title: Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations.
abstract: BACKGROUND
  DNA methylation is an epigenetic mechanism that has been increasingly investigated in observational human studies, particularly on blood leukocyte DNA. Characterizing the degree and determinants of DNA methylation stability can provide critical information for the design and conduction of human epigenetic studies.
  
  
  METHODS
  We measured DNA methylation in 12 gene-promoter regions (APC, p16, p53, RASSF1A, CDH13, eNOS, ET-1, IFNγ, IL-6, TNFα, iNOS, and hTERT) and 2 of non-long terminal repeat elements, i.e., L1 and Alu in blood samples obtained from 63 healthy individuals at baseline (Day 1) and after three days (Day 4). DNA methylation was measured by bisulfite-PCR-Pyrosequencing. We calculated intraclass correlation coefficients (ICCs) to measure the within-individual stability of DNA methylation between Day 1 and 4, subtracted of pyrosequencing error and adjusted for multiple covariates.
  
  
  RESULTS
  Methylation markers showed different temporal behaviors ranging from high (IL-6, ICC = 0.89) to low stability (APC, ICC = 0.08) between Day 1 and 4. Multiple sequence and marker characteristics were associated with the degree of variation. Density of CpG dinucleotides nearby the sequence analyzed (measured as CpG(o/e) or G+C content within ±200 bp) was positively associated with DNA methylation stability. The 3' proximity to repeat elements and range of DNA methylation on Day 1 were also positively associated with methylation stability. An inverted U-shaped correlation was observed between mean DNA methylation on Day 1 and stability.
  
  
  CONCLUSIONS
  The degree of short-term DNA methylation stability is marker-dependent and associated with sequence characteristics and methylation levels.
authors: Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, Massachusetts, United States of America. hmbyun@hsph.harvard.edu
authors: Hyang-Min
authors: HM
authors: Byun
authors: Francesco
authors: F
authors: Nordio
authors: Brent A
authors: BA
authors: Coull
authors: Letizia
authors: L
authors: Tarantini
authors: Lifang
authors: L
authors: Hou
authors: Matteo
authors: M
authors: Bonzini
authors: Pietro
authors: P
authors: Apostoli
authors: Pier Alberto
authors: PA
authors: Bertazzi
authors: Andrea
authors: A
authors: Baccarelli
mesh_terms: D025601:Adenomatous Polyposis Coli Protein / Q000235:genetics; D001482:Base Composition / Q000235:genetics; D015820:Cadherins / Q000235:genetics; D019941:Cyclin-Dependent Kinase Inhibitor p16; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics*; D006801:Humans; D008297:Male; D009363:Neoplasm Proteins / Q000235:genetics; D052247:Nitric Oxide Synthase Type II / Q000235:genetics; D052250:Nitric Oxide Synthase Type III / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D019098:Telomerase / Q000235:genetics; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: C555337:APC protein, human; D025601:Adenomatous Polyposis Coli Protein; C000614131:CDKN2A protein, human; D015820:Cadherins; D019941:Cyclin-Dependent Kinase Inhibitor p16; C099972:H-cadherin; D009363:Neoplasm Proteins; C411762:RASSF1 protein, human; D014409:Tumor Necrosis Factor-alpha; D016159:Tumor Suppressor Protein p53; D025521:Tumor Suppressor Proteins; C496314:NOS3 protein, human; D052247:Nitric Oxide Synthase Type II; D052250:Nitric Oxide Synthase Type III; C509186:TERT protein, human; D019098:Telomerase