Fig. 9

Compartment switch is regulated by multi-factors. a Hi-C heatmap showing the compartmentalization of the C19Q region in EpiGo-Control (dCas9) cells (chr19: 40,000,000–50,000,000). H3K9me3, RNA-seq, and PC1 tracks are also shown. Red box, A-to-B switched regions upon dCas9-KRAB induction. Green box, A-to-A regions upon dCas9-KRAB induction. b Hi-C heatmap showing the compartmentalization of the C19Q region in EpiGo-KRAB cells. All the data processing and display are the same as a. c Boxplots showing the dCas9-KRAB target sequence density for A-to-A and A-to-B regions in dCas9 and dCas9-KRAB cells. Only compartment A regions with target sequences were selected for analysis. P values calculated by Wilcoxon rank-sum test (two-sided) are also shown. d Left, boxplots showing the gene density in each class for mouse cell lines (MEF A-to-CC B, MEF B-to-CC A, MEF A-to-CC B, MEF B-to-CC A). Right, boxplots showing the gene density in each class for human cell lines (hES A-to-TB B, hES B-to-TB A, hES A-to-TB B, hES B-to-TB A). MEF, mouse embryonic fibroblast; CC, cumulus cells; hES, human embryonic stem cells; TB, trophectoderm. Hi-C data were obtained from GSE52457 and GSE139430. P values calculated by Wilcoxon rank-sum test (two-sided) are also shown. e Boxplots showing the gene density in each class. Whole genome compartment A/B and all chr19 compartment A/B in dCas9 cells are similarly analyzed and shown as control. P values calculated by Wilcoxon rank-sum test (two-sided) are also shown. f Left, boxplots showing the gene expression level in each class. Right, boxplots showing the H3K27ac enrichment at promoters for genes located in each class. Whole genome compartment A/B and all chr19 compartment A/B in dCas9 cells were are similarly analyzed and shown as controls. P values calculated by Wilcoxon rank-sum test (two-sided) are also shown. g Boxplots showing the average distance towards A/B borders in each class. Whole genome compartments A/B and all chr19 compartments A/B in dCas9 cells were used as control. All A-to-B regions in chr19q arm with dCas9-KRAB targets were similarly analyzed and shown. P values calculated by Wilcoxon rank-sum test (two-sided) are also shown