Journal Article

Obesity-associated variants within FTO form long-range functional connections with IRX3

Naranjo, Silvia, Gómez-Marín, Carlos, Gomez-Skarmeta, Jose Luis, Wasserman, Nora F., Sung, Hoon-Ki, Nóbrega, Marcelo A., Sakabe, Noboru J., Sobreira, Débora R., Nagy, Andras, Gamazon, Eric R., Manzanares, Miguel, Credidio, Flavia L., Shen, Michael, Puviindran, Vijitha, Tena, Juan J., Hui, Chi-Chung, Kim, Kyoung-Han, Tam, Davis, Lee, Ju Hee, Vakili, Niki Alizadeh, Aneas, Ivy, Son, Joe Eun, Cox, Nancy J., Smemo, Scott, Acemel, Rafael D.

2014

Overview

Obesity-associated noncoding sequences within FTO are functionally connected with IRX3 , and long-range enhancers in this region recapitulate aspects of IRX3 expression, suggesting that the obesity-associated interval is part of IRX3 regulation; Irx3 -deficient mice have lower body weight and are resistant to diet-induced obesity, suggesting IRX3 as a novel determinant of body mass and composition. Genetic links to obesity The search for genetic correlates of obesity has highlighted a noncoding region in the FTO gene: variations within this intron are associated with increased risk for obesity and type 2 diabetes. Although the biological actions of FTO have been intensely scrutinized, it is still not clear how these genetic variants influence FTO expression and biology. This paper shows that these noncoding sequences are functionally connected — at megabase distances — with the homeobox gene IRX3 . The obesity-associated interval appears to belong to the regulatory functions of IRX3 , rather than FTO . In addition, mice lacking Irx3 have reduced body weight and are resistant to diet-induced obesity. Taken together, the data suggest that IRX3 is an important metabolic regulator associated with human obesity and type 2 diabetes. Genome-wide association studies (GWAS) have reproducibly associated variants within introns of FTO with increased risk for obesity and type 2 diabetes (T2D) 1 , 2 , 3 . 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 4 , 5 , 6 . However, no direct connection between the obesity-associated variants and FTO expression or function has been made 7 , 8 , 9 . 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.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 38/23 / 38/39 / 38/43 / 42/44 / 45 / 631/208/200 / 631/208/729/743 / 631/337/572/2102 / 64/116 / 64/60 / 692/699/2743/393 / Adipose tissue / Adipose Tissue - metabolism / Alpha-Ketoglutarate-Dependent Dioxygenase FTO / Animals / Artificial chromosomes / Basal Metabolism - genetics / Body Mass Index / Body weight / Body Weight - genetics / Brain / Brain - metabolism / Diabetes Mellitus, Type 2 - genetics / Diet / Gene expression / Genes, Dominant - genetics / Genetic aspects / Genome-wide association studies / Genomes / Genomics / Homeobox genes / Homeodomain Proteins - genetics / Homeodomain Proteins - metabolism / Homeotic genes / Humanities and Social Sciences / Humans / Hypothalamus - metabolism / Introns - genetics / letter / Male / Mice / Mixed Function Oxygenases - genetics / multidisciplinary / Obesity / Obesity - genetics / Oxo-Acid-Lyases - genetics / Phenotype / Physiological aspects / Polymorphism, Single Nucleotide - genetics / Promoter Regions, Genetic - genetics / Properties / Proteins - genetics / Rodents / Science / Single nucleotide polymorphisms / Thinness - genetics / Transcription Factors - deficiency / Transcription Factors - genetics / Transcription Factors - metabolism / Weight control / Zebrafish - embryology / Zebrafish - genetics