Figure 4

Methylome profiling in DNMT3A and DNMT3B-deficient embryos. (A) mRNA expression of Dnmt3a/b genes in embryos. Expression was measured by RT-qPCR on 5 to 10 pooled embryos and is depicted as a ratio relative to the expression of two housekeeping genes (Actb and Rpl13a). The primers used for RT-qPCR were designed in the last exons to amplify all isoforms. Blast, blastocyst; Epb, epiblast; Emb, embryo. (B) Pairwise comparison of CpG methylation in 400 bp tiles in wild-type (WT) compared with Dnmt3a-/- and Dnmt3b-/- E8.5 embryos. (C) Distribution of CpG methylation in RefSeq genes and 10 kb of flanking sequences in WT, Dnmt3a-/- or Dnmt3b-/- E8.5 embryos. (D) Number of 400 bp tiles that lose or gain more than 10% methylation in Dnmt3a-/- and Dnmt3b-/- compared with WT E8.5 embryos. (E) Detailed representation of the extent of methylation loss detected in 400 bp tiles in Dnmt3a-/- and Dnmt3b-/- compared with WT E8.5 embryos. (F) Boxplot representing the distribution of CpG methylation in the whole genome (400 bp tiles), exons, introns and transposable elements (TEs) in WT, Dnmt3a-/- and Dnmt3b-/- E8.5 embryos. Only sequences with >50% methylation in WT E8.5 embryos are considered. (G) Distribution of CpG methylation in several families of transposable elements in WT, Dnmt3a-/- and Dnmt3b-/- E8.5 embryos. IAP, intracisternal A-particle; LINE, long interspersed nuclear element; SINE, short interspersed nuclear element.