Fig. 4: Greater loss of DNA methylation upon UHRF1 depletion than upon DNMT1 depletion; UHRF1 regulates DNA methylation at DNMT1, DNMT3A and DNMT3B sites.
From: Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells
A Volcano plot of differentially methylated regions (DMRs, 1 kb bins) after 4 days of depletion of UHRF1 and/or DNMT1. Blue dots: hypomethylated regions (>25% loss of methylation, q-value < 0.01), red dots: hypermethylated regions (>25% gain of methylation, q-value < 0.01). Gray dots: no significant change. The p value is corrected to q-value using sliding linear model (SLIM). B Venn diagram of the hypomethylated regions in the indicated cell lines, 4 days after depletion of the proteins. C Workflow used to quantitatively compare WGBS methylation values to the in vitro preferences of DNMT1, DNMT3A and DNMT3B. D Higher levels of H3K36me3 correlate with larger losses of DNA methylation in CpG islands. The CGIs were ranked by H3K36me3 level in HCT116 cells and split into 10 equally sized bins. DNA methylation differences were estimated from biological triplicates. Lines = median; box = 25th–75th percentile; whiskers = 1.5 × interquartile range from box. The p value is from Spearman’s correlation tests. Source data are provided as a Source data file.
