title: Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers.
abstract: BACKGROUND
  The mechanisms by which genetic variants, such as single nucleotide polymorphisms (SNPs), identified in genome-wide association studies act to influence body mass remain unknown for most of these SNPs, which continue to puzzle the scientific community. Recent evidence points to the epigenetic and chromatin states of the genome as having important roles.
  
  
  METHODS
  We genotyped 355 healthy young individuals for 52 known obesity-associated SNPs and obtained DNA methylation levels in their blood using the Illumina 450 K BeadChip. Associations between alleles and methylation at proximal cytosine residues were tested using a linear model adjusted for age, sex, weight category, and a proxy for blood cell type counts. For replication in other tissues, we used two open-access datasets (skin fibroblasts, n = 62; four brain regions, n = 121-133) and an additional dataset in subcutaneous and visceral fat (n = 149).
  
  
  RESULTS
  We found that alleles at 28 of these obesity-associated SNPs associate with methylation levels at 107 proximal CpG sites. Out of 107 CpG sites, 38 are located in gene promoters, including genes strongly implicated in obesity (MIR148A, BDNF, PTPMT1, NR1H3, MGAT1, SCGB3A1, HOXC12, PMAIP1, PSIP1, RPS10-NUDT3, RPS10, SKOR1, MAP2K5, SIX5, AGRN, IMMP1L, ELP4, ITIH4, SEMA3G, POMC, ADCY3, SSPN, LGR4, TUFM, MIR4721, SULT1A1, SULT1A2, APOBR, CLN3, SPNS1, SH2B1, ATXN2L, and IL27). Interestingly, the associated SNPs are in known eQTLs for some of these genes. We also found that the 107 CpGs are enriched in enhancers in peripheral blood mononuclear cells. Finally, our results indicate that some of these associations are not blood-specific as we successfully replicated four associations in skin fibroblasts.
  
  
  CONCLUSIONS
  Our results strongly suggest that many obesity-associated SNPs are associated with proximal gene regulation, which was reflected by association of obesity risk allele genotypes with differential DNA methylation. This study highlights the importance of DNA methylation and other chromatin marks as a way to understand the molecular basis of genetic variants associated with human diseases and traits.
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. sarah.voisin.aeris@gmail.com.
authors.forename: Sarah
authors.initials: S
authors.lastname: Voisin
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. markus.almen@imbim.uu.se.|Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden. markus.almen@imbim.uu.se.
authors.forename: Markus Sällman
authors.initials: MS
authors.lastname: Almén
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. galina.zheleznyakova@neuro.uu.se.
authors.forename: Galina Y
authors.initials: GY
authors.lastname: Zheleznyakova
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. lina.llundberg@gmail.com.
authors.forename: Lina
authors.initials: L
authors.lastname: Lundberg
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. sanaz.zr@gmail.com.
authors.forename: Sanaz
authors.initials: S
authors.lastname: Zarei
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. sandra.r.castillo@hotmail.se.
authors.forename: Sandra
authors.initials: S
authors.lastname: Castillo
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. fia.e@hotmail.com.
authors.forename: Fia Ence
authors.initials: FE
authors.lastname: Eriksson
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. emil.nilsson@neuro.uu.se.
authors.forename: Emil K
authors.initials: EK
authors.lastname: Nilsson
authors.affiliation: Medical Faculty, IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany. Matthias.Blueher@medizin.uni-leipzig.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Blüher
authors.affiliation: Medical Faculty, IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany. Yvonne.Boettcher@medizin.uni-leipzig.de.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Böttcher
authors.affiliation: Medical Faculty, IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany. peter.kovacs@medizin.uni-leipzig.de.
authors.forename: Peter
authors.initials: P
authors.lastname: Kovacs
authors.affiliation: Latvian Biomedical Research and Study Center, Ratsupites 1, Riga, LV-1067, Latvia. klovins@biomed.lu.lv.
authors.forename: Janis
authors.initials: J
authors.lastname: Klovins
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. mathias.rask-andersen@neuro.uu.se.
authors.forename: Mathias
authors.initials: M
authors.lastname: Rask-Andersen
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden. Helgi.Schioth@neuro.uu.se.
authors.forename: Helgi B
authors.initials: HB
authors.lastname: Schiöth
mesh_terms: D000273:Adipose Tissue / Q000378:metabolism; D000293:Adolescent; D000328:Adult; D000368:Aged; D000483:Alleles; D001921:Brain / Q000378:metabolism; D018899:CpG Islands; D019175:DNA Methylation; D004742:Enhancer Elements, Genetic; D005260:Female; D005347:Fibroblasts / Q000378:metabolism; D006801:Humans; D008297:Male; D008875:Middle Aged; D009765:Obesity / Q000097:blood / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D055815:Young Adult