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Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ
Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10382156/ https://www.ncbi.nlm.nih.gov/pubmed/37503920 http://dx.doi.org/10.7554/eLife.87672 |
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author | Tan, Zhi Yang Cai, Shujun Noble, Alex J Chen, Jon K Shi, Jian Gan, Lu |
author_facet | Tan, Zhi Yang Cai, Shujun Noble, Alex J Chen, Jon K Shi, Jian Gan, Lu |
author_sort | Tan, Zhi Yang |
collection | PubMed |
description | Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ 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 situ. 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 ex vivo (in nuclear lysates), but not in situ. 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 in situ. |
format | Online Article Text |
id | pubmed-10382156 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-103821562023-07-29 Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ Tan, Zhi Yang Cai, Shujun Noble, Alex J Chen, Jon K Shi, Jian Gan, Lu eLife Cell Biology Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ 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 situ. 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 ex vivo (in nuclear lysates), but not in situ. 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 in situ. eLife Sciences Publications, Ltd 2023-07-28 /pmc/articles/PMC10382156/ /pubmed/37503920 http://dx.doi.org/10.7554/eLife.87672 Text en © 2023, Tan, Cai, Noble et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Cell Biology Tan, Zhi Yang Cai, Shujun Noble, Alex J Chen, Jon K Shi, Jian Gan, Lu Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ |
title | Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ |
title_full | Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ |
title_fullStr | Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ |
title_full_unstemmed | Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ |
title_short | Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ |
title_sort | heterogeneous non-canonical nucleosomes predominate in yeast cells in situ |
topic | Cell Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10382156/ https://www.ncbi.nlm.nih.gov/pubmed/37503920 http://dx.doi.org/10.7554/eLife.87672 |
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