DNA methylation is dynamically reprogrammed at two developmental periods, in primordial germ cells and pre-implantation embryos, via distinct phases of DNA demethylation and de novo methylation. Here we show that ribosomal DNA (rDNA) promoters are hypomethylated in sperm and oocytes; this hypomethyaltion was maintained during pre-implantation development. A DNA methylation analysis of embryonic and extra-embryonic cells on embryonic day 7.5 (E7.5) revealed that the rDNA promoter was slightly methylated in embryonic and extra-embryonic regions. Intriguingly, this hypomethylated status was observed throughout germ cell development on E13.5 and E18.5. In contrast, fetal somatic cells in gonad and liver acquired methylation on E13.5, which was maintained in adult tissues. These findings indicate a unique rDNA methylation signature in the germ cell lineage. (C) 2017 Elsevier Inc. All rights reserved.