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. 2024 Jun 12;26(6):991–1002. doi: 10.1038/s41556-024-01424-9

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2024

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

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Fig. 1 — a, Combined Hi-C contact linear genomic distances density plots from two replicates of young and old pro-B cells. Colour shading refers to compartments (pink), TADs and loops (green), and close interactions (yellow). b, Example of Hi-C contact heatmaps, visualized with Juicebox using Coverage (sqrt) normalization. Difference heatmap (right) shows regions with increased (red) and decreased interactions (blue) in old pro-B cells. c, PC1 of young and old pro-B cells from Hi-C compartment analysis. Numbers of significantly changed euchromatic (A) and heterochromatic (B) bins of 100 kb are indicated in each quadrant. Significantly changed bins were obtained using a two-pass MD method with a one-sided chi-squared test P < 0.01. d, Difference of aggregate H3K27ac and H3K27me3 (n = 2) signals within significantly switched bins identified in c. e, Differential expression (n = 4) for genes associated with each category identified in c from RNA-seq analysis. The top and bottom of each box (in d and e) represents the 75th and 25th percentile, respectively, with a line at the median. Whiskers extend by 1.5× the interquartile range. P values were determined by two-sided Wilcoxon signed-rank test. f, Chromatin state of Ebf1 locus in young and old pro-B cells. Top tracks show Hi-C compartment PC1, with orange indicating compartment A and blue indicating compartment B. Lower tracks show normalized ChIP–seq and RNA-seq tracks. Clint1 (right) serves as a control gene located in compartment A that is unaffected by age. g. Hi-C heatmaps of the Ebf1 locus. Interactions with greater than twofold change in old pro-B cells are marked by black circles/arcs (reduced) or the blue square/arc (increased). Numbers represent the ratio of Hi-C PETs in old pro-B cells compared with young pro-B cells. h, Nuclear positioning assayed by FISH. Representative nuclei from young and old pro-B cells and non-B cells from Rag2^−/− mice are shown. Probe colours are as indicated. Dashed lines delineate the nuclear periphery. i, Distance between Ebf1 locus and nuclear periphery in pro-B cells and non-B cells (n = 100) is shown. The red line indicates the median value; P values based on unpaired two-sided t-tests.

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