Extended Data Fig. 6: Verification of H3K27me3-H3K36me3 co-enrichment in MulTI-Tag.

a) Genome browser screenshot showing H3K27me3 (red) and H3K36me3 (teal) enrichment from ENCODE ChIP-seq (rows 1, 2, 5, and 6) or bulk MulTI-Tag (rows 3, 4, 7, and 8) in K562 cells (rows 1-4) or H1 hESCs (rows 5-8) at the PCSK9 gene. Colored boxes indicate co-enrichment of H3K27me3 and H3K36me3 in the same gene in H1 hESCs. b) Heatmaps describing the enrichment of H3K27me3 (red) and H3K36me3 (teal) signal from ENCODE ChIP-seq (left) or bulk MulTI-Tag (right) in H1 hESCs in 86 genes for which 1) a MulTI-Tag H3K27me3 peak overlapped a 2 kb window surrounding the TSS, and 2) a MulTI-Tag H3K36me3 peak overlapped the gene body. Selected genes of interest, including those involved in metabolic and developmental signaling, are highlighted at right. c) Violin plots describing the number of normalized counts for H3K27me3 (red) and H3K36me3 (teal) mapping to the top 100 genes as classified by the percentage of single H1 hESCs enriched with H3K27me3 (left), H3K36me3 (right), or co-enriched for H3K27me3 and H3K36me3 (center) in the genes in question. ENCODE ChIP-seq (white), CUT&Tag (light grey), bulk MulTI-Tag (medium grey) and aggregate single cell MulTI-Tag (dark grey) counts are displayed for each category. P-values derived from student’s t-tests are listed above violins. d) Violin plots describing ENCODE RNA-seq counts mapping to the top 100 genes as classified by the percentage of single H1 hESCs enriched with H3K27me3 (left), H3K36me3 (right), or co-enriched for H3K27me3 and H3K36me3 (center) in the genes in question.