Genome-wide methylation patterns in mammalian placentas show both large-scale divergence and gene-specific similarities.

(A) Phylogenetic tree of the species studied and the classification of their placenta types. Branch lengths are not to scale. (B) Density curves of average percent methylation in non-overlapping 20 kb windows in mammalian placentas. For comparison, the methylation distribution for brain tissue is shown in beige for some species and human cord blood is shown in aquamarine. The opossum brain sample was fetal whereas the other brain samples were postnatal. The interquartile range and medians are shown as black bars and white dots, respectively, for the placenta samples. Mouse brain data is from Hon et al. [19] (GSE42836), human placenta data is from Schroeder et al [21] (GSE25930). (C) Comparison of global methylation patterns in select species after liftOver to the human genome and smoothing (for full figure, see S4 Fig). Human placenta PMDs, as determined by HMM, are shown in black bars at top. (D) Comparison of methylation patterns at the CNTNAP2 locus in select species (for full figure, see S5 Fig). Raw species CpG site methylation wig data were graphed on the UCSC Genome Browser without preprocessing. Black line represents 50% methylation. Genes of interest are orange. EEM = extra-embryonic membrane.