Fig. 3

DNMT1 maintenance-dependent methylation patterns are critical for suppressing LTR retrotransposons. a Methylation at two neighboring TEs, LTRs (blue rectangle) and LINEs (green oval), in DKO and 1KO cells. b Methylation of RRMRs in WT and KO cells. Each dot represents the overall methylation of one RRMR. c Overlap of DKO cell RRMRs with all repetitive elements in the mouse genome. scRNA small-scan RNA, SINE short interspersed nuclear element. d Composition of repetitive elements in the mouse genome. e, f Correlation of LTR methylation in DKO or 1KO cells with WT. Color represents two-dimensional transformed density. g DNMT1 displays different efficiencies during the maintenance of LTR subtype methylation. The percentage of members within each LTR subtype falling into each of six ranges was calculated and transformed to color intensity. LTR subtypes are ordered by percentage within the highest methylation range, 0.5–1, then second highest. Shown in blue are the top 7 LTR subtypes whose members retain high methylation in DKO.