Fig. 5

Low-dose arecoline effects on the methylome of NFs and CAL27 cells. A Global-wide average methylation of C, CG, CHG and CHH. Bar showed the number of each type of methylated C sites (mCG, mCHG and mCHH) and their proportion in all mC sites. B Mean methylation of NFs and CAL27 cells with or without low-dose arecoline treatment levels in different gene elements. C Methylation patterns of CGI and its surrounding regions of each sample. D Principal component analysis (PCA) for DNA methylation states of 24,949 CpG sites with 16 human cell lines. The PC1 axis clearly distinguishes NFs groups from CAL27 groups, while the PC2 axis distinguishes low-dose arecoline treatment groups from control groups. E Pairwise Pearson correlation coefficients (PCC) were calculated for comparison among methylomes of NFs and CAL27 cells with or without low-dose arecoline treatment. Samples were hierarchically clustered with the Euclidean distance method. The color scale indicates the degree of correlation. The correlation matrix and heat map were generated using R software. F Pairwise comparison of genome-wide DMR methylation level distribution density between control group and low-dose arecoline treated group in NFs and CAL27s. Density increases from blue to red. DMR density increases from white to red. G Violin plot of genome-wide methylation level distribution of DMR in NFs and CAL27s with or without low-dose arecoline treatment. The Y-axis represents the methylation level, and the violin width represents the number of DMRs for that methylation level. The middlebox plot reflects the distribution of DMR methylation levels from another perspective. The average methylation level of DMR between the two groups was calculated using the t-test to calculate the p-value statistics in the plot. C1E, CAL27 cells with low-dose arecoline treatment; C1C, CAL27 cells without low-dose arecoline treatment; NF1E, NFs with low-dose arecoline treatment; NF1C, NFs without low-dose arecoline treatment