Overall epigenetic patterns in human PG and AG embryos. (a) Schematic of the generation of human haploid parthenogenetic (PG) and androgenetic (AG) embryos used for RNA-seq, post-bisulfite adaptor tagging (PBAT) sequencing, DNase l hypersensitive sites sequencing (DNase-seq) and H3K27me3 ultra-low-input micrococcal nuclease-based native ChIP-seq (ULI-NChIP-seq). The blue dots mean that experimental data are from this study, while the yellow dots mean the data are from Yuan et al., 2023 [16]. For DNA methylation, four replicates of AG or PG (AG/PG) morulae were used: AG/PG_R1 (n = 1), AG/PG_R2 (n = 1), AG/PG_R3 (n = 2), AG/PG_R4 (n = 2); two replicates of AG or PG blastocysts were used: AG/PG_R1 (n = 1), AG/PG_R2 (n = 1). For DNase-seq, two replicates of AG or PG blastocysts were used: AG/PG_R1 (n = 1), AG/PG_R2 (n = 1). For ULI-NChIP-seq of H3K27me3, two replicates of AG or PG blastocysts were used: AG/PG_R1 (n = 2), AG/PG_R2 (n = 2). ‘n’ represents the number of embryos used in each replicate. (b) A heat map showing the DHS signal, H3K27me3 signal and CpG methylation levels (CpG ML) of genomic regions in PG and AG haploid embryos. The genome is divided into four groups of regions according to the DHS and H3K27me3 signal. Regions in group I only show a DHS signal but no H3K27me3 signal in any embryos. Regions in group II show both DHS and H3K27me3 signals in embryos. Regions in group III only show the H3K27me3 signal but no DHS signal in any embryos. Regions in group IV show neither a H3K27me3 signal nor DHS signal in any embryos. 8C represents an eight-cell embryo; Bla represents blastocyst; Mor represents morula. (c) Bar plot showing the percentage of genomic regions (bins) with differential DHS signal (left), H3K27me3 signal (middle) and DNA methylation (right) between AG (paternal) and PG (maternal) embryos. The percentage of differential DHS at eight-cell stage is calculated by the ratio of m/n, where m indicates the number of regions marked by the parentally specific DHSs in the eight-cell embryos, and n indicates the number of regions marked by the DHSs in either PG or AG eight-cell embryos. Similar methods were applied to calculate the percentages of regions with differential H3K27me3 signal or DNA methylation. (d) A heat map showing gene expression, DNA methylation and H3K27me3 signal in the gene promoters with both PG-specific DNA methylation and AG-specific H3K27me3 at blastocyst stage. (e–f) Genome browser view of DNA methylation and H3K27me3 signal in two imprinted genes, GLIS3 (e) and RASGRF1 (f). (g) A schematic model showing the relationship between parentally specific epigenetic status and gene expression. Paternally (Pat, also as AG) specific H3K27me3 and maternally (Mat, also as PG) specific DNA methylation could be associated with repression of the alleles.