Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ

Abstract

Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes <i>in situ</i> (inside cells) resembles the canonical structure determined <i>in vitro</i> 25 years ago. Nucleosome structure <i>in situ</i> is otherwise poorly understood. Using cryo-electron tomography (cryo-ET) and 3D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected <i>in situ</i>. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found <i>ex vivo</i> (in nuclear lysates), but not <i>in situ</i>. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome's DNA is partially detached <i>in situ</i>.