Fig. 6: Enrichment of CCCG or CGGG sequences in mouse repeat elements that are DNMT3C targets.

a Image of the L1MdA and IAPEz-int elements showing the frequencies of CpG sites, CCCG + CGGG sites and fraction of CpG sites in CCCG or CGGG context, all expressed as o/e frequencies averaged over 50 bps. “Expected” values were determined using the C and G content of the entry. The annotated ORFs of the elements are indicated. Note the clustering of CCCG/CGGG sites in the promoter of L1MdA and at several regions in the body of IAPEz. b Frequency of CG sites in a CCCG or CGGG context in mouse repeat elements. The figure shows data for three LINE elements and three ERVK elements that are validated DNMT3C targets¹². As a control, two ERVK elements are shown, which are not methylated by DNMT3C. In addition, data are shown for examples of one murine ERV1 and ERVL element that both are also not targeted by DNMT3C and for one human ERV2 element. For the L1 elements, the promoter regions were used for the analysis, in all other cases the entire sequence of the element was used. See Supplementary Table 5 and Supplementary Fig. 10 for more information. The p-value was determined by a two-flanked T-test assuming unequal variance. c Methylation rates of two designed repeat substrates with sequences taken from known DNMT3C targets. Shown are averages of three experiments, error bars represent the SD. Data points are indicated by circles. P-values were determined by a two-sided T-test assuming equal variance, n.s. not significant. See also Supplementary Fig. 4.