Supplementary Figure 4: Epigenetic switch of DNA methylation with H3K9me3 on LTR regions.
From: Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development
a, Scatterplots show the association tests between log2-transformed H3K27me3 / input ratio and DNA methylation level during pre-implantation embryos on specific LTR families. Different colors represent four major family of the LTRs, including ERVK, ERV1, MaLR and ERVL (two-sided association test, n = 7 biologically independent samples. The x-axis represents the Pearson's correlation coefficients and the y-axis represents P-value of the tests. The blue horizontal line in each plot correspond p-value of 0.05 significance threshold. The total number of significant positive (+) and negative (−) correlations (P-value < 0.05) for each annotation is shown at the top of each plot. b, Boxplots show the log2-transformed H3K9me3 / input ratio, log2-transformed H3K27me3 / input ratio, DNA methylation, ATAC signal and expression level of the 28 H3K27me3 increased LTR during pre-implantation development. Statistical significance between stages was evaluated based on one-sided Wilcoxon test, * represent p-value < 0.05, *** represent p-value < 0.001. n = 28 different LTRs. The center represents the median value and the upper/lower line represent 5% and 95% quantile for the boxplots. c, Scatterplots show the association tests between log2-transformed H3K27me3 / input ratio and DNA methylation level during pre-implantation embryos on specific LTR families (two-sided association test, n = 7 biologically independent samples). Different colors represent four major family of the LTRs, including ERVK, ERV1, MaLR and ERVL. The total number of significant positive (+) and negative (−) correlations (P-value < 0.05) for each family is shown at the top of each plot. d, Graphs show the averaged expression level of Chaf1a, Sumo2, Trim28 and Zfp809. RNA-seq has been performed 2 times for MII oocyte, morula, 3 times for 8-cell and 4 times for 2-cell, 4-cellICM and TE. Results for each experiment are plotted as individual points with the average value indicated by the black line.
