Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells

Genomics. 2014 Dec;104(6 Pt B):538-44. doi: 10.1016/j.ygeno.2014.09.009. Epub 2014 Sep 29.


In the current study, we have used HT-TREBS to individually analyze the DNA methylation pattern of 4799 IAP LTR retrotransposons in embryonic stem, somatic and Neuro2A cells. According to the results, half of the loci within this family show constant methylation patterns between the three cell types whereas the remaining half display variable levels of methylation. About half of the variably methylated IAP LTRs tend to be hypomethylated in ES cells, and nearly all in this group are hypomethylated in Neuro2A cells. The observed hypomethylation in both cell types occur in a non-uniform, locus-specific manner and to various degrees of severity, with some of them being easily detectible by COBRA. Overall, this study demonstrates the feasibility of HT-TREBS to study DNA methylation changes at retrotransposons in a locus-specific manner in multiple cell types and further suggests the potential utility of this technique in developing epigenetic biomarkers for tracking disease progression.

Keywords: DNA methylation; Endogenous retrovirus; Epigenetic biomarkers; Epigenomes; IAP LTR; Retrotransposons.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cell Line, Tumor
  • DNA Methylation*
  • Embryonic Stem Cells / metabolism*
  • Epigenesis, Genetic*
  • Genome
  • Mice
  • Mice, Inbred C57BL
  • Neoplasms / genetics*
  • Neoplasms / metabolism
  • Retroelements*
  • Sequence Analysis, DNA / methods
  • Terminal Repeat Sequences*


  • Retroelements