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Fig. 3 | Genome Biology

Fig. 3

From: CTCF and cohesin promote focal detachment of DNA from the nuclear lamina

Fig. 3

CTCF binding sites locally detach from the NL by cohesin-mediated long-range DNA interactions. A LaminB1 z-scores around active and inactive genes, CTCF binding sites, and random locations in LADs defined in the mESC PT clone, visualized as an average signal with 95% confidence interval of the mean (top panel) and heatmap (bottom panel). In the heatmap, rows represent individual sites and missing data is shown as gray tiles. Genes are filtered to be positioned at least 100 kb from CTCF binding sites, and vice-versa for CTCF binding sites. B Average scores around CTCF binding sites, active genes, and random locations in LADs for the epigenetic data sets, as described in Fig. 1C. C Average LaminB1 z-scores as in A following a protein depletion time course (0 h, 6 h, and 24 h) of CTCF, RAD21, WAPL, and a combination of CTCF and WAPL. Note that the PT data in panels A and C are from distinct sets of experiments; all data in C were obtained with the same batch of Lamin B1 antibody, which is different from the batch used for the data in A. The PT data from panel C lack an auxin-treated time point and are therefore not used in the other figures, but are better suited for direct comparisons with the untreated conditions (0 h) in the other clones in this panel (see also Additional file 1: Fig. S6A). D Similar plot to Fig. 2A, but showing the fraction of CTCF binding sites in iLADs and LADs that overlap with loop anchors. Loop anchor data is from ref. [36] E CTCF binding sites that overlap with loop anchors are classified based on LAD overlap. The bar plot shows the positioning of their looping partners in iLAD or LAD regions. F Illustration of the detachment score, defined as the difference between the LaminB1 score at the CTCF binding site and its 100-kb flanking region (see the “Methods” section). G The distribution of the detachment score (F) for CTCF binding sites, separated by loop anchor overlap and anchor positioning. CTCF binding sites within 100kb from LAD borders are excluded. A Wilcoxon test followed by Benjamini–Hochberg multiple testing correction was used to test for statistical significance. H Average counts-per-million (cpm) normalized ATAC-seq signals as in B for CTCF-AID and RAD21-AID cell lines without (0 h) and with (24 h) IAA-induced protein depletion

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