Histone marks for inactive genes in X1 NBs. (A) Average H3K27me3 ChIP-seq profile across X1-, X2-, and Xins-enriched loci in X1 NBs across three biological replicates following outlier removal. The y-axis represents the difference in coverage between sample and input, and the x-axis represents signal 2.5 kb upstream of and downstream from the TSS. (B) H3K27me3 ChIP-seq profiles following outlier removal for X2 genes from high to low X2 proportional ranking. H3K27me3 signal increases with an increase in proportion of X2 gene expression, indicative of these high-ranking X2 genes being transcriptionally silenced or lowly expressed in NBs. (C) Average H3K4me1 ChIP-seq profiles following outlier removal across X1-, X2-, and Xins-enriched loci in X1 NBs. The y-axis represents the absolute difference in coverage between sample and input, and the x-axis represents signal 2.5 kb upstream of and downstream from the TSS. (D) H3K4me1 ChIP-seq profiles following outlier removal for X2 genes from high to low X2 proportional ranking. Highly ranked X2 genes have a H3K4me1 signal at the promoter-proximal region, and a decrease in X2 ranking coincides with a peak shift −1 kb downstream from the TSS. (E) H3K4me3, H3K36me3, H3K4me1, and H3K27me3 NB ChIP-seq profiles for highly expressed Xins genes. The y-axis scale represents percentage coverage for each mark, and 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).
