Fig. 1

Enhancers constitute the major epigenomic alterations in AEC differentiation. A) Left: Volcano plot (left) of differential gene expression during differentiation in the 2D model. Blue = AT2 (D0) enriched genes, red = AT1-like (D6) enriched genes. Right: Heatmap of known known AT1 and AT2 cell marker gene expression in RNAseq from 2D AEC differentiation model at the indicated days. Colors are scaled by row; blue = low expression, red = high expression. B) Unsupervised hierarchical cluster analysis of R-squared correlation matrix of chromatin-mark occupancy demonstrates similarity across the major known epigenetic marks. Darker green = more highly correlated genomic distribution, white = less correlated distribution patterns across the genome. Colored annotation panels along the side of the heatmap correspond to the days in culture (greyscale) and epigenetic mark (colors) being measured. UMR = unmethylated regions, LMR = low methylation regions, PMR = partially methylated regions. Numbers on heatmap indicate R correlation value rounded to nearest tenth. C) PIANO diagram showing correlation between loss or gain of epigenetic mark and changes in expression of the nearest-neighbor gene. Red scale = significance of enrichment for genes with gain in expression during AEC differentiation, blue = significance of enrichment for genes with loss in expression during AEC differentiation. Increasing size of circle containing epigenetic mark = more regions associated with gene expression changes, smaller size of circle = fewer epigenetic regions associated with gene expression changes. The thickness of the grey connecting lines indicates the number of genes that are associated with both epigenetic marks, thicker = more genes associated with both marks, thinner = fewer genes.