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.