Figure 1: Pluripotency features and DNA methylation profiles of NT2 cells upon RA induction.
From: Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster
(a) Expression of OCT4, DNMT1, DNMT3a and DNMT3b in untreated NT2 cells (control) and cells treated for 3, 7, 14 and 21 days with RA. qRT–PCR measurements with at least three biological replicates were internally normalized to the corresponding β-actin expression levels. s.d.'s are indicated by error bars. (b) Microscopic images of NT2 cells showing the expression of enhanced green fluorescent protein (EGFP) under the control of the OCT4 promoter (first row) and the same cells after treatment with RA for 7 days (second row). The first column shows the light microscopic images (phase contrast), the second column EGFP fluorescence, and the third column an overlay. Scale bar 200 μm. (c) Density plot showing the distribution of the AVB values (x axis) of 3,091 non-CpG methylation states interrogated by the Infinium450K BeadChip, measured in uninduced NT2 cells (black, mean=0.27) and cells treated for 7 days (blue, mean=0.13) and 14 days (purple, mean=0.11) with RA. (d) Scatter plots showing the comparison of Illumina DNA methylation profiles (including non-CpG sites) of untreated NT2 cells with profiles of cells treated for 7 days (left plot) and 14 days (right plot) with RA. Red dots and numbers indicate differentially methylated sites. (e) Bar diagram showing the association of all sites interrogated by the Infinium450K BeadChip (control), RA-induced hypomethylated sites (hypo.) and hypermethylated sites (hyper.) with CGIs, shelf and shore regions. (f) Bar diagram showing the correlation of RA-induced differentially methylated sites (hypo- or hypermethylated compared with controls) identified using the Infinium450K BeadChip with annotated enhancer regions.
