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Summary  Single Nucleotide Polymorphisms in  FTO  intron 1 have been associated with obesity risk, leading to the hypothesis that  FTO  is the obesity‐related gene. However, other studies have shown that the  FTO  gene is part of the regulatory domain of the neighboring  IRX3  gene and that enhancers in  FTO  intron 1 regulate  IRX3 . While  Irx3  activity was shown to be necessary in the hypothalamus for the metabolic function of  Irx3  in mouse, no enhancers with hypothalamic activity have been demonstrated in the risk‐associated region within  FTO . In order to identify potential enhancers at the human  FTO  locus  in vivo , we tested regulatory activity in  FTO  intron 1 using BAC transgenesis in zebrafish. A minimal  gata2  promoter‐GFP cassette was inserted 1.3 kb upstream of the obesity associated SNP rs9939609 in a human  FTO  BAC plasmid. In addition to the previously identified expression domains in notochord and kidney, human  FTO  BAC:GFP transgenic zebrafish larvae expressed GFP in the ventral posterior tuberculum, the posterior hypothalamus and the anterior brainstem, which are also expression domains of zebrafish  irx3a . In contrast, an in‐frame insertion of a GFP cassette at the  FTO  start codon resulted in weak ubiquitous GFP expression indicating that the promoter of  FTO  does likely not react to enhancers located in the obesity risk‐associated region. genesis 53:640–651, 2015. © 2015 The Authors. genesis Published by Wiley Periodicals, Inc.

BAC transgenic zebrafish reveal hypothalamic enhancer activity around obesity associated SNP rs9939609 within the human FTO gene