Fig. 2

KDM3B is essential to regulate H3K9me1/me2 histone modifications and chromatin accessibility. a Correlation heatmap of genome-wide enrichment for H3K9me1, H3K9me2 or H3K9me3 ChIP-seq data in NB4 cells expressing scrambled control versus shKDM3B, organized and ordered using hierarchical clustering, is shown. Each modification type was then scaled to 0–1 and the R coefficient was determined with Spearman’s correlation. Colors indicate no correlation (red), intermediate correlation (yellow), and strong correlation (blue). b Plots showing the genome-wide correlation from H3K9me1, H3K9me2 or H3K9me3 ChIP-seq in NB4 cells expressing scrambled control versus shKDM3B, respectively. c Signal intensity plot representing changes in H3K9me1, H3K9me2 and H3K9me3 ChIP-seq signal at promoters regions or gene body following silencing of KDM3B in NB4 cells. The enriched regions were extended ± 3 kb from their midpoint. d Genome browser tracks of H3K9me1, H3K9me2 and H3K9me3 ChIP-seq data at the C11orf95, CBX4 and CDK2AP1 loci following silencing of KDM3B in NB4 cells. e Chromatin accessibility in NB4 cells expressing scrambled control versus shKDM3B at promoters regions. The enriched regions were extended ± 0.5 kb from their midpoint. f Genome browser tracks of ATAC-seq data at the C11orf95, CBX4 and CDK2AP1 loci following silencing of KDM3B in NB4 cells. g Venn diagram representing overlap of accessible sites in NB4 cells expressing scrambled control versus shKDM3B. h TF motif analysis of different regions in NB4 cells expressing scrambled control versus shKDM3B in all chromatin accessible sites. The scale of the circles represents motif enrichment