Molecular Dynamics-Guided All-Atom Reconstruction of Cryo-ET Maps Reveals Mechanisms of Histone Tail-Mediated Chromatin Compaction

Abstract

Dynamics and physical state of chromatin are crucial in regulating gene expression, DNA replication, and repair. Intrinsically disordered histone tails were previously recognized as key modulators of chromatin states. However, detailed atomistic mechanisms by which histone tail dynamics are associated with chromatin compaction and higher-order chromatin organization remain poorly understood. In this work, we combine extensive all-atom molecular dynamics simulations of tri-nucleosomes with cryo-electron tomography (Cryo-ET) of native nucleosome arrays to investigate histone tail-mediated chromatin folding. Our approach offers distinct advantages as it elucidates realistic inter- and intra-nucleosomal interactions and DNA conformations derived from physics-based MD simulations, enabling a more accurate and physically grounded interpretation of Cryo-ET data. The results reveal that histone tails promote chromatin compaction and constrain tri-nucleosome unfolding via three major patterns: through histone-DNA interactions, histone H2A-H4 and H3-H4 tail-tail interactions. Notably, the distributions of MD-generated structural parameters of tri-nucleosomes with truncated histone tails were found to be in strong agreement with those of experimental open chromatin arrays with widely spaced nucleosomes, whereas the system with histone tails resembled more condensed chromatin. These findings provide mechanistic insights into how histone tails may mediate chromatin folding at the atomistic scale and underscore the dual role of histone tails in both structural compaction and inter-nucleosomal communication.