Supplementary Figure 10: Lineage-specific de novo methylation in embryos cultured in vitro.
From: Dynamic epigenomic landscapes during early lineage specification in mouse embryos
a Chromosome-wide view of CG methylation for tissues isolated from in vivo E6.5 embryos (red) and IVC embryos (blue, replicate 1). The second replicate of IVC embryos showed similar patterns (data not shown). b The average methylation levels near active (green, FPKM≥10) or silenced (black, FPKM≤1) genes for IVC epiblast and VE (replicate 1). Similar observations were made for replicate 2 (data not shown). c The enrichment (logratio of observed/expected) of various types of genomic elements for regions hypermethylated in IVC epiblast compared to E5.5 or E6.5 epiblast in the genome. d A model of allele and lineage-specific DNA methylation reprogramming in mouse early embryos. After fertilization, the maternal allele inherits gene body DNA methylation pattern from oocyte to blastocyst. Gene body methylation then occurs in postimplantation embryos on both alleles during de novo methylation. Such pattern is retained in extraembryonic tissues but is gradually diminished in embryonic tissues. On the other hand, the paternal allele in preimplantation embryos undergoes mega-base chromatin compartment A-specific demethylation. During de novo methylation, VE preferentially gains DNA methylation in compartment A while epiblast shows even DNA methylation in both compartments. The differences between epiblast and VE are likely in part contributed by the differential expression of Dnmts
