Genome-Wide DNA Methylation in Saliva and Body Size of Adolescent Girls

References

• Ng M , FlemingT , RobinsonMet al. Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: a systematic analysis for the Global Burden of Disease Study 2013 . Lancet6736 , 1 – 16 ( 2014 ).
   Google Scholar
• Vuorela N , SahaM-T , SaloM . Prevalence of overweight and obesity in 5- and 12-year-old Finnish children in 1986 and 2006 . Acta Paediatr.98 , 507 – 512 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Vuorela N , SahaMT , SaloMK . Change in prevalence of overweight and obesity in Finnish children – comparison between 1974 and 2001 . Acta Paediatr.100 , 109 – 115 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Park MH , SovioU , VinerRM , HardyRJ , KinraS . Overweight in childhood, adolescence and adulthood and cardiovascular risk in later life: pooled analysis of three British birth cohorts . PLoS ONE8 , 3 – 8 ( 2013 ).
   Web of Science ®Google Scholar
• Hebebrand J , HinneyA . Environmental and genetic risk factors in obesity . Child Adolesc. Psychiatr. Clin. N. Am.18 , 83 – 94 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Locke AE , KahaliB , BerndtSIet al. Genetic studies of body mass index yield new insights for obesity biology . Nature518 , 197 – 206 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Boks MP , DerksEM , WeisenbergerDJ , StrengmanE , JansonE , IrisE . The relationship of DNA methylation with age, gender and genotype in twins and healthy controls . PLoS ONE4 , 21 – 23 ( 2009 ).
   Web of Science ®Google Scholar
• Horvath S . DNA methylation age of human tissues and cell types . Genome Biol.14 , R115 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Meissner A , MikkelsenTS , GuHet al. Genome-scale DNA methylation maps of pluripotent and differentiated cells . Nature454 , 766 – 770 ( 2010 ).
   Web of Science ®Google Scholar
• Breitling LP , YangR , KornB , BurwinkelB , BrennerH . Tobacco-smoking-related differential DNA methylation: 27K discovery and replication . Am. J. Hum. Genet.88 , 450 – 457 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Wang D , LiuX , ZhouYet al. Individual variation and longitudinal pattern of genome-wide DNA methylation from birth to the first two years of life . Epigenetics7 , 594 – 605 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Alisch RS , BarwickBG , ChopraPet al. Age-associated DNA methylation in pediatric populations age-associated DNA methylation in pediatric populations . Genome Res.22 , 623 – 632 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Jacoby M , GohrbandtS , ClausseV , BronsNH , MullerCP . Interindividual variability and co-regulation of DNA methylation differ among blood cell populations . Epigenetics7 , 1421 – 1434 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• van Dijk SJ , MolloyPL , VarinliH , MorrisonJL , MuhlhauslerBS . Epigenetics and human obesity . Int. J. Obes. (Lond.)39 , 1 – 13 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Ziller MJ , GuH , MüllerFet al. Charting a dynamic DNA methylation landscape of the human genome . Nature500 , 477 – 481 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Adalsteinsson BT , GudnasonH , AspelundTet al. Heterogeneity in white blood cells has potential to confound DNA methylation measurements . PLoS ONE7 , 1 – 9 ( 2012 ).
   Web of Science ®Google Scholar
• Talens RP , BoomsmaDI , TobiEWet al. Variation, patterns, and temporal stability of DNA methylation: considerations for epigenetic epidemiology . FASEB J.24 , 3135 – 3144 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Dolinoy DC . The agouti mouse model: an epigenetic biosensor for nutritional and environmental alterations on the fetal epigenome . Mutr. Rev.29 , 997 – 1003 ( 2008 ).
   Google Scholar
• Öst A , LempradlA , CasasEet al. Paternal diet defines offspring chromatin state and intergenerational obesity . Cell159 , 1352 – 1364 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Lavebratt C , AlmgrenM , EkströmTJ . Epigenetic regulation in obesity . Int. J. Obes.36 , 757 – 765 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Drake AJ , McPhersonRC , GodfreyKMet al. An unbalanced maternal diet in pregnancy associates with offspring epigenetic changes in genes controlling glucocorticoid action and foetal growth . Clin. Endocrinol. (Oxf.)77 , 808 – 815 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Huang R-C , GalatiJC , BurrowsSet al. DNA methylation of the IGF2/H19 imprinting control region and adiposity distribution in young adults . Clin. Epigenetics4 , 21 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Almén MS , NilssonEK , JacobssonJAet al. Genome-wide analysis reveals DNA methylation markers that vary with both age and obesity . Gene548 , 61 – 67 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Xu X , SuS , BarnesVAet al. A genome-wide methylation study on obesity: differential variability and differential methylation . Epigenetics8 , 522 – 533 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Plagemann A , HarderT , BrunnMet al. Hypothalamic proopiomelanocortin promoter methylation becomes altered by early overfeeding: an epigenetic model of obesity and the metabolic syndrome . J. Physiol.587 , 4963 – 4976 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Kuroda A , RauchTA , TodorovIet al. Insulin gene expression is regulated by DNA methylation . PLoS ONE4 , e6953 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Demerath EW , GuanW , GroveMLet al. Epigenome-wide association study (EWAS) of BMI, BMI change, and waist circumference in African American adults identifies multiple replicated loci . Hum. Mol. Genet.24 , 4464 – 4479 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Dick KJ , NelsonCP , TsaprouniLet al. DNA methylation and body-mass index: a genome-wide analysis . Lancet6736 , 1 – 9 ( 2014 ).
   Google Scholar
• Moleres A , CampiónJ , MilagroFIet al. Differential DNA methylation patterns between high and low responders to a weight loss intervention in overweight or obese adolescents: the EVASYON study . FASEB J.27 , 2504 – 2512 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Godfrey KM , SheppardA , GluckmanPDet al. Epigenetic gene promoter methylation at birth is associated with child’s later adiposity . Diabetes60 , 1528 – 1534 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Relton CL , GroomA , St PourcainBet al. DNA methylation patterns in cord blood DNA and body size in childhood . PLoS ONE7 , e31821 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• GitHub: Victorian-Bioinformatics-Consortium . https://github.com/Victorian-Bioinformatics-Consortium/nesoni .
   Google Scholar
• Krueger F , AndrewsSR . Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications . Bioinformatics27 , 1571 – 1572 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Langmead B , SalzbergS . Fast gapped-read alignment with Bowtie 2 . Nat. Methods9 , 357 – 359 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Jaffe AE , MurakamiP , LeeHet al. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies . Int. J. Epidemiol.41 , 200 – 209 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Hou C-D . A simple approximation for the distribution of the weighted combination of non-independent or independent probabilities . Stat. Probab. Lett.73 , 179 – 187 ( 2005 ).
   Web of Science ®Google Scholar
• Aryee MJ , JaffeAE , Corrada-BravoHet al. Minfi: a flexible and comprehensive bioconductor package for the analysis of Infinium DNA methylation microarrays . Bioinformatics30 , 1363 – 1369 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Turner SD . qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots . bioRxiv doi:10.1101/005165 ( 2014 ) ( Epub ahead of print ).
   Google Scholar
• Zhang K , CuiS , ChangS , ZhangL , WangJ . i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study . Nucleic Acids Res.38 , 90 – 95 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Iwen KAH , SenyamanO , SchwartzAet al. Melanocortin crosstalk with adipose functions: ACTH directly induces insulin resistance, promotes a pro-inflammatory adipokine profile and stimulates UCP-1 in adipocytes . J. Endocrinol.196 , 465 – 472 ( 2004 ).
   Google Scholar
• Li W , JiaoH , WangKet al. A genome wide association study of plasma uric acid levels in obese cases and never-overweight controls . Obesity21 , 490 – 494 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Turcot V , GroomA , McConnellJCet al. Bioinformatic selection of putative epigenetically regulated loci associated with obesity using gene expression data . Gene499 , 99 – 107 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Zhang Z , HaoC , LiCet al. Mutation of SLC35D3 causes metabolic syndrome by impairing dopamine signaling in striatal D1 neurons . PLoS Genet.10 , e1004124 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Schmidt AM , MooreKJ . The semaphorin 3E/PlexinD1 axis regulates macrophage inflammation in obesity . Cell Metab.18 , 461 – 462 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Hoeflich A , RussoVC . Physiology and pathophysiology of IGFBP-1 and IGFBP-2 – consensus and dissent on metabolic control and malignant potential . Best Pract. Res. Clin. Endocrinol. Metab.29 , 685 – 700 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Gauthier BR , WollheimCB . Synaptotagmins bind calcium to release insulin . Am. J. Physiol. Endocrinol. Metab.295 , E1279 – E1286 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Do DN , StratheAB , OstersenT , JensenJ , MarkT . Genome-wide association study reveals genetic architecture of eating behavior in pigs and its implications for humans obesity by comparative mapping . PLoS ONE8 , e71509 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Girardet C , ButlerAA . Neural melanocortin receptors in obesity and related metabolic disorders . Biochim. Biophys. Acta1842 , 482 – 494 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Chakraborty A , KoldobskiyMA , BelloNTet al. Inositol pyrophosphates inhibit akt signaling, thereby regulating insulin sensitivity and weight gain . Cell143 , 897 – 910 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Lee M , KimMK , KimS , ParkH , ParkC , ParkHK . Gender-based differences on the association between salt-sensitive genes and obesity in Korean children aged between 8 and 9 years . PLoS ONE10 , e0120111 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Hoyo C , FortnerK , MurthaAPet al. Association of cord blood methylation fractions at imprinted and birth weight . Cancer Causes Control2 , 635 – 645 ( 2012 ).
   Google Scholar
• Cordova-Palomera A , AlemanyS , FatjoM , NenadicI , FanL , GonzaA . Birth weight, working memory and epigenetic signatures in IGF2 and related genes: a MZ twin study . PLoS ONE9 , e103639 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Martínez JA , MilagroFI , ClaycombeKJ , SchalinskeKL . Epigenetics in adipose tissue, obesity, weight loss, and diabetes . Adv. Nutr.5 , 71 – 81 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Movérare-Skrtic S , MellströmD , VandenputL , EhrichM , OhlssonC . Peripheral blood leukocyte distribution and body mass index are associated with the methylation pattern of the androgen receptor promoter . Endocrine35 , 204 – 210 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Hidalgo B , IrvinMR , ShaJet al. Epigenome-wide association study of fasting measures of glucose, insulin, and HOMA-IR in the genetics of lipid lowering drugs and diet network study . Diabetes63 , 801 – 807 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Breton C V , SiegmundKD , JoubertBRet al. Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation . PLoS ONE9 , e99716 ( 2009 ).
   Google Scholar
• Besingi W , JohanssonÅ . Smoke-related DNA methylation changes in the etiology of human disease . Hum. Mol. Genet.23 , 2290 – 2297 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Stueve TR , WolffMS , PajakA , TeitelbaumSL , ChenJ . CYP19A1 promoter methylation in saliva associated with milestones of pubertal timing in urban girls . BMC Pediatr.14 , 78 ( 2009 ).
   Google Scholar
• Lomniczi A , LocheA , CastellanoJMet al. Epigenetic control of female puberty . Nat. Neurosci.16 , 281 – 289 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Freedman DS , WangJ , MaynardLMet al. Relation of BMI to fat and fat-free mass among children and adolescents . Int. J. Obes.29 , 1 – 8 ( 2004 ).
   Web of Science ®Google Scholar
• Houseman EA , AccomandoWP , KoestlerDCet al. DNA methylation arrays as surrogate measures of cell mixture distribution . BMC Bioinformatics13 , 86 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Zou J , LippertC , HeckermanD , AryeeM , ListgartenJ . Epigenome-wide association studies without the need for cell-type composition . Nat. Methods11 , 309 – 311 ( 2014 ).
   PubMed Web of Science ®Google Scholar