Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization

Paweł Trzaskoma, Błażej Ruszczycki, Byoungkoo Lee, Katarzyna K. Pels, Katarzyna Krawczyk, Grzegorz Bokota, Andrzej A. Szczepankiewicz, Jesse Aaron, Agnieszka Walczak, Małgorzata A. Śliwińska, Adriana Magalska, Michal Kadlof, Artur Wolny, Zofia Parteka, Sebastian Arabasz, Magdalena Kiss-Arabasz, Dariusz Plewczyński, Yijun Ruan () and Grzegorz M. Wilczyński ()
Additional contact information
Paweł Trzaskoma: Polish Academy of Sciences
Błażej Ruszczycki: Polish Academy of Sciences
Byoungkoo Lee: The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr
Katarzyna K. Pels: Polish Academy of Sciences
Katarzyna Krawczyk: Polish Academy of Sciences
Grzegorz Bokota: University of Warsaw
Andrzej A. Szczepankiewicz: Polish Academy of Sciences
Jesse Aaron: Howard Hughes Medical Institute
Agnieszka Walczak: Polish Academy of Sciences
Małgorzata A. Śliwińska: Polish Academy of Sciences
Adriana Magalska: Polish Academy of Sciences
Michal Kadlof: University of Warsaw
Artur Wolny: Polish Academy of Sciences
Zofia Parteka: University of Warsaw
Sebastian Arabasz: Łukasiewicz Research NETWORK – PORT Polish Center for Technology Development
Magdalena Kiss-Arabasz: Łukasiewicz Research NETWORK – PORT Polish Center for Technology Development
Dariusz Plewczyński: University of Warsaw
Yijun Ruan: The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr
Grzegorz M. Wilczyński: Polish Academy of Sciences

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: Abstract The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of an electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5 × 5 × 30 nm in xyz dimensions) that is superior to the current super-resolution by fluorescence light microscopy. We apply 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualize a large number of distinctive 3D chromatin folding structures in ultra-resolution. We further quantitatively characterize the reconstituted chromatin folding structures by identifying sub-domains, and uncover a high level heterogeneity of chromatin folding ultrastructures in individual nuclei, suggestive of extensive dynamic fluidity in 3D chromatin states.

Date: 2020
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DOI: 10.1038/s41467-020-15987-2

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