Gene expression changes upon modulation of DNMT3A transcripts.

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Gene expression changes upon modulation of DNMT3A transcripts. Gene expression changes upon modulation of DNMT3A transcripts. (A–F) Scatter plots of gene expression (GE; Affymetrix Gene ST 1.0 microarray) upon KD (A–C) or OE (D–F) of transcripts 1+3 (A, D), transcript 2 (B, E), and transcript 4 (C, F), as compared with scrambled shRNA controls or empty control vectors (mean log2 values of normalized data; n = 3). Numbers of genes that reached statistical significance (adj. P < 0.05) and at least 1.5-fold up- or down-regulation are indicated in red and blue, respectively. (G) To visualize that gene expression changes upon KD and OE of transcript 2 occurred preferentially in opposite directions, the scatter plot depicts significant down-regulation (blue) and up-regulation (red) upon KD of transcript 2 in the data for OE of transcript 2 (Fischer's t test). (H) DNAm changes of CpGs upon KD of transcript 2 were matched to differential expression of the corresponding genes. Hypermethylated CpGs in promoter regions were associated with down-regulation of gene expression and vice versa (R = −0.23, R = −0.42 and R = −0.33, respectively; n = 3). (I, J) GO analysis was performed to classify gene expression changes upon KD (I) and OE (J) of transcript 2. Tanja Božić et al. LSA 2018;1:e201800153 © 2018 Božić et al.