Effect of TDG knockdown on 5fC distribution. (a) The ratio of methylation was plotted for TDG wild-type (WT) MEFs versus TDG± ES cells for the group of CGIs that show the highest 5fC enrichment in ES cells and a control group of all CGIs. The 5fC-enriched CGIs have higher methylation in the MEFs than the ES cells. (b) The ratio of methylation for WT MEFs (in red), or TDG KO MEFs (in blue), versus the ES cells. The 43 CGIs with the biggest increase in 5fC upon TDG KD have higher methylation in MEFs than ES cells and this increase is bigger in the absence of TDG. (c) Two example profiles (Hic1 and Csf2ra) show the overlap between 5fC CGI peaks in TDG KD ES cells and 5mC peaks at CGIs in TDG KO MEFs. The dotted grey line marks the transcription start site whereas the solid black lines represent CGIs. The shaded grey areas are the regions that are enriched for 5fC over control. RPKM, reads per kilobase per million mapped reads.