Extended Data Fig. 3: H3K36me3 deposition is not strongly impacted in absence of DNA methylation.
From: DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency
a. 2D scatterplot showing H3K27me3 and H3K36me3 enrichment over genome-wide 10kb bins in WT ESCs. Data points are coloured by 5mC levels in WT ESCs. 10kb bins with ≥10 CpGs covered by ≥5 reads are shown (n=252,812), and the density of datapoints is included. b. 2D scatterplot showing H3K27me3 and H3K36me3 enrichment over genome-wide 10kb bins in WT EpiLCs. Data points are coloured by 5mC levels in WT EpiLCs. 10kb bins with ≥10 CpGs covered by ≥5 reads are shown (n=252,559), and the density of datapoints is included. c. 2D scatterplot showing H3K36me3 enrichment over genome-wide 10kb bins in WT and TKO ESCs. Data points are coloured by 5mC levels in WT ESCs as in a, and density of datapoints is included. d. 2D scatterplot showing H3K36me3 enrichment over genome-wide 10kb bins in WT and TKO EpiLCs. Data points are coloured by 5mC levels in WT EpiLCs as in b, and density of data points is included. e. 2D scatterplot showing H3K27me3 enrichment over genome-wide 10kb bins in WT and TKO EpiLCs, as in Fig. 1c. Data points are coloured by the relative change in H3K36me3 enrichment in TKO versus WT EpiLCs, and density of datapoints is included. f. Violin plot showing the distribution of H3K36me3 level change in TKO EpiLCs compared to WT EpiLCs. 10kb bins are categorized based on H3K27me3 dynamics in WT and TKO EpiLCs; No H3K27me3: insufficient H3K27me3 levels (CPM<1) in either WT or TKO EpiLCs, not DE: H3K27me3 levels do not significantly change between WT and TKO EpiLCs, Down TKO: relative loss of H3K27me3 in TKO EpiLCs, Up TKO: relative enrichment of H3K27me3 in TKO EpiLCs compared to WT EpiLCs.
