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. 2022 Apr 19;13:2139. doi: 10.1038/s41467-022-29696-5

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© The Author(s) 2022

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 Tiled-MCC contact matrices of the Nanog locus in wild-type mES cells (top-right) and auxin-treated CTCF-AID mES cells (bottom-left) at 500 bp resolution. b Differential contact matrix of the Nanog locus in which interactions enriched in WT mES cells are indicated in red and interactions enriched in auxin-treated CTCF-AID mES cells are indicated in blue. a–b Gene annotation (genes of interest in red, coding genes in black, non-coding genes in gray), DNase hypersensitive sites (DHS), and ChIP-seq data for CTCF, Cohesin (RAD21), H3K27ac, H3K4me3, and H3K4me1 are shown below the matrices. The axes of the DHS and ChIP-seq profiles are scaled to signal and have the following ranges: DHS = 0–10.25; CTCF = 0–3092; RAD21 = 0–3414; H3K27ac = 0–58; H3K4me3 = 0–90; H3K4me1 = 0–2064. Enhancers of interest are indicated in green below the DHS profiles. The orientations of CTCF motifs at prominent CTCF-binding sites are indicated by arrowheads (forward orientation in red; reverse orientation in blue). The dashed circles and oval in b highlight the following interactions of interest (from left to right): Nanog promoter and far upstream enhancer; Nanog promoter and downstream super-enhancer; Slc2a3 promoter and downstream super-enhancer; Foxj2 proximal cis-regulatory elements and upstream super-enhancer. The interactions between the Nanog and Slc2a3 promoters with the enhancers in the region appear unchanged upon CTCF depletion (despite the loss of CTCF-mediated interactions directly upstream of the Slc2a3 promoter), whereas the interactions between the proximal cis-regulatory elements of Foxj2 and the super-enhancer are increased. c Expression of Nanog, Slc2a3, and Foxj2 in untreated (left) and auxin-treated (right) CTCF-AID mES cells, derived from RNA-seq data, normalized for fragments per kilobase of the transcript, per million mapped reads (FPKM). The bars represent the average of n = 3 replicates and the error bars indicate the standard error of the mean. Significant (*) and non-significant (n.s.) changes in expression are indicated. Nanog: P = 0.7030; Slc2a3: P = 0.1774; Foxj2: P = 0.0001 (calculated using Cuffdiff analysis and adjusted for multiple comparisons, as previously decribed²⁷). Source data are provided as a Source Data file.