Figure 5

Knockdown of DNMT1 restrains global DNA methylation and regulates gene expression related to differentiation in THP-1 cells. (a) Box plot representing methylation level after BMIQ normalization of each sample. Methylation levels were analyzed by Illumina 850 K Methylation EPIC array. The minimum value, maximum value, and lower and upper quartiles were used for plotting. The line in the middle of each bar indicates the median value. For all cases, the P-values are less than 0.0001. The P-values were calculated by one-way ANOVA followed by Tukey’s multiple comparisons test. (b) Box plot showing the methylation level (β-value) of the hypomethylated CpG islands in DNMT1 knockdown THP-1 cells. The boxes extend from the 25th to the 75th percentiles and the line in the middle of the box indicates the median value. The P-values were calculated by unpaired two-tailed t-test. ****P < 0.0001. (c) Combined analysis of gene expression profiling and DNA methylation array in DNMT1 knockdown THP-1 cells. The genes which are upregulated and showed reduced promoter methylation level by DNMT1 depletion were used for plotting. The box plot represents 25th–75th percentiles with midlines indicating the median values. The heatmap was generated using the RPKM values for each gene. The P-values were calculated by paired two-tailed t-test. ****P < 0.0001. (d) Visualization of GO analysis results of the specified genes in (C). The color of the bubble indicates the log P-value for each GO term. The circle size indicates the frequency of the GO term in the underlying GO database. (e) Combined analysis of gene expression profiles and DNA methylation arrays in UHRF1-depleted THP-1 cells. The genes which are upregulated and showed reduced promoter methylation level by UHRF1 depletion were used for plotting. The box plot represents the 25th–75th percentiles, with midlines indicating the median values. The heat map was generated by RPKM values for each gene. The P-values were calculated by paired two-tailed t-test. ***P < 0.001. (f) Visualization of GO analysis results of the genes specified in (e). The color of the bubble indicates the log of the P-value for each GO term. The size of the circle indicates the frequency of the GO term in the underlying GO database.