Figure 2.

Global methylation analysis of endogenous retrovirus copies nearby and distant from genes. (A) DNA methylation status of ERV copies relative to their TSS or (B) TTS (same dataset of copies for both panels. Note that fewer copies are present in panel B as in some cases the LTR analyzed was not the LTR closest to the TTS. The number of total copies studied in each category (n) is indicated above the bars. Distances were chosen based on Figure 1. Examples of bisulfite sequencing of copies (C) far from or (D,E) close to genes. The following cartoon legend applies for all figures: blue dashed lines represent introns and an arrow inside the ERV copy indicates the ERV sense of transcription. Empty circles represent unmethylated CpGs and filled ones are methylated CpGs (red for ERVs, blue for genes and black for flanking sequences). Each row of CpGs represents one sequenced bisulfite clone and each block of CpGs represents one sample. The tissue where the copy was studied is depicted below each block. For all DNA methylation data see Additional file 2, Figures S1 (MeDIP) and S2 (bisulfite) in Additional file 3. bp: base pairs; CGI: CpG Island; ERV: endogenous retrovirus; ETn/MusD: Early transposon/Mus musculus type D; IAP: Intracisternal (A) Particle; LTR: long terminal repeat; TSS: transcription start site; TTS: transcription termination site.