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. 2018 Feb 7;7:e31977. doi: 10.7554/eLife.31977

Figure 2. Overlap of WGBS hypomethylation and ATAC-seq open chromatin peaks with regulatory annotation.

(A) Methylation levels in percent (y-axis) and log2 CpG density (x-axis) of UMR and LMR regulatory regions with the dashed line indicating the CpG-number (30 CpGs) that distinguishes LMRs and UMRs. (B) Log2 Fold Enrichment (log2FE) of LMRs (green shape), UMRs (blue shape) in various islet annotations is shown. These annotations include islet chromatin states, islet relevant TFBS (FOXA2, MAFB, NKX2.2, NKX6.1, PDX1), islet eQTLs, WGBS derived T2D-associated islet disease DMRs (dDMRs) and ATAC-seq open chromatin peaks. The dDMRs were derived from 6 T2D and eight non-diabetic individuals by Volkov et al. (2017) and dDMRs (orange shape) were also tested for enrichment in the aforementioned islet regulatory annotations. For all annotations, the empirically determined Bonferroni adjusted P-value is ≤0.00032 unless otherwise indicated by the shape: a dot corresponds to an Bonferroni adjusted p-value<0.00032 while the three triangles indicates Bonferroni adjusted p-values>0.00032: UMR enrichment adjusted P-value for weak enhancers = 1; dDMR enrichment adjusted P-value for MAFB = 0.006 and dDMR enrichment adjusted P-value for islet eQTLs = 0.01.

Figure 2—source data 1. LMR_UMR_source_MThurner_Oct_2017.tds is associated with primary Figure 2 Bed file providing coordinates of WGBS hypomethylated regulatory regions defined as UMRs and LMRs.
elife-31977-fig2-data1.tds (1.3MB, tds)
DOI: 10.7554/eLife.31977.007

Figure 2.

Figure 2—figure supplement 1. Identification and removal of Partially Methylated Domains (PMDs) and additional characterisation of regulatory regions.

Figure 2—figure supplement 1.

(A-B) Density distribution of the alpha value (A) before and (B) after removing PMDs (green curve in (A)) on chromosome 22. Alpha values represent a summary statistic derived from DNA methylation of windows of 100 CpGs and represents an indication of the polarisation status of methylation values in the genome which is expected to contain either highly methylated or unmethylated regions. Distributions with alpha <1 indicate methylation levels that are bimodal with either 0 or one methylation. Alpha = 1 corresponds to a uniform distribution of methylation; and distributions with alpha >1 tend to have primarily intermediate methylation levels. The red and green curve in (A) represent the non-PMD (red) and PMD regions (green) in the genome. (C) Number of peaks (x-axis) and mapped and filtered reads (y-axis) per ATAC-seq islet preparation. The dashed line indicates the mean read number. (D) Log2 Fold Enrichment (log2FE, x-axis) and associated -log10 Bonferroni adjusted P-values (y-axis) of LMRs (circle), UMRs (triangle) in various islet annotations (colours) is shown. These annotations include islet chromatin states, islet relevant TFBS (FOXA2, MAFB, NKX2.2, NKX6.1, PDX1), islet eQTLs, WGBS derived T2D-associated islet disease DMRs (dDMRs) and ATAC-seq open chromatin peaks. dDMRs (square) were also tested for enrichment in the aforementioned islet regulatory annotations. The results cluster near -log10 P-value of 3.5 since most Bonferroni adjusted P-values were more extreme than 0.00032.