The obesity-associated SNPs in intron 1 of the FTO gene affect primary transcript levels

Abstract

As shown by genome-wide association studies single-nucleotide polymorphisms (SNPs) within intron 1 of the FTO gene are associated with the body mass index and type II diabetes, although the functional significance of these SNPs has remained unclear. Using primer extension assays, we have determined the ratio of allelic FTO transcript levels in unspliced heterogeneous nuclear RNA preparations from blood of individuals heterozygous for SNP rs9939609. Allelic expression ratios of the neighboring RPGRIP1L gene were investigated in individuals who were heterozygous for SNP rs4784319 and heterozygous or homozygous for rs9939609. In each of five individuals, the FTO transcripts containing the A (risk) allele of rs9939609 were more abundant than those with T allele (mean 1.38; 95% confidence interval 1.31-1.44). Similar results were obtained in a fibroblast sample. We also observed skewed allelic expression of the RPGRIP1L gene in blood, but skewing was independent of the FTO genotype. Our data suggest that increased expression of FTO is associated with increased body mass.

Figure 1

Physical map of the FTO and RPGRIP1L loci. The FTO and RPGRIP1L genes are located on the long arm of chromosome 16, share a CpG island with 51 CpG dinucleotides and are transcribed in opposite directions. The obesity-associated SNPs are in strong LD and located within intron 1 of the FTO gene. The variants used in this study as well as the CUTL1-binding site identified by Stratigopoulos et al are indicated.

Figure 2

Allelic expression studies. (a) Allelic expression of the FTO gene in five individuals. The ratio of the two alleles of SNP rs9939609 is skewed in favor of the A (risk) allele in all individuals investigated. Results are displayed as diamonds, in which the horizontal line represents the mean value and the top and bottom of the diamonds represent the 95% confidence interval. (b) Allelic expression of the RPGRIP1L gene in six individuals with different FTO genotypes. In each individual, the ratio of the two alleles of SNP rs4784319 is skewed in favor of the T allele, independently of the FTO genotype.