Extended Data Fig. 2: Features of embryonic LADs, analysis of gene expression and oocyte DamID.

a, Left, chromosome plots comparing Dam and Dam–lamin B1 DamID profiles in 2-cell embryos, 8-cell embryos and embryonic stem cells. Right, genome-wide comparison scatter plots of Dam and Dam–lamin B1 scores per 100-kb bin in 2- and 8-cell embryos and embryonic stem cells (right panel). DamID scores were calculated based on n = 3 independent biological replicates. r = Spearman’s rho. b, Average CpG density, AT content and DNaseI hypersensitivity sites (DHS)¹⁰ over LAD boundaries. c, Percentage overlap of LADs in embryos with constitutive LADs (associating with the lamina in embryonic stem cells, astrocytes, neural precursor cells and mouse embryonic fibroblasts)^8,37. d, CpG density, A/T content, DNase hypersensitivity (DHS) and minor ZGA gene expression at the 2-cell stage in genomic regions reorganizing in respect to the nuclear periphery during the zygote to 2-cell stage transition. Violin plots show the 25th and 75th percentiles (white boxes), median (black horizontal line) and values at most 1.5 × IQR. For CpG density, A/T content and DHS, n = number of bins; for minor ZGA expression, n = number of minor ZGA genes. Wilcoxon rank-sum test P values shown (two-sided). DHS data from ref. ¹³, expression data from ref. ¹⁹. e, Percentage overlap of the de novo iLAD at the 2-cell stage with constitutive LADs (as defined for c). f, Heat map of gene expression Z-scores at different stages of early embryonic development, depicting only genes in LADs specific to the 2-cell stage. These genomic regions contain 957 genes of which the 155 expressed genes are presented in the heat map (see Methods). g, Percentage of minor ZGA genes of total number of genes in iLADs (purple) and LADs (green). h, Example regions of LAD dynamics between the zygote and 2-cell stage (left top) and the 2-cell and 8-cell stage (right top). For each region, the mRNA expression levels are depicted in RPKM (red). The bottom panels display two examples of LAD dynamics between the zygote, 2-cell and 8-cell stages. The location of two genes in the 2-cell-specific LADs is indicated with a dotted line and the expression levels (RPKM) of the corresponding genes is displayed as violin plots. Violin plots show median (black points) and values at most 1.5 × IQR. n = biologically independent samples; zygote (n = 4), 2-cell (n = 10) and 8-cell (n = 28). i, Chromosome plot comparing Dam and Dam–lamin B1 profiles in oocytes and zygotes. j, Chromosome plots comparing Dam and Dam–lamin B1 DamID population and single-cell profiles in oocytes and zygotes.