Skip to main content
. 2023 Jul 24;6(10):e202302101. doi: 10.26508/lsa.202302101

Figure 4. Reversible disruption of inter-TAD polycomb clustering by 1,6-HD.

Figure 4.

(A) Hi-C maps of the three adjacent TADs on chromosome 5 (mm9) containing En2, Shh, and Mnx1 polycomb targets from WT (Ring1B+/+) and Ring1B−/− mESCs at 5 kb resolution. Genes, fosmid probe–binding locations, H3K27me3, and RING1B ChIP-seq profiles are shown between the two Hi-C maps (data from the study of Boyle et al [2020]). Black arrowheads indicate enriched interactions between the three polycomb target genes in WT cells and reduced interactions in Ring1B−/− cells. (B) Representative images of 3D-FISH for En2, Shh, and Mnx1 in untreated, 1,6-HD–treated, and recovered WT cells. (C, E) Bar plots providing categorical analysis of the spatial location of each of the three polycomb (C) and non-polycomb (E) probes shown in A relative to each other in untreated, 2,5-HD–treated, 1,6-HD–treated, and recovered WT cells. Categories are as in Fig 3. Differences in clustering and dispersal identified using Fisher’s exact test; ∗∗ P ≤ 0.01, ∗∗∗ P ≤ 0.001, ∗∗∗∗ P ≤ 0.0001. (D) Scatter plots depicting the interprobe distances between each of the two fosmid probe pairs indicated on x and y axes with the separation between the third pair indicated by the color in the color bar for polycomb target loci in WT cells. Dashed red box indicates non-dispersed alleles with at least two sets of interprobe distances <400 nm. (F) As in C but for untreated, 1,6-HD–treated, and recovered Ring1B−/− cells. Data for a biological replicate are in Fig S4. Data and statistical evaluation are summarised in Tables S4 and S5.