DNA Sequence and Histone Variant H2A.Z Jointly Govern Nucleosome Unwrapping Pathways

Abstract

Nucleosome unwrapping governs chromatin accessibility and gene regulation, yet the molecular determinants of unwrapping directionality remain poorly understood. Using atomistic and SIRAH coarse-grained umbrella sampling simulations, we show that DNA sequence and histone variant composition jointly tune a directional preference for nucleosome unwrapping. For both the ASP and Widom-601 sequences, unwrapping initiates asymmetrically from a preferred DNA end, with progressive disengagement of the H3 N-terminal tail providing the molecular switch that determines directionality in the Widom-601 system. Substitution of canonical H2A with the variant H2A.Z reverses this directional preference, shifting unwrapping to the opposite DNA end and altering the free energy landscape. SIRAH coarse-grained simulations faithfully reproduce these sequence- and variant-dependent unwrapping pathways and their qualitative free energy features, though quantitative barrier heights differ from atomistic values, identifying a target for further force field refinement. Comparing the H3 tail flexibility from atomistic simulations with published solution NMR amide intensities for two Widom-601 constructs corroborates the fast-timescale tail dynamics and points to a sequence-dependent, microsecond-millisecond exchange component at the H3 tail-core junction. Together, these results establish H3 tail - DNA disengagement, corroborated by NMR data, as a key mechanistic determinant of unwrapping directionality, reveal how a single histone variant substitution can reverse this preference, and validate SIRAH as an efficient framework for large-scale chromatin simulations.