Fig. 5

Identification of novel DMRs using the MEA pipeline. Allele-specific DNAme levels were calculated over 133,065 regions containing INDELs but lacking SNVs (representing novel informative regions gained employing MEA) using C57BL/6 J x DBA/2 J ICM WGBS data [11]. a Maternal versus paternal DNAme levels and CpG density (data point size) are plotted for informative regions overlapping with at least 10 CpGs from which allele-specific DNAme levels can be ascertained (746 data points). b CpG density (data point size) and allele-specific DNAme levels are shown, as in (a) over the subset of novel informative regions +/− 200 bp from annotated TSSs (with at least five informative CpGs on both alleles). Representative novel informative regions for which screenshots are provided are circled in red. c-d UCSC genome browser screenshots of differentially methylated regions (dashed boxes) near the promoters of the Kiss1 and Lpar6 genes. Tracks from Wang et al. [11] are included to illustrate differences in pipeline sensitivity. DNAme tracks of male and female germ cells [25, 26] as well as E7.5 embryos [11] are also shown, along with the location of informative CpGs (highlighted in blue)