Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ

• Published in: eLife Vol. 12
• Main Authors: Tan, Zhi Yang, Cai, Shujun, Noble, Alex J, Chen, Jon K, Shi, Jian, Gan, Lu
• Format: Journal Article
• Language: English
• Published: England eLife Science Publications, Ltd 28.07.2023; eLife Sciences Publications Ltd; eLife Sciences Publications, Ltd
• Subjects: Analysis; Cell Biology; Chromatin; Chromosomes and Gene Expression; Classification; cryo-ET; cryo-FIB; Crystal structure; Histone H2A; Lysates; nucleosome; Nucleosomes; Scientific equipment and supplies industry; Yeast; United States; cryo-FIB; cell biology; chromosomes; nucleosome; cryo-ET; chromatin; gene expression; S. cerevisiae
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.87672

Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes (inside cells) resembles the canonical structure determined 25 years ago. Nucleosome structure 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 . 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 (in nuclear lysates), but not . 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 .