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Fig. 1 | Epigenetics & Chromatin

Fig. 1

From: Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

Fig. 1

Cell line generation and overall changes seen in methylation levels. a Experimental approach: WT hTERT1604 fibroblasts were transfected with shRNA-containing plasmid and grown in selective medium; colonies of resistant cells were expanded, and three (d8, d10, d16) showing reduced DNMT1 levels were then analysed using genome-wide methylation and transcription arrays on the Illumina platform. b Levels of DNMT1 mRNA in cell lines from array and qPCR: error bars represent 95% confidence intervals around median, and standard error of the mean (SEM), respectively. All three knockdown (KD) lines were significantly depleted at p < 0.05 for both assays (except d8 array). c Overall methylation levels in WT and KD cells as measured by 450K: a β value of 1 equates to 100% methylation. Median values are indicated by the line, and whiskers represent interquartile range. The positions of the medians are also indicated at right (arrowheads). d The difference in median β value between each KD cell line and WT is shown first for all sites assayed (see c above) and then for each type of genomic element. CGI, CpG island; shore, region adjacent to CGI; shelf, adjacent to shore; sea, all other. See also Additional file 3: Fig. S2B. e Probe density distributions; in KD there is a decrease in the number of fully methylated sites (β closer to 1) and an increase in the number of unmethylated sites (β closer to 0), as well as in probes showing intermediate levels of methylation (arrow). f Numbers of sites (×104) showing significant changes in methylation (FDR < 0.05) compared to WT: the set of common sites is largest in each case, with close to twice as many sites commonly losing methylation in comparison with those gaining

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