Ectopic deposition of H3K27me3 leads to formation of new chromatin repressive loops. (A) Schema illustrating the antagonistic role of the PRC2 complex (involving the histone methyltransferase CLF) and the histone demethylase REF6 to control H3K27me3 homeostasis and chromatin remodeling. (B) Heatmap of C-Hi-C data showing ref6-5 specific loops (reSLs). (C) Examples of reSLs detected by C-Hi-C. C-Hi-C interaction signal (blue lines) and H3K27me3 ChIP-seq signal in wild type (black peaks) and ref6-5 (red peaks) are represented. (D) Model of chromatin contacts organization in wild type and ref6-5 mutant. (E) Histogram representing the percentage of genes (observed [O] or expected [E]) involved in reSLs that are either hyper- or hypomethylated in ref6-5 compared to WT. To obtain the expected proportion, we shuffled the H3K27me3 signals 1000 times to obtain the randomized gene counts. The mean of the 1000 permutations was used to determine the expected proportions. Asterisk indicates significant difference (P-value < 2.2 × 10–16, test of proportions). The bottom pie chart represents the percentage of ref6-5 hypermethylated genes involved in reSLs. The box plot displays the H3K27me3 levels of the 40% of ref6-5 hypermethylated genes involved on reSLs. (F) Scatterplot of log2 (ref6-5/wild-type gene expression fold change) for pairs of genes interacting specifically in ref6-5 compared to wild-type.
