title: X chromosome-wide analysis identifies DNA methylation sites influenced by cigarette smoking.
abstract: BACKGROUND
  Tobacco smoking is a major cause of chronic disease worldwide. Smoking may induce cellular and molecular changes including epigenetic modification, with both short-term and long-term modification patterns that may contribute to phenotypic expression of diseases. Recent epigenome-wide association studies (EWAS) have identified dozens of smoking-related DNA methylation (DNAm) sites. However, the X chromosomal DNAm sites have been largely overlooked due to a lack of an analytical framework for dealing with the sex-dimorphic distribution. To identify novel smoking-related DNAm sites on the X chromosome, we examined the modality of each X chromosomal DNAm site and conducted a sex-specific association study of cigarette smoking.
  
  
  RESULTS
  We used a discovery sample of 139 middle-age twins, and three replication samples of 78 twins, 464 and 333 unrelated individuals including 47, 17, 22, and 89 current smokers, respectively. After correction for multiple testing, the top smoking-related DNAm sites in BCOR and TSC22D3 were significantly hypermethylated and hypomethylated, respectively, among current smokers. These smoking-associated sites were replicated with meta-analysis p-values of 9.17 × 10(-12) and 1.61 × 10(-9). For both sites, the smoking effects on methylation levels were larger in males than that in females.
  
  
  CONCLUSIONS
  Our findings highlight the importance of investigating X chromosome methylation patterns and their associations with environmental exposures and disease phenotypes and demonstrate a robust statistical methodology for such study. Existing EWAS of human diseases should incorporate the X chromosomal sites to complete a comprehensive epigenome-wide scan.
authors.affiliation: Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE #3049, Atlanta, GA 30322 USA.
authors.forename: Daniella
authors.initials: D
authors.lastname: Klebaner
authors.affiliation: Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE #3049, Atlanta, GA 30322 USA.
authors.forename: Yunfeng
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE #3049, Atlanta, GA 30322 USA.
authors.forename: Qin
authors.initials: Q
authors.lastname: Hui
authors.affiliation: School of Nursing, Yale University, Orange, CT USA.
authors.forename: Jacquelyn Y
authors.initials: JY
authors.lastname: Taylor
authors.affiliation: Vietnam Era Twin Registry and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA USA.
authors.forename: Jack
authors.initials: J
authors.lastname: Goldberg
authors.affiliation: Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE #3049, Atlanta, GA 30322 USA.
authors.forename: Viola
authors.initials: V
authors.lastname: Vaccarino
authors.affiliation: Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE #3049, Atlanta, GA 30322 USA.|Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA USA.
authors.forename: Yan V
authors.initials: YV
authors.lastname: Sun
mesh_terms: D041321:Chromosomes, Human, X / Q000187:drug effects* / Q000235:genetics; D019175:DNA Methylation / Q000187:drug effects*; D044127:Epigenesis, Genetic / Q000187:drug effects; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D011518:Proto-Oncogene Proteins / Q000187:drug effects / Q000235:genetics; D012097:Repressor Proteins / Q000187:drug effects / Q000235:genetics; D012907:Smoking / Q000009:adverse effects*; D014157:Transcription Factors / Q000187:drug effects / Q000235:genetics
chemical_list: C411984:BCOR protein, human; D011518:Proto-Oncogene Proteins; D012097:Repressor Proteins; C404226:TSC22D3 protein, human; D014157:Transcription Factors
keywords: DNA methylation; Epigenetics; Epigenome; Epigenome-wide association study; Heritability; Methylome; Smoking; Twin; X chromosome