Non-random distribution of methyl-CpG sites and non-CpG methylation in the human rDNA promoter identified by next generation bisulfite sequencing

Abstract

A next generation bisulfite sequencing (NGBS) was used to study rDNA promoter methylation in human brain using postmortem samples of the parietal cortex. Qualitative analysis of patterns of CpG methylation was performed at the individual rDNA unit level. CpG site-specific differences in methylation frequency were observed with the core promoter harboring three out of four most methylated CpGs. Moreover, there was an overall trend towards co-methylation for all possible pairs of 26 CpG sites. The hypermethylated CpGs from the core promoter were also most likely to be co-methylated. Finally, although rare, non-CpG (CpH) methylation was detected at several sites with one of them confirmed using the PspGI-qPCR assay. Similar trends were observed in samples from control individuals as well as patients suffering of Alzheimer’s disease (AD), mild cognitive impairment (MCI) or ataxia telangiectasia (AT). Taken together, while some methyl-CpG sites including those in the core promoter may have relatively greater inhibitory effect on rRNA transcription, co-methylation at multiple sites may be required for full and/or long lasting silencing of human rDNA.

How alcohol drinking affects our genes: an epigenetic point of view

“…Difficulties in recognizing this particular type of methylation caused a delay in the understanding and explanation of some molecular mechanisms involving stem cell differentiation and neuronal development. Otherwise, this technical bias can be overcome by the recent next generation bisulfite sequencing assays (Guo et al 2014;Pietrzak et al 2016). The family of DNA methyltransferases enzymes (DNMTs) catalyzes the methylation reaction.…”

Epigenetic roles in the malignant transformation of gastric mucosal cells

“…The current knowledge on gene methylation is far from being accurate and comprehensive. Future studies focusing on the following aspects will be more valuable: (1) longitudinal studies: large-scale DNA methylation profiling of clinical tissue specimens—longitudinal, dynamic cohort studies that analyze serial clinical specimens obtained from individual patients at various stages, from inflammation, intestinal metaplasia, and atypical hyperplasia to gastric cancer, are particularly inadequate; a genome-wide longitudinal study of DNA methylation based on such specimens will provide more accurate and comprehensive results; (2) data mining: collection and analysis of the data on gene methylation in normal gastric mucosa, precancerous lesions, and gastric cancer in various populations—exploration of the methylation pattern changes that occur during the malignant transformation of gastric mucosa using large-scale data mining allows a complete understanding of the gene methylation characteristics related to the malignant transformation of gastric mucosa as well as the differentiation of the key methylation changes from the numerous accompanying changes; and (3) non-CpG methylation: non-CpG methylation is an emerging field of research [28, 29]. However, a few data have been obtained for gastric cancer.…”

Non-CpG Methylation Revised

“…"Epigenetic science", as part of the bio-medical science, is no exception and is therefore subject to continuous revision and adjustment. This is the case of the new perspective suggested by the increasing evidence that non-CpG methylation of DNA is a discrete event and retains its functional role [2][3][4][5].…”

“…Once established during embryonic neurogenesis, non-CpG methylation is conserved during adult life and can account for 53% of total 5-mC, representing the main form of neuronal DNA methylation [33]. Evidence of differential non-CpG methylation correlated to brain pathology and brain aging has been collected both through gene-specific and genome-wide analyses [4,5,[34][35][36][37]. My laboratory further contributed to this field, taking advantage of the unbiased approach described above, showing that differential non-CpG methylation is associated with the modulated expression of specific genes in the brain of human patients with Alzheimer's disease and Tuberous Sclerosis [38][39][40][41].…”