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. 2021 Jan 4;12:41. doi: 10.1038/s41467-020-20292-z

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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. 4 — a Examples of TAD (black triangles) and sub-TAD (light blue triangles) positions in the haploid X chromosome in individual nuclei with 77,770 unique contacts. b Percentage of TAD and sub-TAD boundaries per cell (excluding TAD boundaries for the same cells) found as sub-TAD boundaries in the snHi-C maps after 50% downsampling. Downsampling was performed 10 times. At the top: TAD boundaries are highlighted with blue lines, sub-TAD boundaries located inside TADs are highlighted with red lines. Boxplots represent the median, interquartile range, maximum and minimum. ****p-value < 0.0001 using the Mann–Whitney two-sided test. n = 20 cells. c Genomic regions with alternative chromatin folding patterns in individual cells. Positions of sub-TADs and TADs identified in bulk BG3 in situ Hi-C data (top panels) are highlighted with light gray and dark gray rectangles, respectively. Positions of TAD boundaries in bulk BG3 in situ Hi-C data are shown with vertical light gray lines. d Heatmaps showing log₂ values of contact enrichment between genomic regions belonging to putative A- (negative PC1 values) and B- (positive PC1 values) compartments (saddle plot). PC1 profile is constructed using the bulk BG3 in situ Hi-C data. e Contact probability P_c(s) between transcriptionally active (red) and inactive (blue) genomic bins in the snHi-C data. The light blue shading shows the genomic distances corresponding to the average TAD size in single nuclei. f Average plot of long-range interactions between top 1000 regions of A compartment annotated by bulk Hi-C data (in bulk Hi-C and merged snHi-C). g Average plot of long-range interactions between top 1000 regions of B compartment annotated by bulk Hi-C data (in bulk Hi-C and merged snHi-C). h Average plot of interactions between top 500 regions enriched in MSL (in bulk Hi-C and merged snHi-C) on chromosome X. i Average plot of interactions between top 500 regions enriched in dRING (in bulk Hi-C and merged snHi-C).