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. 2014 Dec 11;10(12):e1004868. doi: 10.1371/journal.pgen.1004868

Figure 4. Unique regulation of tandem repeat-containing regions.

Figure 4

A, DNA methylation dynamics of transposable elements. Mean methylation levels of CpGs in various classes of SINEs, LINEs, LTRs and DNA repeats and SVA subfamilies are shown. SVA_A showed an especially high methylation level in blastocysts (59.2%). B, Proportions of repeat copies overlapping>70% methylated windows in human blastocysts. We analyzed only SINEs, LINEs, LTRs, DNA repeats, SVAs and satellites with>100 copies in the human genome. The top ten repeat names with the highest proportions are shown. The raw data are shown in S4 Table. C, Relationships between methylation levels and CpG densities. Mean methylation levels of CpGs in SVA_A are plotted against CpG densities. D, MER34C2 copies overlapping>70% methylated windows in human blastocysts. 39 MER34C2 copies are all tandemly repeated within the PTPRN2 gene locus. E, Proportions of maternal and paternal gDMRs containing VNTRs. Counts of gDMRs with VNTRs and total gDMRs are indicated. F, Proportions of mean methylation levels of CGIs with and without VNTRs in human blastocysts. Only autosomal CGIs hypermethylated in both gametes were analyzed. 118 of 499 CGIs with VNTRs and 31 of 2,222 CGIs without VNTRs showed>70% methylation (P = 0, chi-square test). G, Characteristics of VNTRs highly methylated in blastocysts. Using Tandem Repeats Finder [41], the size of the consensus pattern, the number of tandemly aligned copies and the alignment score were compared between VNTRs of <50% methylated CGIs and>70% methylated CGIs shown in (F). The alignment score calculated by Tandem Repeat Finder reflects the degree of similarity between repeat copies. When several VNTRs were found in a CGI, the VNTR with the highest alignment score was analyzed. Boxes represent lower and upper quartiles and horizontal lines indicate the median. Whiskers extend to the most extreme data points within 1.5 times the interquartile range from the boxes. The Mann-Whitney U test was used to calculate P-values. No sequence motif was found among the consensus patterns of the>70% methylated CGIs using DREME [42]. H, Mean methylation levels of CpGs in ALR. Oocytes showed the highest methylation level (80.6%).