Extended Data Fig. 3: Genome-wide characterization of the bipartite signature.

a and b, Bipartite (a) and bivalent (b) gene rank (x axis) and corresponding rate of correct bipartite and bivalent classification obtained through genome browser visual inspection of individual loci (y axis, fraction of bipartite true-positive, Methods) in E10.5 K20^tdTomato/+ progenitors and E14.5, E18.5 and P4 Drg11^{vPrV-ZsGreen/+} barrelette neurons. c, Aggregate plot showing profile of H3K27me3 around the transcription start site (TSS) in E14.5Bip genes (top 100 genes ranked by bipartiteness scores in E14.5 Drg11^{vPrV-ZsGreen/+} barrelette neurons) with long gene length (>10 kb). Promoters (defined as 1 kb upstream to 500 bp downstream of TSS) and gene bodies (from 1 kb to 3 kb downstream of TSS) are highlighted. Note that H3K27me3 on gene bodies does not stretch further than 2-3 kb downstream of the TSS, even when genes are long. d, Genome browser profiles of representative bipartite IEGs (Fos, Egr1) in mouse ESCs. Note that the H3K27me3 mark is deposited not only on downstream (gene body) but also upstream regions of these H3K27ac promoters. e, Scatterplots showing promoter H3K27ac (x axis) and gene body H3K27me3 (y axis) signals in E14.5 rhombomere 3 (r3)-derived K20^tdTomato/+ hindbrain cells. E14.5Bip genes identified in Drg11^{vPrV-ZsGreen/+} barrelette neurons are mapped (red dots). Dashed lines indicate thresholds corresponding to a 5% false discovery rate (FDR) based on a gaussian mixture model with two components (for foreground and background, see Methods). Barrelette neuron E14.5Bip genes show high levels of promoter H3K27ac and gene body H3K27me3 indicating that they are bipartite also in r3-derived K20^tdTomato/+ hindbrain cells. f, CpG average observed/expected (o/e) ratios in a 100 bp window in E14.5Bip and E14.5Biv gene loci. Bins overlapping with the promoter, TSS, and gene body are indicated. g, Transcription factor binding motifs specifically enriched in E14.5Bip as compared to E14.5Biv promoters (Methods).