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. 2022 Oct 5;13:991751. doi: 10.3389/fphar.2022.991751

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Copyright © 2022 Buocikova, Tyciakova, Pilalis, Mastrokalou, Urbanova, Matuskova, Demkova, Medova, Longhin, Rundén-Pran, Dusinska, Rios-Mondragon, Cimpan, Gabelova, Soltysova, Smolkova and Chatziioannou.

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Integration of decitabine (DAC)-induced DNA methylation and gene expression changes. The number of (A) hypomethylated and (B) hypermethylated genes after DAC treatment in JIMT-1 and T-47D cell lines (p-value ≤ 0.01; abs(log2FC) ≥ 1, FDR p-value ≤ 0.5 set as cut-offs for DNA methylation and gene expression, respectively); Volcano scatter plots showing the distribution -log10 (p-value) (y-axis) and log2FC (x-axis) of methylation-mediated changes in mRNA expression induced by exposure to DAC compared to non-treated controls for (C) JIMT-1 and (D) T-47D cells. In each plot, significantly up-regulated entities are highlighted by red and down-regulated by blue. Non-significant findings are presented as grey dots; Heatmaps depict (E) all DAC-induced DNA methylation-mediated gene expression changes in JIMT-1 and T-47D cells, and (F) the top 20 differentially regulated genes, respectively; Circos graphs show the integration of methylation and gene expression changes in (G) JIMT-1 and (H) T-47D cells. The outer circle is the chromosome idiogram of the human genome (based on G-banding, centromere highlighted in red). Blue outer circos plots demonstrate the culmination of methylation data (p < 0.01). The second plot represents hypomethylated and up-regulated (green dots) and hypermethylated and down-regulated (red dots) genes. The inner plot shows the chromosomal location of the top 50 hypomethylated/up-regulated (violet) and hypermethylated/down-regulated (yellow) genes.