Extended Data Fig. 9: CNS-specific genes are associated with Rest/Nrsf binding and de-repression.
From: The changing mouse embryo transcriptome at whole tissue and single-cell resolution
a, H3K27me3 fold-decrease and RNA fold-change. Each bar represents a cluster of genes in a tissue type. The height represents RNA fold-increase between the earliest and latest time points, and the colours represent H3K27me3 ChIP signal fold decrease. The arrows point to the strongest decrease of H3K27me3 that happens in Cluster 34 in brain samples. b, Nrsf target enrichment in individual clusters. Bonferroni-corrected P values are calculated based on hypergeometric tests. Sample size (equal to that of Extended Data Fig. 2): Cluster 1 n = 121 genes, Cluster 2 n = 196 genes, Cluster 3 n = 693 genes, Cluster 4 n = 65 genes, Cluster 5 n = 474 genes, Cluster 6 n = 95 genes, Cluster 7 n = 226 genes, Cluster 8 n = 106 genes, Cluster 9 n = 103 genes, Cluster 10 n = 2182 genes, Cluster 11 n = 563 genes, Cluster 12 n = 536 genes, Cluster 13 n = 93 genes, Cluster 14 n = 341 genes, Cluster 15 n = 219 genes, Cluster 16 n = 1176 genes, Cluster 17 n = 338 genes, Cluster 18 n = 37 genes, Cluster 19 n = 45 genes, Cluster 20 n = 1319 genes, Cluster 21 n = 801 genes, Cluster 22 n = 44 genes, Cluster 23 n = 95 genes, Cluster 24 n = 283 genes, Cluster 25 n = 138 genes, Cluster 26 n = 30 genes, Cluster 27 n = 68 genes, Cluster 28 n = 200 genes, Cluster 29 n = 56 genes, Cluster 30 n = 236 genes, Cluster 31 n = 90 genes, Cluster 32 n = 256 genes, Cluster 33 n = 1,008 genes, Cluster 34 n = 3,073 genes, Ubiquitous n = 3,000 genes. c, Abundance of Nrsf mRNA in forebrain. The individual data points are shown as individual bars. d–f, Averaged H3K27me3 profiles near promoter regions (x-axis) for liver ChIP–seq signals over Cluster 10 genes (d), forebrain ChIP–seq signals over Cluster 34 genes (e) and forebrain ChIP–seq signals over Rest-targeted genes in Cluster 34 (f).
