Within both these pseudogenes, oocytes maintained low levels of methylation, whereas somatic cells maintained high levels of methylation.
Retrotransposons also maintained high levels of CG methylation, although satellite repeats showed lower methylation levels (Additional file 2: Figure S2C).
In fact, methylation of the exocyclic NH group maintained high affinity for the tri-methylene 2-aminobenzimidazole derivative, while a drop in affinity was observed for the annular N-methylation.
These elements (and some single-copy loci) were previously shown to require continuous de novo methylation in order to maintain high levels of methylation in serum-grown ESCs (Arand et al., 2012), indicating that DNA methylation maintenance is inefficient at these loci.
Indeed, it has been previously observed that Dnmt3a/Dnmt3b double knockout ESCs lose global methylation slowly over consecutive passages (Jackson et al., 2004; Arand et al., 2012), while Dnmt3a and Dnmt3b are needed to maintain high levels of methylation at LINE1s due to inefficient methylation maintenance at these regions (Arand et al., 2012).
A recent evolutionary study determined that while the majority of CGIs may actively avoid DNA methylation, some CGIs are likely to maintain high CpG contents via methylation-independent processes such as biased gene conversion.
Consequently, genomic regions with relatively dense germline methylation have low CpG O/ E and regions with little or no germline methylation maintain high levels of CpG O/ E. It is important to note that CpG O/ E could be influenced by either the number of methylated CpG sites or the proportion of cells incurring methylation at a given locus.
The expression information in the present study provides strong support for the suggestion that HD-tuins family HDACs are important in Arabidopsis SE and are more likely to regulate histone modifications in target genes to maintain a high methylation status during SE.
In contrast, regions that undergo weak germline DNA methylation (hypomethylated) maintain high CpGO/E.
A persistence of dispersed methylation profiles at CpG dyads can be caused by constantly maintaining high levels of highly oxidized forms (not detectable by bisulfite sequencing) and/or by a loss (impaired maintenance) and re-gain of 5mC by de novo methylation.
