Fig. 8
From: Chromatin variation associated with liver metabolism is mediated by transposable elements
Differential DNA methylation at TEs can impact chromatin accessibility variation across inbred strains. a A model of TE contribution to chromatin variation through differential DNA methylation. b Genome browser view of differentially methylated TEs with variable chromatin accessibility. ChIP-seq tracks of three liver TF and input from C57BL/6J and A/J livers are also shown. CpG sites within the highlighted accessible chromatin sites are shown in blue. c Bisulfite sequencing in A/J and C57BL/6J liver of the highlighted region in b. Filled circles represent methylated CpGs, whereas open circles represent unmethylated CpGs. d Boxplot of CpG methylation variance among the seven strains within variable chromatin sites that contain TEs, other repeat elements or unique sequences. Box plots show the median value, and whiskers show distribution of first and third quartile. e Percentage of differential methylated (DM) vs other CpGs in TE sequences. Differential methylation was defined from RRBS data of 25 inbred strains (see “Methods” section) (**indicates p < 0.001, Fisher’s exact test)