title: 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.
authors.affiliation: Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY 40292, United States; Department of Neurological Surgery, University of Louisville, Louisville, KY 40292, United States.
authors.forename: Maciej
authors.initials: M
authors.lastname: Pietrzak
authors.affiliation: Division of Biostatistics and Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, United States.
authors.forename: Grzegorz A
authors.initials: GA
authors.lastname: Rempala
authors.affiliation: Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, United States.
authors.forename: Peter T
authors.initials: PT
authors.lastname: Nelson
authors.affiliation: Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY 40292, United States; Department of Neurological Surgery, University of Louisville, Louisville, KY 40292, United States; Department of Pharmacology & Toxicology, University of Louisville, Louisville, KY 40292, United States. Electronic address: michal.hetman@louisville.edu.
authors.forename: Michal
authors.initials: M
authors.lastname: Hetman
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics; D001260:Ataxia Telangiectasia / Q000235:genetics; D001483:Base Sequence; D001921:Brain / Q000166:cytology; D060825:Cognitive Dysfunction / Q000235:genetics; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019636:Neurodegenerative Diseases / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal
keywords: Aging; Brain; DNA methylation; Neurodegeneration; Nucleolus; rDNA