Extended Data Fig. 3: Correlation between DNMT3A1 and H3K27me3 across gene bodies and gene expression analysis for Dnmt3a1–/– mouse brain.
a, Heatmaps of H3K4me3, H3K27me3 and DNMT3A1 across genes (left) in P18 Dnmt3a-FLAG cortex. Genes were ranked by H3K4me3 occupancy, and the curves represent smoothing cubic splines (right) fitted by the median signals of H3K27me3 and DNMT3A1 across each gene. b, Unchanged expression levels of DNA methylation regulators in Dnmt3a1–/– cortex. TPM: transcripts per million. WT, n = 3; Dnmt3a1 KO, n = 3 biological replicates. Data are shown as mean ± s.d. *** P = 0.0002 (two-sided unpaired t test). c, RT-qPCR verification of depletion of Dnmt3a1 full-length transcripts and down-regulation of neural development-related genes in P21 Dnmt3a1–/– cerebral cortex. The expression level of each gene was normalized to that of Gapdh. WT, n = 4; Dnmt3a1 KO, n = 5 biological replicates. Data are shown as mean with s.d. P values for Dnmt3a1, **** P < 0.0001; Neurod6, * P = 0.0173; Bdnf, * P = 0.0280; Wnt7a, *** P = 0.0002 (two-sided unpaired t tests). d,e, Heatmaps highlighting the relative expression level of members in gene sets synapse assembly (d) and neuromuscular process (e). f, RT-qPCR verification of expression changes for selected members in gene sets synapse assembly and neuromuscular process in P21 Dnmt3a1–/– cerebral cortex. WT, n = 4; Dnmt3a1 KO, n = 5 biological replicates. Data are shown as mean ± s.d. P values for Wnt5a, ** P = 0.0081; Homer1, * P = 0.0215; Shank1, *** P = 0.0006; Shank2, ** P = 0.0053 (two-sided unpaired t tests). g, GSEA of Dnmt3a1–/– hippocampal transcriptome. Top dysregulated gene sets were listed and ranked by NES. h, Enrichment plots for down-regulated gene set regulation of synaptic transmission in Dnmt3a1–/– hippocampus. i, Heatmap and average density of wildtype DNMT3A1 binding across DEGs (up- or down-DEGs) and non-DEGs (other) of Dnmt3a1–/– cortex. Input was subtracted from the signal of DNMT3A1 ChIP-seq. Genes are ordered by P values, with up-DEGs and down-DEGs on the top and bottom ends, respectively.
