Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of nucleosome arrays

Jia Gao, Hongyun Li, Song Tan, Ruobo Zhou and Tae-Hee Lee ()
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Jia Gao: The Pennsylvania State University, Department of Chemistry
Hongyun Li: The Pennsylvania State University, Department of Chemistry
Song Tan: The Pennsylvania State University, Department of Biochemistry and Molecular Biology
Ruobo Zhou: The Pennsylvania State University, Department of Chemistry
Tae-Hee Lee: The Pennsylvania State University, Department of Chemistry

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Chromatin condensation is dynamically regulated throughout the cell cycle and plays key roles in modulating gene accessibility. The DNA-histone dynamics in the nucleosome are central to the regulation mechanisms of chromatin condensation, which remain poorly understood. Employing fluorescence recovery after photobleaching, optical super-resolution imaging, and microrheology with optical tweezers, we investigated the roles of various parameters in regulating phase-separation of 12-mer nucleosome arrays. Here, we show that histone H4 tail lysine residues are the main drivers of liquid-liquid phase separation of nucleosome arrays. We also show that the condensed liquid-like droplets comprise a mobile fraction and a relatively immobile structural scaffold. Histone chaperone Nap1 and histone H3 tail acetylation enhance DNA-histone dynamics within this scaffold, thereby lowering the overall viscosity of the droplets. These results suggest that histone chaperone and histone H3/H4 tails play critical roles in regulating chromatin condensation and gene accessibility in condensed chromatin.

Date: 2025
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DOI: 10.1038/s41467-025-65701-3

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