomic loci, suggesting a more complex scenario than canonical LLPS 10,13,14 . Recent in vitro studies of condensate formation on DNA suggest that liquid phase condensation that requires a condensation surface can be accurately described as wetting by a sub-saturated liquid phase 23,24 . Our work in an embryonic model system suggests that the formation of clusters enriched in recruited Pol II might proceed similarly by liquid phase wetting with chromatin as a condensation surface.…”

Co-condensation of proteins with single- and double-stranded DNA

“…FUS-ssDNA co-condensate have liquid-like properties (see above). Capillary forces are mechanical forces that are generated by a fluid when contacting a surface (de Gennes, Brochard-Wyart and Quéré, 2004; Quail et al ., 2020). Given that self-interactions of the FUS-ssDNA polymer can generate a liquid phase, it is tempting to speculate that this can give rise to generalized capillary forces for liquid phases consisting of collapsed self-interacting polymers.…”

“…Such condensates have been suggested to play an important role in the generation of transcriptional hubs that could coordinate the expression of several genes and mediate enhancer function (Cho et al ., 2018; Sabari et al ., 2018; Guo et al ., 2019; Henninger et al ., 2021). Recently it was shown that a pioneer transcription factor can form co-condensates together with DNA in vitro (Quail et al ., 2020). Some membrane-less compartment in the cell nucleus, such as the nucleolus, show all the features of liquid-like condensates (Brangwynne, Mitchison and Hyman, 2011; Feric et al ., 2016).…”