Fig. 4: DNA methylation patterns of normal and tumorigenic cells.

a Principal component analysis of DNA methylation at TSS-distal and TSS proximal poised enhancer regions (En-Pd and En-Pp, based on ENCODE postnatal 0 days mouse lung, ENCSR538YJF). The shape of the dots reflects the sample type, as normal lung (Normal) or GFP⁺ tumours (Tumour). The colour indicates mouse lineages used. Coloured shading is drawn around the Normal (light blue) and Tumour (purple) samples. b DNA methylation deconvolution by MeDeCom analysis shows three identified latent methylation components (LMC 1–3). Colours indicate the proportion of LMCs for each sample. Samples are clustered within each mouse lineage (Sftpc, Scgb1a1 or Hopx) and according to sample type (Normal/Tumour). c Association of LMCs with cell type-specific gene signatures based on published single-cell RNA sequencing data¹⁷. Genes are ranked by their correlation of promoter methylation with the respective LMC. Enrichment scores are running sums calculated using the Gene Set Enrichment Analysis algorithm. d Heatmap of regions that were differentially methylated between Scgb1a1 and Sftpc normal samples. The methylation value is shown as beta values ranging from 0 to 1 visualized by the heatmap colours blue to red. For tumours, the label of each column shows the proposed originating cell type, while the colours below depict their originating lineage. e Average methylation across the Scgb1a1 and Sftpc genes for normal samples from Scgb1a1 and Sftpc lines and Club and AT2 originated tumours. Pink bars highlight regions with DNA methylation differences between normal lineages, while blue bars highlight regions with differences in tumours from distinct origins. ENCODE cCRE, showing candidate Cis-Regulatory elements, cHMM lung P0 showing ChromHMM regions in mouse lung, postnatal 0 days, and ATAC lung P0 showing ATAC-seq peaks in postnatal 0-day-old lung are UCSC tracks under the same name. f TF motif enrichment analysis of the differentially methylated regions (DMRs). Each column represents one comparison (e.g. Scgb1a1 normal vs. tumour) in one direction (e.g. hypermethylation in second, as in hypermethylated in tumours). The colour of the dots shows the enrichment of the DMRs for the motifs compared to random genomic regions. The size of the dots reflects on the –log₁₀(p value) of the enrichment analysis. Empty lines show the lack of significant enrichment.