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Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM)
Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that u...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9288481/ https://www.ncbi.nlm.nih.gov/pubmed/35842472 http://dx.doi.org/10.1038/s41598-022-16028-2 |
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author | Li, Yue Agrawal, Vasundhara Virk, Ranya K. A. Roth, Eric Li, Wing Shun Eshein, Adam Frederick, Jane Huang, Kai Almassalha, Luay Bleher, Reiner Carignano, Marcelo A. Szleifer, Igal Dravid, Vinayak P. Backman, Vadim |
author_facet | Li, Yue Agrawal, Vasundhara Virk, Ranya K. A. Roth, Eric Li, Wing Shun Eshein, Adam Frederick, Jane Huang, Kai Almassalha, Luay Bleher, Reiner Carignano, Marcelo A. Szleifer, Igal Dravid, Vinayak P. Backman, Vadim |
author_sort | Li, Yue |
collection | PubMed |
description | Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei. |
format | Online Article Text |
id | pubmed-9288481 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-92884812022-07-18 Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM) Li, Yue Agrawal, Vasundhara Virk, Ranya K. A. Roth, Eric Li, Wing Shun Eshein, Adam Frederick, Jane Huang, Kai Almassalha, Luay Bleher, Reiner Carignano, Marcelo A. Szleifer, Igal Dravid, Vinayak P. Backman, Vadim Sci Rep Article Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei. Nature Publishing Group UK 2022-07-16 /pmc/articles/PMC9288481/ /pubmed/35842472 http://dx.doi.org/10.1038/s41598-022-16028-2 Text en © The Author(s) 2022, corrected publication 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Li, Yue Agrawal, Vasundhara Virk, Ranya K. A. Roth, Eric Li, Wing Shun Eshein, Adam Frederick, Jane Huang, Kai Almassalha, Luay Bleher, Reiner Carignano, Marcelo A. Szleifer, Igal Dravid, Vinayak P. Backman, Vadim Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM) |
title | Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM) |
title_full | Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM) |
title_fullStr | Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM) |
title_full_unstemmed | Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM) |
title_short | Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM) |
title_sort | analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (chromstem) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9288481/ https://www.ncbi.nlm.nih.gov/pubmed/35842472 http://dx.doi.org/10.1038/s41598-022-16028-2 |
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