Fig. 4

Read-level analysis of WGBS data points to epigenetic dysregulation in cell type-specific genes. a Illustration of strategy for pinpointing cell type-specific loss of methylation from read-level WGBS data. Searching for differentially methylated read clusters in 100 bp genomic bins enables inferences about changes taking place in individual cell types. Clusters comprise least 4 reads (see Methods); single reads are shown here for simplicity. Hypomethylated read clusters specific to F/F mice likely originate from AgRP neurons, whereas substantially methylated read clusters specific to F/F mice may arise from secondary effects in other cell types. b For each bin with both a cluster unique to F/F and a cluster unique to +/+ mice, average methylation levels of the unique clusters are shown in a density plot. Bins in ‘sector 2’ are defined by the simultaneous absence of a substantially methylated (≥ 55%) read cluster in +/+ mice and appearance of a novel hypomethylated (≤ 45%) read cluster in +/+ mice. ‘Sector 4’ is defined conversely. c Circos plot showing density of sectors 2 and 4 bins located in promoter regions of genes. Right: Venn diagram shows minimal overlap of sectors 2 and 4 promoter bins. d Promoter bins for differentially expressed genes specific to the molecularly defined ARH neural cell types Gm8773/Tac1, Arx/Nr5a2, Tbx19, unassigned2, Slc17a6/Trhr, and Trh/Lef1²⁵ are enriched in sector 4 relative to sector 2, suggesting that these cell types contribute to the observed hypermethylation in F/F ARH neurons as a whole. Bars represent −log₁₀(p) of χ² tests comparing cell type-specific sectors 2 and 4 bins relative to a background list of all sectors 2 and 4 bins (*p < 0.05). Numbers in parentheses represent ratio of sector 2:sector 4 bin counts. e Plot showing the location of promoter bins for differentially expressed genes specific to Arx/Nr5a2 ARH neurons. Plot coordinates follow the same convention as b.