1
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Hansen GT, Sobreira DR, Weber ZT, Thornburg AG, Aneas I, Zhang L, Sakabe NJ, Joslin AC, Haddad GA, Strobel SM, Laber S, Sultana F, Sahebdel F, Khan K, Li YI, Claussnitzer M, Ye L, Battaglino RA, Nóbrega MA. Genetics of sexually dimorphic adipose distribution in humans. Nat Genet 2023; 55:461-470. [PMID: 36797366 PMCID: PMC10375400 DOI: 10.1038/s41588-023-01306-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/23/2023] [Indexed: 02/18/2023]
Abstract
Obesity-associated morbidity is exacerbated by abdominal obesity, which can be measured as the waist-to-hip ratio adjusted for the body mass index (WHRadjBMI). Here we identify genes associated with obesity and WHRadjBMI and characterize allele-sensitive enhancers that are predicted to regulate WHRadjBMI genes in women. We found that several waist-to-hip ratio-associated variants map within primate-specific Alu retrotransposons harboring a DNA motif associated with adipocyte differentiation. This suggests that a genetic component of adipose distribution in humans may involve co-option of retrotransposons as adipose enhancers. We evaluated the role of the strongest female WHRadjBMI-associated gene, SNX10, in adipose biology. We determined that it is required for human adipocyte differentiation and function and participates in diet-induced adipose expansion in female mice, but not males. Our data identify genes and regulatory mechanisms that underlie female-specific adipose distribution and mediate metabolic dysfunction in women.
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Affiliation(s)
- Grace T Hansen
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Pritzker School of Medicine, University of Chicago, Chicago, IL, USA.
| | - Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Zachary T Weber
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Li Zhang
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Amelia C Joslin
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Gabriela A Haddad
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Sophie M Strobel
- Broad Institute of MIT and Harvard, Boston, MA, USA
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Samantha Laber
- Broad Institute of MIT and Harvard, Boston, MA, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Farhath Sultana
- Department of Rehabilitation Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Faezeh Sahebdel
- Department of Rehabilitation Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Kohinoor Khan
- Department of Rehabilitation Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Yang I Li
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, USA
- Massachussetts General Hospital, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at the Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Liang Ye
- Department of Rehabilitation Medicine, University of Minnesota, Minneapolis, MN, USA.
| | - Ricardo A Battaglino
- Department of Rehabilitation Medicine, University of Minnesota, Minneapolis, MN, USA.
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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2
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Sobreira DR, Joslin AC, Zhang Q, Williamson I, Hansen GT, Farris KM, Sakabe NJ, Sinnott-Armstrong N, Bozek G, Jensen-Cody SO, Flippo KH, Ober C, Bickmore WA, Potthoff M, Chen M, Claussnitzer M, Aneas I, Nóbrega MA. Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5. Science 2021; 372:1085-1091. [PMID: 34083488 PMCID: PMC8386003 DOI: 10.1126/science.abf1008] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/28/2021] [Indexed: 12/11/2022]
Abstract
Whereas coding variants often have pleiotropic effects across multiple tissues, noncoding variants are thought to mediate their phenotypic effects by specific tissue and temporal regulation of gene expression. Here, we investigated the genetic and functional architecture of a genomic region within the FTO gene that is strongly associated with obesity risk. We show that multiple variants on a common haplotype modify the regulatory properties of several enhancers targeting IRX3 and IRX5 from megabase distances. We demonstrate that these enhancers affect gene expression in multiple tissues, including adipose and brain, and impart regulatory effects during a restricted temporal window. Our data indicate that the genetic architecture of disease-associated loci may involve extensive pleiotropy, allelic heterogeneity, shared allelic effects across tissues, and temporally restricted effects.
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Affiliation(s)
- Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Amelia C Joslin
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Qi Zhang
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Grace T Hansen
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn M Farris
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University, Stanford 94305 CA, USA
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Grazyna Bozek
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Sharon O Jensen-Cody
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Kyle H Flippo
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Matthew Potthoff
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Mengjie Chen
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Melina Claussnitzer
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02131, USA
| | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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3
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4
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Sakabe NJ, Aneas I, Knoblauch N, Sobreira DR, Clark N, Paz C, Horth C, Ziffra R, Kaur H, Liu X, Anderson R, Morrison J, Cheung VC, Grotegut C, Reddy TE, Jacobsson B, Hallman M, Teramo K, Murtha A, Kessler J, Grobman W, Zhang G, Muglia LJ, Rana S, Lynch VJ, Crawford GE, Ober C, He X, Nóbrega MA. Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth. Sci Adv 2020; 6:eabc8696. [PMID: 33268355 PMCID: PMC7710387 DOI: 10.1126/sciadv.abc8696] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/19/2020] [Indexed: 05/29/2023]
Abstract
While a genetic component of preterm birth (PTB) has long been recognized and recently mapped by genome-wide association studies (GWASs), the molecular determinants underlying PTB remain elusive. This stems in part from an incomplete availability of functional genomic annotations in human cell types relevant to pregnancy and PTB. We generated transcriptome (RNA-seq), epigenome (ChIP-seq of H3K27ac, H3K4me1, and H3K4me3 histone modifications), open chromatin (ATAC-seq), and chromatin interaction (promoter capture Hi-C) annotations of cultured primary decidua-derived mesenchymal stromal/stem cells and in vitro differentiated decidual stromal cells and developed a computational framework to integrate these functional annotations with results from a GWAS of gestational duration in 56,384 women. Using these resources, we uncovered additional loci associated with gestational duration and target genes of associated loci. Our strategy illustrates how functional annotations in pregnancy-relevant cell types aid in the experimental follow-up of GWAS for PTB and, likely, other pregnancy-related conditions.
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Affiliation(s)
- Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Knoblauch
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Debora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Nicole Clark
- Department of Pediatrics, Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA
| | - Cristina Paz
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Horth
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Ryan Ziffra
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Harjot Kaur
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Xiao Liu
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Rebecca Anderson
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Jean Morrison
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Virginia C Cheung
- Department of Neurology and Institute for Stem Cell Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chad Grotegut
- Department of Obstetrics and Gynecology, Duke University Health System, Durham, NC 27713, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, University of Gothenberg, Gothenberg, Sweden
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalization, Institute of Public Health, Oslo, Norway
| | - Mikko Hallman
- Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Kari Teramo
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Amy Murtha
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Duke University School of Medicine, Durham, NC 27713, USA
| | - John Kessler
- Department of Neurology and Institute for Stem Cell Medicine, Northwestern University, Chicago, IL 60611, USA
| | - William Grobman
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ge Zhang
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Louis J Muglia
- Department of Obstetrics and Gynecology, University of Chicago, Chicago IL 60637, USA
| | - Sarosh Rana
- Department of Obstetrics and Gynecology, University of Chicago, Chicago IL 60637, USA
| | - Vincent J Lynch
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Gregory E Crawford
- Department of Pediatrics, Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
- Department of Obstetrics and Gynecology, University of Chicago, Chicago IL 60637, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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5
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El Khattabi L, Zhao H, Kalchschmidt J, Young N, Jung S, Van Blerkom P, Kieffer-Kwon P, Kieffer-Kwon KR, Park S, Wang X, Krebs J, Tripathi S, Sakabe N, Sobreira DR, Huang SC, Rao SSP, Pruett N, Chauss D, Sadler E, Lopez A, Nóbrega MA, Aiden EL, Asturias FJ, Casellas R. A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers. Cell 2019; 178:1145-1158.e20. [PMID: 31402173 PMCID: PMC7533040 DOI: 10.1016/j.cell.2019.07.011] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/24/2019] [Accepted: 07/09/2019] [Indexed: 12/11/2022]
Abstract
While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.
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Affiliation(s)
| | - Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | | | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Peter Van Blerkom
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | | | | | - Solji Park
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Xiang Wang
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Jordan Krebs
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | | | - Noboru Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Su-Chen Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Daniel Chauss
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Erica Sadler
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Andrea Lopez
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
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6
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Montefiori LE, Sobreira DR, Sakabe NJ, Aneas I, Joslin AC, Hansen GT, Bozek G, Moskowitz IP, McNally EM, Nóbrega MA. A promoter interaction map for cardiovascular disease genetics. eLife 2018; 7:e35788. [PMID: 29988018 PMCID: PMC6053306 DOI: 10.7554/elife.35788] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/21/2018] [Indexed: 12/17/2022] Open
Abstract
Over 500 genetic loci have been associated with risk of cardiovascular diseases (CVDs); however, most loci are located in gene-distal non-coding regions and their target genes are not known. Here, we generated high-resolution promoter capture Hi-C (PCHi-C) maps in human induced pluripotent stem cells (iPSCs) and iPSC-derived cardiomyocytes (CMs) to provide a resource for identifying and prioritizing the functional targets of CVD associations. We validate these maps by demonstrating that promoters preferentially contact distal sequences enriched for tissue-specific transcription factor motifs and are enriched for chromatin marks that correlate with dynamic changes in gene expression. Using the CM PCHi-C map, we linked 1999 CVD-associated SNPs to 347 target genes. Remarkably, more than 90% of SNP-target gene interactions did not involve the nearest gene, while 40% of SNPs interacted with at least two genes, demonstrating the importance of considering long-range chromatin interactions when interpreting functional targets of disease loci.
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Affiliation(s)
| | - Debora R Sobreira
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Noboru J Sakabe
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Ivy Aneas
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Amelia C Joslin
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Grace T Hansen
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Grazyna Bozek
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Ivan P Moskowitz
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
- Department of Pediatrics and PathologyThe University of ChicagoChicagoUnited States
| | - Elizabeth M McNally
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoUnited States
| | - Marcelo A Nóbrega
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
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Nóbrega MA, Gómez-Skarmeta JL. Editorial. Semin Cell Dev Biol 2016; 57:1. [PMID: 27499506 DOI: 10.1016/j.semcdb.2016.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Smemo S, Tena JJ, Kim KH, Gamazon ER, Sakabe NJ, Gómez-Marín C, Aneas I, Credidio FL, Sobreira DR, Wasserman NF, Lee JH, Puviindran V, Tam D, Shen M, Son JE, Vakili NA, Sung HK, Naranjo S, Acemel RD, Manzanares M, Nagy A, Cox NJ, Hui CC, Gomez-Skarmeta JL, Nóbrega MA. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature 2014; 507:371-5. [PMID: 24646999 PMCID: PMC4113484 DOI: 10.1038/nature13138] [Citation(s) in RCA: 853] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 02/10/2014] [Indexed: 12/18/2022]
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.
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Affiliation(s)
- Scott Smemo
- 1] Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA [2]
| | - Juan J Tena
- 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]
| | - Kyoung-Han Kim
- 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]
| | - Eric R Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Carlos Gómez-Marín
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain
| | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Flavia L Credidio
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Nora F Wasserman
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Ju Hee Lee
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Vijitha Puviindran
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Davis Tam
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Michael Shen
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Joe Eun Son
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5T 3H7, Canada
| | - Niki Alizadeh Vakili
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hoon-Ki Sung
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5T 3H7, Canada
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain
| | - Miguel Manzanares
- Cardiovascular Development and Repair Department, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5T 3H7, Canada
| | - Nancy J Cox
- 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
| | - Chi-Chung Hui
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
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9
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Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM. Megabase deletions of gene deserts result in viable mice. Nature 2004; 431:988-93. [PMID: 15496924 DOI: 10.1038/nature03022] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Accepted: 09/08/2004] [Indexed: 12/24/2022]
Abstract
The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals.
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