Fig. 6: Transcripts initiate from cryptic intragenic promoters in Dnmt mutant embryos.

a Genome browser tracks of WGBS and RNA-seq profiles at the Mgl2 locus in WT and Dnmt mutant embryos. One WGBS replicates and three RNA-seq replicates are shown. RepeatMasker annotations are displayed in yellow below the tracks. b Boxplot of the ratio of RNA-seq read counts in downstream exons compared to the first exon in WT and DKO embryos for all expressed genes with at least 5 exons (n = 12,898). Exon n represents the last exon of the gene. ns: not significant; *p < 0.05; **p < 0.01; ***p < 0.001 (Wilcoxon test). c Metaplots representing the CpG density and the CpG methylation levels in 5 kb sequences flanking cryptic intragenic initiation sites or canonical RefSeq TSS. d Genome browser tracks of RNA-seq, DNAse-seq and NRF1 ChIP-seq profiles at the Mgl2 locus in WT and Dnmt triple knockout (TKO) ES cells. Two replicates are shown. e The genome browser tracks on the top display Mgl2 RNA-seq profiles upon NRF1 knockdown in TKO ES cells. The boxplot on the bottom shows the quantification of Mgl2 expression measured by RNA-seq (plotted as FPKM) upon mock and NRF1 knockdown in TKO ES cells (n = 3 replicates). In the boxplots the line indicates the median, the box limits indicate the upper and lower quartiles and the whiskers extend to 1.5 IQR from the quartiles.