Additional file 2: of Epigenome-wide DNA methylation regulates cardinal pathological features of psoriasis

Figure S1. Characterisation of DMPs. (a) Distribution of DMPs across different genomic regions; separate study of localization of hyper- and hypomethylated DMPs. (b) Figure showing comparison of frequency of DMPs and total probes in 450 k array across different genomic regions. *Indicates significantly enriched regions according to hypergeometric test. (c) Overlap of DMPs across regions containing repeat elements, (d) their distribution over genomic regions and (e) sub-classification into different types of repeat elements. Figure S2. Characterisation of differential CGI. (a) Hierarchical clustering of differential CGI. Normal samples are marked in light green and disease samples are marked with dark green. (b) Distribution of DMPs over CGI and associated regions (shores and shelves) and non-CGI regions (Open Sea); separate classification of hyper- and hypomethylated DMPs across CGI and associated regions. (c) Extent of hyper- and hypomethylation over CGI and associated shores and shelves. Figure S3. Characterisation of differential promoters. (a) Heatmap of differentially methylated promoters. Normal samples are marked in light green and disease samples are marked with dark green. (b) Classification of differential promoters into hyper- and hypomethylation; overlap of hyper- and hypomethylayed promoters with CGI and associated regions and non-CGI regions. (c) Validation of candidate promoter methylation in additional samples by qMSP. (d) Gene expression analysis of corresponding genes between disease and adjacent normal samples. Figure S4. Verification of complete methylation of promoter-pCpGL constructs. Unmethylated and methylated promoter constructs were digested with methylation sensitive restriction enzymes (HinP1I, AciI, HpaII) and run on 1% agarose gel. Lane1: 100 bp ladder; 2: SELENBP1 unmethylated uncut construct; 3: SELENBP1 unmethylated cut; 4: SELENBP1 methylated cut; Lane5: 100 bp ladder; 6: S100A9 unmethylated uncut construct; 7: S100A9 unmethylated cut; 8: S100A9 methylated cut. Figure S5. Description of Histopathological features studied :(a) × 10 magnification images of histopathological sections of adjacent normal and psoriatic disease tissue samples, (b) × 40 magnification image of stratum corneum in samples with and without Munro’s microabscess. (c) × 40 magnification image of stratum corneum and stratum spinosum junction showing Kogoj’s microabscess and focal hypergranulosis. Figure S6. Correlation of methylation status of sites with R > 0.6 with rete peg length. (a) Heatmap of sites correlated (r > 0.6) with rete peg elongation. (b) PCA with highly correlated (R > 0.7) sites. (PDF 1185 kb