Fig. 1. AMs from mice with muco-obstructive lung disease are epigenetically distinct from WT AMs.

a Graphical representation of the experimental workflow, created with www.biorender.com. b Distribution of Scnn1b-transgenic (Tg) vs. wild-type (WT) airway macrophage (AM) DNA methylation differences of differentially methylated regions (DMR), defined by DSS. DMRs are characterized by at least three CpGs with an adjusted (adj.) P value < 0.05, a width of >50 bp, and an average change of methylation >0.1. Hierarchical clustering of c DMRs methylation levels and f differentially accessible regions (DAR) accessibility. e Volcano plot of the chromatin accessibility analysis, performed with DiffBind. DARs: adj. P value < 0.05, absolute log2 fold change >1. Red dots: increased accessibility in Scnn1b-Tg AMs; blue dots reduced accessibility in Scnn1b-Tg AMs. Annotation and enrichment of d DMRs and g DARs to gene regulatory regions, as determined by the LOLA method. h Integrated analysis of overlapping DARs and DMRs. The gray diagonal represents the linear regression. Shaded areas are confidence intervals of the correlation coefficient at 95%. Correlation coefficients and P values were calculated by the Pearson correlation method. i Locus plot of selected DMRs and DARs showing average methylation and chromatin accessibility of Scnn1b-Tg AMs and WT AMs. Shaded areas indicate 95% confidence intervals. Motif enrichment of j DMRs and k DARs (adj. P value < 0.05) stratified in hypo- and hypermethylated DMRs and open and closed DARs, respectively. l Predicted upstream regulator analysis of chromatin accessibility changes. Tagmentation-based whole-genome bisulfite sequencing (tWGBS), Scnn1b-Tg (n = 3) vs. WT (n = 4); Assay for transposase-accessible chromatin sequencing (ATACseq), Scnn1b-Tg (n = 4) vs. WT (n = 3). Source data are provided as a Source Data file.