Extended Data Fig. 4: YAP activation causes regional DNA demethylation in canonical YAP target genes.
a, DNA dot blot of genomic 5mC and 5hmC levels in 1-month-old Mst1/2 mutant livers (top panels). The blot was then stained with methylene blue as loading control (bottom panels). Images are representative of two independent experiments. b, 5mC and 5hmC validation at the indicated rDMRs in Mst1/2 mutant livers. Methylation (top panel) and hydroxymethylation (bottom panel) levels were determined by MBD-qPCR and hMeDIP-qPCR, respectively (n = 4). Values represent mean ± s.e.m. P values are calculated with unpaired two-tailed Student’s t-test. c, Genomic tracks displaying MBD-seq and H3K4me1 ChIP-seq reads at the rDMR loci of the indicated YAP target genes. Grey columns represent YAP-induced rDMRs. The cloning-based locus-specific bisulfite sequencing sites are also marked. Note the robust enhancer mark H3K4me1 occupancy at the YAP-induced rDMRs. d, Cloning-based traditional bisulfite sequencing (left panels) and TAB-seq (right panels) of CpG sites at the rDMR loci of YAP target genes. All sequencing results include 10 independent clones.
