Extended Data Figure 1: H3K36me2/3 mark transcriptionally active euchromatin.
a) ChIP-seq normalized reads of H3K36me2 were plotted relative to averagepercentage of CpG methylation in mMSCs for 100kb non-overlapping bins (n = 25,624). Pearson’s correlation coefficient is indicated.
b) Quantification of ChIP-seq normalized reads for DNMT3A1, DNMT3B and averagedCpG methylation within H3K36me2/3 (n = 591), H3K27me3 (n = 283), or H3K9me3 (n = 545) domains. P-values were < 2.2 × 10−16 for all pair-wise comparisons as determined by Wilcoxon’s rank sum test (two-sided), except for DNMT3B (P = 3.73 × 10−14) between H3K27me3 and H3K9me3 domains. Boxes represent median and 25th-75th percentiles, whiskers are minimum to maximum with discrete points representing outliers.
c) Quantification of ChIP-seq normalized reads for gene expression, H3K4me1 andH3K27ac within H3K36me2/3 (n = 591), H3K27me3 (n = 283), or H3K9me3 (n = 545) domains. P-values were < 2.2 × 10−16 for all pair-wise comparisons as determined by Wilcoxon’s rank sum test (two-sided), except for gene expression (P = 1.72 × 10−6) between H3K27me3 and H3K9me3 domains. Boxes represent median and 25th-75th percentiles, whiskers are minimum to maximum with discrete points representing outliers.
d) 3D genome browser representation of Hi-C chromatin conformation data from mousemyoblasts compared to ChIP-seq normalized reads for histone PTMs in mMSCs at Chr4: 52.2-99.1 Mb. Levels of CpG methylation are depicted as a heat map (blue/low; white/intermediate; red/high). Refseq genes are annotated at the bottom. For H3K36me3 and H3K36me2, data are representative of two independent ChIP-seq experiments; for H3K27me3 and H3K9me3, ChIP-seq was performed once and an independent ChIP was performed in which genomic regions of selective enrichment and depletion were confirmed by qPCR. WGBS was performed once.