Kozlowska, M. | Search bioRxiv

bioRxiv2026

DNA Sequence Differentially Modulates Histone Core and Tail Interactions in Canonical and Centromeric Nucleosomes

Human centromeric chromatin is a specialized chromatin domain characterized by CENP-A-containing nucleosomes interspersed with canonical histone H3 nucleosomes. It is assembled on tandem repeats of -satellite DNA and defines centromere identity. How histone variant identity and DNA sequence jointly shape nucleosome structure and histone-DNA interactions that underpin centromeric chromatin formation remains incompletely understood. Here, we investigate the structural plasticity of the histone core and nucleosomal DNA, histone tail dynamics and DNA-sequence dependent changes for canonical (H3) and centromeric (CENP-A) nucleosomes using the SIRAH coarse-grained molecular dynamics (CG-MD) simulations. Nucleosomes containing -satellite positioning sequence (ASP) and Widom 601 DNA sequence are systematically analyzed and compared. Our simulations reveal that the centromeric nucleosome exhibits a more stable histone core with lower structural plasticity and the histone tails engage DNA differently with an overall reduction in the histone-DNA contacts compared to the canonical nucleosome. Further investigation of CENP-N binding to the CENP-A nucleosome demonstrates substantial modulation of nucleosomal DNA dynamics and histone-DNA interactions. Replacing the ASP DNA sequence with the Widom 601 sequence preserves the stability of both types of the histone core while markedly altering histone-tail dynamics. The conformational dynamics of canonical nucleosomes is more strongly affected by the Widom 601 DNA sequence than those of their centromeric counterparts. However, CENP-N binding induces more spatially extensive changes in DNA geometry in Widom 601 than in ASP DNA. Our findings suggest that DNA sequence and histone composition have residue-level differences translating into distinct nucleosome dynamics, which could be among the determinants governing the structural and dynamic properties of centromeric chromatin and its biological function.

biophysics↗

bioRxiv2025

Structural dynamics in the CENP-A nucleosome impacted by protein-protein interactions with centromere protein N

Noncanonical nucleosomes at the centromere contain the histone variant CENP-A, playing a crucial role in chromosome segregation. CENP-A is highly regulated and its centromeric organization is partially regulated by the centromere protein N (CENP-N). Despite its importance, the protein-protein interactions within the complex formed between CENP-A nucleosomes and CENP-N remain poorly understood at a molecular level. Here, we employ the SIRAH coarse-grained molecular dynamics (MD) simulations to investigate the binding interface and structural rearrangements of proteins in the CENP-A nucleosome complexed with CENP-N. We aim to assess the stability of the CENP-A nucleosome and the change in its plasticity upon the CENP-N binding. By the set of {micro}s-long MDs, we reveal enhanced flexibility in the N-terminal region of CENP-A and stabilization of its RG loop in the complex with CENP-N. This is demonstrated to have rather minor effects on the overall stability of the nucleosome and changing its compactness. Nevertheless, the data suggest the binding of CENP-N allosterically changes the conformational states of CENP-A and impacts its interactions with other proteins in the histone core. A distance-based contact map analysis further elucidates key residues mediating the interaction between CENP-A and CENP-N, while umbrella sampling simulations quantify their binding free energy, which remains challenging to measure experimentally.

biophysics↗