title: Obesity-associated variants within FTO form long-range functional connections with IRX3.
abstract: Genome-wide association studies (GWAS) have reproducibly associated variants within introns of FTO with increased risk for obesity and type 2 diabetes (T2D). Although the molecular mechanisms linking these noncoding variants with obesity are not immediately obvious, subsequent studies in mice demonstrated that FTO expression levels influence body mass and composition phenotypes. However, no direct connection between the obesity-associated variants and FTO expression or function has been made. Here we show that the obesity-associated noncoding sequences within FTO are functionally connected, at megabase distances, with the homeobox gene IRX3. The obesity-associated FTO region directly interacts with the promoters of IRX3 as well as FTO in the human, mouse and zebrafish genomes. Furthermore, long-range enhancers within this region recapitulate aspects of IRX3 expression, suggesting that the obesity-associated interval belongs to the regulatory landscape of IRX3. Consistent with this, obesity-associated single nucleotide polymorphisms are associated with expression of IRX3, but not FTO, in human brains. A direct link between IRX3 expression and regulation of body mass and composition is demonstrated by a reduction in body weight of 25 to 30% in Irx3-deficient mice, primarily through the loss of fat mass and increase in basal metabolic rate with browning of white adipose tissue. Finally, hypothalamic expression of a dominant-negative form of Irx3 reproduces the metabolic phenotypes of Irx3-deficient mice. Our data suggest that IRX3 is a functional long-range target of obesity-associated variants within FTO and represents a novel determinant of body mass and composition.
authors.affiliation: 1] Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA [2].
authors.forename: Scott
authors.initials: S
authors.lastname: Smemo
authors.affiliation: 1] Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain [2].
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Tena
authors.affiliation: 1] Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada [2].
authors.forename: Kyoung-Han
authors.initials: KH
authors.lastname: Kim
authors.affiliation: Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Eric R
authors.initials: ER
authors.lastname: Gamazon
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Noboru J
authors.initials: NJ
authors.lastname: Sakabe
authors.affiliation: Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Gómez-Marín
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Ivy
authors.initials: I
authors.lastname: Aneas
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Flavia L
authors.initials: FL
authors.lastname: Credidio
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Débora R
authors.initials: DR
authors.lastname: Sobreira
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Nora F
authors.initials: NF
authors.lastname: Wasserman
authors.affiliation: Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
authors.forename: Ju Hee
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
authors.forename: Vijitha
authors.initials: V
authors.lastname: Puviindran
authors.affiliation: Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
authors.forename: Davis
authors.initials: D
authors.lastname: Tam
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Shen
authors.affiliation: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5T 3H7, Canada.
authors.forename: Joe Eun
authors.initials: JE
authors.lastname: Son
authors.affiliation: Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
authors.forename: Niki Alizadeh
authors.initials: NA
authors.lastname: Vakili
authors.affiliation: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5T 3H7, Canada.
authors.forename: Hoon-Ki
authors.initials: HK
authors.lastname: Sung
authors.affiliation: Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain.
authors.forename: Silvia
authors.initials: S
authors.lastname: Naranjo
authors.affiliation: Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain.
authors.forename: Rafael D
authors.initials: RD
authors.lastname: Acemel
authors.affiliation: Cardiovascular Development and Repair Department, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Manzanares
authors.affiliation: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5T 3H7, Canada.
authors.forename: Andras
authors.initials: A
authors.lastname: Nagy
authors.affiliation: 1] Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA [2] Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Nancy J
authors.initials: NJ
authors.lastname: Cox
authors.affiliation: Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
authors.forename: Chi-Chung
authors.initials: CC
authors.lastname: Hui
authors.affiliation: Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain.
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Gomez-Skarmeta
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Nóbrega
mesh_terms: D000273:Adipose Tissue / Q000378:metabolism; D000071516:Alpha-Ketoglutarate-Dependent Dioxygenase FTO; D000818:Animals; D001481:Basal Metabolism / Q000235:genetics; D015992:Body Mass Index; D001835:Body Weight / Q000235:genetics; D001921:Brain / Q000378:metabolism; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics; D004032:Diet; D005799:Genes, Dominant / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D007031:Hypothalamus / Q000378:metabolism; D007438:Introns / Q000235:genetics*; D008297:Male; D051379:Mice; D006899:Mixed Function Oxygenases / Q000235:genetics*; D009765:Obesity / Q000235:genetics*; D007652:Oxo-Acid-Lyases / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D011506:Proteins / Q000235:genetics*; D013851:Thinness / Q000235:genetics; D014157:Transcription Factors / Q000172:deficiency / Q000235:genetics* / Q000378:metabolism; D015027:Zebrafish / Q000196:embryology / Q000235:genetics
chemical_list: D018398:Homeodomain Proteins; C501598:IRX3 protein, human; C501599:Irx3 protein, mouse; D011506:Proteins; D014157:Transcription Factors; D006899:Mixed Function Oxygenases; C524916:FTO protein, mouse; D000071516:Alpha-Ketoglutarate-Dependent Dioxygenase FTO; C526492:FTO protein, human; D007652:Oxo-Acid-Lyases