Nat Commun 2020 May 1; 11(1):2120
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.
Trzaskoma, Paweł; Ruszczycki, Błażej; Lee, Byoungkoo; Pels, Katarzyna K; Krawczyk, Katarzyna; Bokota, Grzegorz; Szczepankiewicz, Andrzej A; Aaron, Jesse; Walczak, Agnieszka; Śliwińska, Małgorzata A; Magalska, Adriana; Kadlof, Michal; Wolny, Artur; Parteka, Zofia; Arabasz, Sebastian; Kiss-Arabasz, Magdalena; Plewczyński, Dariusz; Ruan, Yijun; and Wilczyński, Grzegorz M, "Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization." (2020). Faculty Research 2020. 87.