Extended Data Fig. 4: DNA hyper-methylation (intragenic regions) and excessive open chromatins link with up-regulated major ZGA genes in human arrested embryos.
a, f. Relative enrichment analysis of a. DMRs, f. differential NDRs between human normal and arrested embryos in different genomic regions. b. The expression levels of genes associated with arrested-specific hypo-DMRs and hyper-DMRs (promoter) in human arrested embryos. c. Heatmap showing the expression levels of DEGs in human arrested embryos compared with human normal embryos (left). Pie charts showing the proportion of DEGs associated with DMRs (promoter or intragenic, right). d, e. The relationship between gene expression and DNA methylation level of DMRs (intragenic) at d. zygote and e. 2-cell stages of major ZGA genes. Up-regulated major ZGA genes with significant changes in DNA methylation levels are labeled in red. g. The spearman correlation coefficients between the normalized chromatin accessibility (core promoter regions) and gene expression levels. The number of biologically independent samples is 20, 20, 22, 22 for human normal zygote to 8-cell embryos; 15, 13, 7, 6 biologically independent samples for human arrested ones. Error bars represent mean ± SEM. h. The average expression levels of genes associated with arrested-specific proximal-merged NDRs (mNDRs) and that associated with normal-specific proximal mNDRs in human arrested embryos. In b, h, data are from 10, 10, 11, 12 biologically independent samples for human normal zygote to 8-cell embryos; 15, 13, 7, 6 biologically independent samples for human arrested ones; each box represents the median, 25% and 75% quartiles; whiskers indicate 1.5 times the interquartile range; unpaired two-sided Student’s t-tests without adjustment. i. Heatmap showing the proximal NDRs that were specifically open in human normal or arrested embryos (left). Pie charts showing the proportion of DEGs associated with arrested or normal-specific mNDRs (proximal, right). j, k. The association between major ZGA genes and differential NDRs (proximal) in j. human arrested zygotes and k. 2-cell embryos. Red dots represent up-regulated major ZGA genes in human arrested embryos occupied with arrested-specific NDRs (proximal). In d, e, j, k, representative major ZGA genes are labeled in purple.
