Imprinted genes and several genomic repeat classes are known to escape the developmental reprogramming of DNA methylation (Guibert et al, 2012). Given the potential biological relevance of these genomic features to our study question, we tested whether DMRs were preferentially associated with SINE, LINE, and LTR repeat elements, as well as imprinted loci. Neither analysis revealed significant enrichments (Supplementary Figures S6 and S7). Only six imprinted genes (Abcc9, Begain, Chst8, Dlgap2, Gata3, and Kcnq1) were present in our list of DMRs, representing 1.2% of all DMR-associated genes, which was not significantly different than that expected by chance (χ2, P>0.05).
