Figure 1: Differential expression and isoform analysis.

(a) Experimental overview (b) DE genes in myoepithelial and luminal (lum) epithelial cell types across three donors, luminal upregulated (red), myoepithelial (myo) upregulated (green). (c) Exon–intron junction mCpGs provide an inherited signature of exon expression. Average number of CpGs (black, bottom panel) and average mCpG levels (whole-genome bisulphite shotgun, 20 bp bins) at exon junctions +/− 200 bp in luminal (solid line with round dots) and myoepithelial (dashed line with triangles). Exons are divided into four groups namely: (1) exons expressed in both the cell types (exon reads per kilobase of transcript per million reads mapped (RPKM) >0.1 in luminal and myoepithelial RM084, purple); (2) luminal-specific exons (isoform exons expressed in luminal but not in myoepithelial, red); (3) myoepithelial-specific exons (isoform exons expressed in myoepithelial but not in luminal, green) and (4) exons not expressed in either cell types (all other exons, blue). A statistical significant difference was observed between the not expressed exons and all other groups, t-test P value <10⁻¹⁸. All other comparisons show weak or no statistically significant difference. (d) H3K36me3 density in exon bodies provides a transient record of exon expression. Average H3K36me3 signal levels for exons in expressed genes (gene RPKM >0.1) in luminal RM080 (red) and myoepithelial RM080 (green). Exons are broken down into four groups namely: (1) exons expressed in both the cell types (exon RPKM >0.1 in luminal and myoepithelial); (2) luminal-specific exons (isoform exons expressed in luminal but not in myoepithelial); (3) myoepithelial-specific exons (isoform exons expressed in myoepithelial but not in luminal); and (4) exons not expressed in either cell types (all other exons). Fold enrichment of average H3K36me3 signal levels within exons revealed an increase H3K36me3 signals in cell type-specific exons in corresponding cell populations. (e) Model of inherited and transient epigenetic exon marking. Exon boundary DNA methylation (black dot) and exon body H3K36me3 (red flag) marking of exons in luminal and myoepithelial cell populations.