Fig. 3: UHRF1 knockdown induces genome-wide loss of DNA methylation and modulates gene transcription.

A The distribution of methylation levels in the whole genome. B The methylation level of CpG sites in the indicated cells. C Number of DML (differentially methylated locus) and DMR (differentially methylated region) in the indicated cells. D Density scatter plot of DNA sites with different methylation levels after UHRF1 knockdown. E Volcano plot for differentially expressed genes between control and UHRF1 knockdown CRL-8024 cells. F Scatter plot showing the correlation between DNA methylation and gene expression (TPM). MeGDP: numeral methylation difference between gene body and promoter. G Distribution of DMR of upregulated genes and downregulated genes. H Scatter plot showing the correlation between DNA methylation changes and gene expression changes (log2 (fold change)) after UHRF1 depletion in CRL-8024 cells. The values of DNA methylation change are depicted in the violin plot. The y-axis represents the numeral methylation difference in the gene body, promoter and MeGDP between the UHRF1 knockdown group and the control groups. I Venn diagram among the four datasets in CRL-8024 cells. The number of oncogenes and tumor suppressors that were upregulated or downregulated after UHRF1 knockdown are shown in the bar graph. P values using Spearman’s correlation coefficient (F) or unpaired Student’s t test (H). ^∗∗∗∗P < 0.0001. Ns not significant.