Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM).
Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM).
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DOI：
10.1038/s41598-022-16028-2
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发表时间：
2022-07-16
影响因子：
4.6
通讯作者：
Backman, Vadim
中科院分区：
文献类型：
--
作者：
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
多长度尺度的染色质组织在转录调控中起着至关重要的作用。破译这些过程的相互作用需要体外染色质结构的高分辨率，三维，定量成像。在此，我们介绍了ChromSTEM，一种利用扫描透射电子显微镜的高角度环形暗场成像和断层扫描结合dna特异性染色的方法。我们利用ChromSTEM对三维染色质构象进行了深度量化，具有高空间分辨率和对比度，允许表征几乎低至DNA碱基对水平的高阶染色质结构。利用ChromSTEM质量密度层析图的质量尺度分析，我们观察到染色质形成了空间上定义明确的高阶结构域，半径约为80 nm。在结构域内，染色质表现出聚合的分形行为和从中心到外围径向降低的质量密度。与其他纳米成像和分析技术不同，我们证明了这种高分辨率成像技术与基于聚合物物理的分析的独特结合使我们能够(i)研究包装域内的染色质构象和（ii）量化与转录相关的染色质结构的统计描述符。我们观察到，即使在同一细胞系中，包装结构域也具有异质形态特性，这表明统计染色质包装在调节真核细胞核内基因表达中的潜在作用。
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.
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染色质物理拓扑，分形结构和基因表达之间的全球关系。
影响因子：
4.6
作者：
Almassalha LM;Tiwari A;Ruhoff PT;Stypula-Cyrus Y;Cherkezyan L;Matsuda H;Dela Cruz MA;Chandler JE;White C;Maneval C;Subramanian H;Szleifer I;Roy HK;Backman V
通讯作者：
Backman V
影响因子：
3.9
作者：
Hansen JC;Connolly M;McDonald CJ;Pan A;Pryamkova A;Ray K;Seidel E;Tamura S;Rogge R;Maeshima K
通讯作者：
Maeshima K
影响因子：
4
作者：
Koberna, K;Ligasová, A;Berezney, R
通讯作者：
Berezney, R
DOI：
10.1073/pnas.0810057105
发表时间：
2008-12-16
影响因子：
11.1
作者：
Eltsov, Mikhail;MacLellan, Kirsty M.;Dubochet, Jacques
通讯作者：
Dubochet, Jacques
影响因子：
7.8
作者：
BELMONT, AS;SEDAT, JW;AGARD, DA
通讯作者：
AGARD, DA