BPS2026 – Comparisons of H3 and CENP-A nucleosome stability using all-atom and coarse-grained simulations

Eukaryotic genomes are intricately organized within the nucleus as chromatin, wherein the fundamental subunit is the nucleosome. A nucleosome consists of DNA wrapped around an octamer of histone proteins, and its structure varies depending on histone variants. One notable variant is centromere protein A (CENP-A), which shares about 50% sequence similarity with canonical histone H3. Previous studies suggest that CENP-A nucleosomes display unique stability, with partially unwrapped DNA that facilitates kinetochore assembly. Disruption of this assembly can lead to mitotic arrest, improper chromosome segregation, or even apoptosis. The precise role of CENP-A N-terminal tails in nucleosome stability remains ambiguous, and their differential influence compared to the rest of the histone core is unclear. To investigate the structural roles of histone cores and N-terminal tails, we employed a mix of all-atom and coarse-grained molecular dynamics simulations of nucleosomes containing canonical H3, CENP-A, hybrids with swapped N-terminal tails, swaps of the α-N helices, swaps of both tails and α-N helices, and tailless variants, using both Widom 601 and centromeric α-satellite DNA. Analysis of DNA termini motion and Markov state models revealed distinct conformational states of the N-terminal tails and DNA positioning. Unlike our all-atom simulations, where the tails frequently remained above the nucleosome surface, the CG models showed that tails often moved into the DNA grooves and contacted the histone core at lower positions. These findings demonstrate that tail positioning and core identity jointly shape nucleosome dynamics. The extended timescales accessible in coarse-grained simulations uncovered alternative stabilizing modes not evident in all-atom trajectories, highlighting how complementary resolutions can provide a more complete picture. Together, these results clarify the differential roles of histone cores and tails in nucleosome stability and underscore the importance of simulation timescales in capturing chromatin dynamics.