DNA hypomethylation and expression of long terminal elements correlate in Lsh−/−mutants. (a) Plot of RNA-seq expression changes versus HELP-seq DNA methylation changes in Lsh−/− versus WT cells. Repeat classes plotted are indicated in various colours (see key). Significant differences detected using EdgeR in RNA-seq reads sequenced between Lsh−/− and WT cells are plotted against significant changes (Fisher’s t-test and Benjamini-Hochberg multiple testing) in HELP-seq reads. Vertical dashed lines indicate −5 and +5 RNA-seq log2-fold change thresholds and horizontal dashed lines indicates −1 and +1 log2-fold change HELP-seq threshold. (b) Boxplot of RNA-seq log2-fold changes at hypomethylated repeat classes. HELP-seq data was filtered for significantly hypomethylated unique repeats and the distribution of their RNA-seq expression levels are shown in boxplot form. (c) Boxplot of HELP-seq log2-fold changes at upregulated unique repeats. RNA-seq data was filtered for significantly upregulated unique repeats and the distribution of their HELP-seq methylation levels are shown in boxplot form.