Hydropathy Landscapes of Histone–DNA Interactions in Chromatin Building Blocks

Histone-DNA interactions define the fundamental building blocks of chromatin, yet their physicochemical organization is most often interpreted through structural and electrostatic descriptors. Here, we apply the Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) scale to multiple aspects of the nucleosome that are critical for DNA packaging, providing a residue-resolved, environment-dependent measure of hydrophobic and hydrophilic character. Using PARCH, we show that nucleobase hydropathy remains largely invariant upon nucleosome formation, whereas the DNA backbone undergoes a pronounced quantitative redistribution, yielding a bimodal hydropathy profile that distinguishes histone-contacting from solvent-exposed regions and arises from periodic histone-DNA contacts and conserved arginine anchors. Extending this framework, we demonstrate that histone core hydropathy is strikingly conserved across species that higher-order assembly into dinucleosomes─key structural intermediates in chromatin fiber formation─selectively reduces DNA backbone hydrophilicity at buried internucleosomal interfaces without altering histone hydropathy, and that the nucleosomal acidic patch remains largely hydropathy-insensitive to DNA wrapping. Finally, we show that cytosine methylation selectively decreases the DNA backbone hydrophilicity, providing a quantitative physicochemical mechanism for enhanced nucleosome stability. Taken together, these results illustrate how small, localized hydropathy modulations at histone-DNA interfaces can have outsized impacts on DNA packaging and chromatin organization and position PARCH as a powerful quantitative framework for mapping physicochemical landscapes across chromatin building blocks and epigenetically regulated states.