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Active Hydrodynamic Theory of Euchromatin and Heterochromatin

S. Alex Rautu1, Alexandra Zidovska2, David Saintillan3, and Michael J. Shelley1,4

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Phys. Rev. X 16, 021009 – Published 9 April, 2026

DOI: https://doi.org/10.1103/8n8h-7gx6

Abstract

The genome contains genetic information essential for a cell’s life. The genome’s spatial organization inside the cell nucleus is critical for its proper function including gene regulation. The two major genomic compartments, euchromatin and heterochromatin, contain largely transcriptionally active and silenced genes, respectively, and exhibit distinct dynamics. In this work, we present a hydrodynamic framework that describes the large-scale behavior of euchromatin and heterochromatin and accounts for the interplay of mechanical forces, active processes, and nuclear confinement. Our model shows contractile stresses from cross-linking proteins lead to the formation of heterochromatin droplets via mechanically driven phase separation. These droplets grow, coalesce, and, in nuclear confinement, wet the boundary. Active processes, such as gene transcription in euchromatin, introduce nonequilibrium fluctuations that drive long-range, coherent motions of chromatin as well as the nucleoplasm and, thus, alter the genome’s spatial organization. These fluctuations also indirectly deform heterochromatin droplets, by continuously changing their shape. Taken together, our findings reveal how active forces, mechanical stresses, and hydrodynamic flows contribute to the genome’s organization at large scales and provide a physical framework for understanding chromatin organization and dynamics in live cells.

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Popular Summary

Chromatin, the functional form of DNA in cells, is a polymer immersed in the nucleoplasmic fluid inside the cell nucleus. It typically segregates into two phases: heterochromatin and euchromatin. Their segregation is often spatially patterned, with euchromatin enriched in the nuclear interior and heterochromatin concentrated near the nuclear envelope. We develop a multiphase continuum model that shows how mechanical forces and flows can drive chromatin phase segregation. Crosslinking proteins within heterochromatin generate contractile forces that pull it together into dropletlike domains that grow and merge over time. Confinement then favors their relocation and spreading along the nuclear envelope, producing a peripheral heterochromatin layer. Transcription-driven active forces in euchromatin drive nucleus-scale flows that deform and reorganize heterochromatin into many different morphologies. Overall, we present a theoretical framework linking active processes in chromatin to its mechanics, nucleus-wide patterning, and motion.

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Phys. Rev. X 16, 021009– Published 9 April, 2026
  • Received 31 March 2025
  • Accepted 23 February 2026
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