Mouse preimplantation imprinting [WGBS]

In mammals, chromatin marks at imprinted genes are asymmetrically inherited from each parent to control gene expression. Many genomic imprints are determined by differentially methylated regions (DMRs), but these have not been comprehensively mapped physically or functionally in mouse preimplantation embryos. To address this, we measured genome-wide DNA methylation in individual haploid uniparental parthenogenetic haploid (ph) and androgenetic haploid (ah) E3.5 blastocysts by micro-whole-genome bisulfite sequencing (µWGBS). For comparison, we also included ahESC and phESC lines in the analysis.Comparison of DNA methylomes from uniparental blastocysts with those of control blastocysts (produced by intracytoplasmic sperm injection) identified 859 DMRs. Haploid ES cells showed overall erosion of those DMRs, in contrast to diploid ES cells that relatively maintained differential methylation. DNA methylation profiling (using micro-WGBS) of mouse E3.5 blastocysts (2 androgenotes, 2 parthenogenotes, 2 ICSI), embyronic stem cells (3 female, 2 male, 4 parthenogenotes, 3 androgenotes), and somatic tissue (kidney, n = 1). Haploid embryos offer the advantage to reduce noise that might have been generated by different alleles in diploid uniparental embryos.