Fig. 2

Variable methylation in TEs is unique to evolutionarily young ERV insertions. a Methylation ranges at the edges of LINEs, SINEs and non-ERV LTRs (denoted LTR*) in B and T cell samples from the WGBS dataset. Each point represents an individual element. Coloured points represent the top candidates in each family, which were selected for bisulphite pyrosequencing validation. b Bisulphite pyrosequencing validation in ear tissue of the top candidates from the WGBS screen in each repeat family. Elements with ≥10 and < 10% range in methylation between individuals are coloured in red and black, respectively. Each point represents an individual and is the average methylation of 2–4 distal CpGs in the element; n ≥ 8 for all elements shown. c Methylation ranges of validated elements grouped by repeat family suggests that variable methylation is uncommon in LINEs, SINEs and non-ERV LTRs, while validated IAP elements have the highest range. Each point represents an individual element. Elements with ≥10 and < 10% range in methylation between individuals are denoted by filled and blank circles, respectively. The thin black dotted line shows the 10% threshold. The thick black dashed lines represent the average methylation range per repeat family. Methylation was assayed in B cells for tsVM-IAPs and in ear tissue for all other types of elements