Differential methylation within endogenous retroviruses is observed when near transcription start sites. (A) DNA methylation comparison between LTRs. Cartoons show the full-length ERV copy relative to the gene studied. Three ERV copies (two ETn/MusDs, and one IAP) located close to gene TSSs show hypomethylation of the LTR near the gene TSS (3' LTR) and hypermethylation of the LTR further from the gene TSS (5' LTR). (B) DNA methylation analysis of 3' and 5' LTRs of ERVs far from genes. No differential methylation between LTRs is generally observed. See Figure S3 in Additional file 3 for all the data (note that the 5' LTR bisulfite sequencing was adapted from . Global methylation profile was compared between both LTRs with a Mann-Whitney U-test, only significant results are shown. ***P <0.001, **P <0.01. 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.
Rebollo et al. Genome Biology 2012 13:R89 doi:10.1186/gb-2012-13-10-r89