Linker histone H1 and H3K56 acetylation are antagonistic regulators of nucleosome dynamics.

H1 linker histones are highly abundant proteins that compact nucleosomes and chromatin to regulate DNA accessibility and transcription. However, the mechanisms that target H1 regulation to specific regions of eukaryotic genomes are unknown. Here we report fluorescence measurements of human H1 regulation of nucleosome dynamics and transcription factor (TF) binding within nucleosomes. H1 does not block TF binding, instead it suppresses nucleosome unwrapping to reduce DNA accessibility within H1-bound nucleosomes. We then investigated H1 regulation by H3K56 and H3K122 acetylation, two transcriptional activating histone post translational modifications (PTMs). Only H3K56 acetylation, which increases nucleosome unwrapping, abolishes H1.0 reduction of TF binding. These findings show that nucleosomes remain dynamic, while H1 is bound and H1 dissociation is not required for TF binding within the nucleosome. Furthermore, our H3K56 acetylation measurements suggest that a single-histone PTM can define regions of the genome that are not regulated by H1.

Histone H3 and H4 N-terminal tails in nucleosome arrays at cellular concentrations probed by magic angle spinning NMR spectroscopy.

Chromatin is a supramolecular assembly of DNA and histone proteins, organized into nucleosome repeat units. The dynamics of chromatin organization regulates DNA accessibility to eukaryotic transcription and DNA repair complexes. Yet, the structural and dynamic properties of chromatin at high concentrations characteristic of the cellular environment (>∼200 mg/mL) are largely unexplored at the molecular level. Here, we apply MAS NMR to directly probe the dynamic histone protein regions in (13)C,(15)N-enriched recombinant nucleosome arrays at cellular chromatin concentrations and conditions designed to emulate distinct states of DNA condensation, with focus on the flexible H3 and H4 N-terminal tails which mediate chromatin compaction. 2D (1)H-(13)C and (1)H-(15)N spectra reveal numerous correlations for H3 and H4 backbone and side-chain atoms, enabling identification of specific residues making up the dynamically disordered N-terminal tail domains. Remarkably, we find that both the H3 and H4 N-terminal tails are overall dynamic even in a highly condensed state. This significant conformational flexibility of the histone tails suggests that they remain available for protein binding in compact chromatin states to enable regulation of heterochromatin. Furthermore, our study provides a foundation for quantitative structural and dynamic investigations of chromatin at physiological concentrations.