Fig. 2: Ectopic H3K36me3 deposition resembles endogenous H3K27me3 genome wide.
From: Addressing the specific roles of histone modifications in transcriptional repression
a Schematic drawing of the domain architecture of the fusions S12N:SD2 and S12N:SD2* with indications of boundaries (amino acid numbers referring to the sequence in WT SUZ12 and SETD2). Asterisk indicates a point mutation introduced to generate catalytic inactive S12N:SD2*. b–e CUT&RUN tracks showing H3K27me3, H3K4me3, and H3K36me3 signals (RPKM) from the indicated cell lines within a representative genomic region that includes the HoxA cluster (b), PRC2 target genes Bmi1, Spag6, and Carlr (c), PRC2 target genes Fgf3 and Fgf15 and the endogenously H3K36me3 positive Fgf4 gene (d), and PRC2 target gene Ntng2 and the endogenously H3K36me3 positive Setx gene (e). The tracks are representative from one biological replicate, performed in biological duplicates (n = 2). CGI annotations (red) are shown below the track. f Mean H3K36me3 CUT&RUN signals (RPKM) in indicated cell lines within a 40 kb window centered on 7732 H3K27me3 positive promoter peaks identified in WT mESCs. g Plot of H3K36me3 CUT&RUN signals (RPM) enrichment within peak boundaries of all H3K27me3 peaks identified in WT mESCs (promoter and non-promoter; n = 22307) for the indicated cell lines quantified using BedTools Multicov. Smoothed lines represent generalized additive model (GAM) fits of mean H3K36me3 signal intensity (RPM) from two independent biological replicates (n = 2), as a function of H3K27me3 CUT&RUN signal intensity (RPM) in WT mESCs (n = 1); shaded ribbons show the 95% confidence interval of the fitted mean (not variability between biological replicates).
