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. 2021 Feb 4;12:789. doi: 10.1038/s41467-020-20753-5

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© The Author(s) 2021

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a Thymidine analogue ¹²⁷I-dU was simultaneously incorporated into HeLa cells for 24 h for chromatin visualization as a replicated DNA signature. IBT reconstructions and deconvolution IBT stacks were represented as 3D renders for 700 tomographic slices. b Replicated DNA images from ¹²⁷I-dU. The first column shows typical raw ion images from 20^th, 200^th, and 400^th depths from the ¹²⁷I-dU channel (green). The second column presents reconstructed ¹²⁷I-dU images by Deconvolution-IBT. The third column corresponds to SILM-IBT images of the same chromatin target and these images were then converted to chromatin density maps (blue to red: low to high). The fourth and fifth columns (zoomed out version) show corresponding chromatin density maps. DNA clusters (n = 10) were assigned to unique colors on the spatial chromatin maps. c HeLa cells were treated with a histone deacetylase (HDAC) inhibitor, Trichostatin A (TSA), for 24 h, after labeling of replicated DNA for 24 h by ⁸¹Br-dU. Four HeLa cells were only labeled by ⁸¹Br-dU without TSA and up to 30 slices were acquired by SIMS. d Another set of four HeLa cells were treated by TSA and imaged. Chromatin density maps were created in the SILM-IBT images from these four cells. The cells that are treated with TSA consistently showed dimmer ion signals and more relaxed DNA features. e Intensity analysis of chromatin (BrdU, n = 4) and TSA treated chromatin (BrdU-TSA, n = 4) for an average of all the eight cells, yielding lower signal levels for TSA treated cells. f Spatial density analysis for peak distributions in a pair of cells with and without TSA, a reduction in the counts of peaks was detected. Insets: 20 × 20 pixels from each BrdU and BrdU-TSA images. g Chromatin features in a HeLa cell imaged using ³¹P channel together with ⁸¹Br-dU labeling for replicated DNA. Upper images: HeLa cell imaged using the IBT data from ⁸¹Br-dU and ³¹P channels, exhibiting 0.42 SSIM values. Lower images: Another HeLa cell for the same ⁸¹Br-dU and ³¹P channels after TSA treatment. IBT-sum images of 30 frames for ⁸¹Br-dU and ³¹P, providing SSIM values of 0.47.