Fig. 1
Overall CG methylation levels and distribution. a Schematic representation of male germ cell development and the cell types analyzed in this study. The interrupted arrow shows that the first round of spermatogenesis skips the stem cell stage. PGC, primordial germ cell. b Developmental changes in the level of CG methylation in the entire genome (line graph) and in 10 kb windows (box plots). Central bar, median; lower and upper box limits, 25th and 75th percentiles, respectively; whiskers, 1.5 times the interquartile range from the 25th to the 75th percentile. The E16.5 PSG data are from Kobayashi et al. [18]. c Distribution of CG methylation across mouse chromosome 1. The methylation levels determined in 500 kb windows are shown for the respective cell types (colored lines). Large PMDs (≥500 kb) identified in P0.5 PSGs by MethylSeekR are highlighted in yellow. The GC contents in 500 kb windows are also shown. cLADs are lamina-associated domains common to embryonic stem cells, neural precursor cells, astrocytes, and embryonic fibroblasts [39]. The CG methylation valleys marked with asterisks are not PMDs but composites of unmethylated CGIs and hypermethylated segments. d Developmental changes in the CG methylation level in 10 kb windows in PMDs and non-PMDs. Those windows overlapping with any PMDs in P0.5 PSGs were considered as PMDs and the rest were considered as non-PMDs. e Transcript levels of genes located in PMDs and non-PMDs. The transcript levels are shown as log2 (FPKM + 1). The PMD genes are RefSeq coding genes whose promoter regions (from 2000 bp upstream to 500 bp downstream of the transcription start site) overlap with any PMDs. The remaining genes are non-PMD