Histone marks for actively transcribed genes in X1 NBs. (A) Average H3K4me3 ChIP-seq coverage profiles across X1-, X2-, and Xins-enriched loci in X1 NBs across biological replicates following outlier removal. The y-axis represents the difference in coverage between sample and input, and the x-axis represents 2.5 kb upstream of and downstream from the TSS. H3K4me3 signal is highest around the promoter-proximal region close to the TSS for X1-enriched loci in NBs consistent with the role of H3K4me3 in active transcription. (B) H3K4me3 ChIP-seq profiles following outlier removal for X2 genes ranked from high to low X2 proportional expression. H3K4me3 signal in NBs decreases with an increase in proportion of X2 expression, indicative of high-ranking X2 genes having a predominant role in post-mitotic progeny as opposed to NBs. (C) Average H3K36me3 ChIP-seq profile across X1-, X2-, and Xins-enriched loci in X1 NBs across biological replicates following outlier removal. The y-axis represents the difference in coverage between sample and input, and the x-axis represents 2.5 kb upstream of and downstream from the TSS. Signal for H3K36me3 is promoter-proximal for Xins genes, whereas the magnitude of signal is greater and shifted 3′ for X1 genes. (D) H3K36me3 ChIP-seq profiles following outlier removal for X2 genes from high to low X2 proportional ranking. H3K36me3 signal in NBs shifts to the 3′ end with a decrease in X2 proportion, consistent with these lowly ranked genes having transcriptional activity in NBs. (E) H3K4me3 and H3K36me3 (active marks) and H3K4me1 and H3K27me3 (suppressive marks) ChIP-seq profiles for highly expressed X1 genes in NBs. The y-axis represents percentage coverage for each mark and allows for the four epigenetic marks to be directly compared. The x-axis represents 1.0 kb upstream of and 2.5 kb downstream from the TSS. Pie charts represent proportional expression for each gene in X1 (dark blue), X2 (light blue), and Xins (orange).
