Supplementary Figure 12: ChIP-seq binding profile and differential binding analysis at TSS of Hdac3, Pol II, and H3K27ac.

a-c, Boxplots of input normalised ChIP-seq in Setd5^+/+, Setd5^+/−, and Setd5^−/−. Signal for 4 different genomic regions: Transcription Start Sites (TSS, n=34159) Gene bodies (n=34151), transcription end sites (TES, n=34159), intergenic ESCs specific enhancers (n=4099) for Hdac3 (a), Pol II (b), and H3K27ac (c). d-f, MA plot of differential binding analysis for Setd5^+/− (left) and Setd5^−/− (right) compared to Setd5^+/+ at TSS using peaks of Hdac3 (d), Pol II (e), and H3K27ac (f). EdgeR likelihood ratio test. g, Boxplots of input normalised ChIP-seq RPKM in Setd5^+/+, Setd5^+/HA, Setd5^+/−, and Setd5^−/−. Signals of Setd5-HA, Pol II, Hdac3, H3K27ac and H4 pan acetylation for 182 genes that show significant (FDR < 0.05) decrease RNA-Pol II binding in Setd5^+/− at TSS. The presence of H3K27ac signal indicates expressed genes. h, Boxplots of ChIP-seq RPKM signal in Setd5^+/+, Setd5^+/−, and Setd5^−/− for 2 different genomic features: TSS having at least one H4 pan acetylation peak (n=3018) and H4 pan acetylation peaks within gene bodies (n=43448 peaks in 9088 gene bodies). TSS is defined as +/- 1.25 kb around gene start position; one-sided Mann–Whitney U test. Boxplots in a, b, c, g, and h represent mean, normalized by input Reads Per Kilobase of genomic regions, per Million mapped reads (RPKM) values of 2 biological replicates from two independent cell lines. Input levels are equal to 1. Outliers, less than 5 or more than 95 percentile of mean RPKM, were removed. The upper, centre, and lower line of the boxplot indicates 75%, 50%, and 25% quantile, respectively. Whiskers extend to the most extreme data point within 1.5-times the interquartile range.