Figure 1

HELP-seq of repetitive genome in mouse. (a) An example of HELP-seq validation. Top: a HELP-seq browser track showing mouse chr2:95100568–951000802 (genomic build mm9) and loss of methylation at the indicated (asterisk) LINE-1. Bottom: bisulfite sequencing validating the HELP-seq profile for the same LINE-1. Average methylation levels are indicated by methylation heat map. (b) Second example of HELP-seq validation. Top: a HELP-seq browser track showing mouse chr15:31097720–31097931 (genomic build mm9) and gain of methylation at indicated (asterisk) genomic locus. Bottom: bisulfite sequencing validating the HELP-seq profile for the same locus. Bisulfite percentages calculated with bisulfite sequencing DNA methylation analysis. For (a) and (b), black square = methylated; white square = unmethylated; grey square = unknown. (c) Methylated-DNA immunoprecipitation of the LINE-1 region at chr2:95100568–951000802. Black = WT; white = Lsh^−/− mutant. (d) Analysis of genome-wide HELP-seq DNA methylation differences at repeat classes between cell line pairs: WT and Lsh^−/− cells, and Dnmt3b^+/− and Dnmt3b^−/− cells. Scale is the calculated odds-ratio (Figure S2 in Additional file 1). Odds ratio >1 hypomethylation in Lsh^−/− or Dnmt3b^−/− indicated by green arrow; odds ratio <1 hypermethylation in Lsh^−/− or Dnmt3b^−/− indicated by red arrow. (e) Analysis of genome-wide HELP-seq DNA methylation differences at repeat class satellites parsed by satellite repeat name. (f) Analysis of genome-wide HELP-seq DNA methylation differences at repeat class LTRs parsed by LTR repeat name. (g) Analysis of genome-wide HELP-seq DNA methylation differences at repeat class LINEs parsed by LINE repeat name. Blue = Lsh^−/− and WT comparison; red = Dnmt3b^−/− and Dnmt3b^+/− comparison.