Histone Surface Exposure Drives Nucleosome Stacking Diversity Through DNA Engagement in Trans

Intrinsic nucleosome dynamics, particularly changes in entry-exit DNA wrapping due to nucleosome breathing, contribute to local chromatin structural heterogeneity. This process exposes otherwise buried histone surfaces, yet the structural mechanisms by which these changes drive diverse nucleosome stacking arrangements remain poorly understood. Here, we determined cryo-EM structures of nucleosome core particles (NCPs) reconstituted with DNA truncated at superhelical locations (SHL) -4.5 and -5.5, mimicking varying extents of histone surface exposure at the nucleosome entry-exit site. We found that the exposed histone surfaces, specifically the H3 αN loop-helix and H2A loop 2, directly engage the DNA gyre of neighboring nucleosomes in a manner analogous to canonical histone-DNA contacts within a nucleosome. These interactions, influenced by the degree of histone surface exposure and ionic strength, act as primary anchors to facilitate the formation of diverse oligonucleosome assemblies. These stacking arrangements predominantly adopt a side-to-face geometries, which is distinct from the commonly observed near-parallel face-to-face inter-nucleosome associations. Our findings provide a structural basis for understanding how entry-exit histone surface exposure generates heterogeneous inter-nucleosome interactions and potentially shapes local chromatin architecture.