Identification of the transcription factor ZEB 1 as a central component of 1 the adipogenic gene regulatory network 2 3

Adipose tissue is a key determinant of whole body metabolism and energy homeostasis. Unraveling the regulatory mechanisms underlying adipogenesis is therefore highly relevant from a biomedical perspective. Our current understanding of fat cell differentiation is centered on the transcriptional cascades driven by the C/EBP protein family and the master regulator PPARγ. To elucidate further components of the adipogenic gene regulatory network, we performed a large-scale transcription factor (TF) screen overexpressing 734 TFs in mouse pre-adipocytes and probed their effect on differentiation. We identified 22 novel pro-adipogenic TFs and characterized the top ranking TF, ZEB1, as being essential for adipogenesis both in vitro and in vivo. Moreover, its expression levels correlate with fat cell differentiation potential in humans. Genomic profiling further revealed that this TF directly targets and controls the expression of most early and late adipogenic regulators, identifying ZEB1 as a central transcriptional component of fat cell differentiation. DOI: http://dx.doi.org/10.7554/eLife.03346.001

[1]  Adelina Rogowska-Wrzesinska,et al.  Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. , 2014, Cell reports.

[2]  Bruce M. Spiegelman,et al.  What We Talk About When We Talk About Fat , 2014, Cell.

[3]  A. James,et al.  Review of Signaling Pathways Governing MSC Osteogenic and Adipogenic Differentiation , 2013, Scientifica.

[4]  Leighton J. Core,et al.  Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription , 2013, Science.

[5]  J. Winkler,et al.  Effectiveness of a Low-Calorie Weight Loss Program in Moderately and Severely Obese Patients , 2013, Obesity Facts.

[6]  S. Raghav,et al.  A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks , 2013, Molecular systems biology.

[7]  M. Lu,et al.  The Transcription Factor Atonal homolog 8 Regulates Gata4 and Friend of Gata-2 during Vertebrate Development , 2013, The Journal of Biological Chemistry.

[8]  Frédérique Lisacek,et al.  Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics , 2013, Nature Methods.

[9]  M. Eisen,et al.  Dual functions of TAF7L in adipocyte differentiation , 2013, eLife.

[10]  Maria Keays,et al.  ArrayExpress update—trends in database growth and links to data analysis tools , 2012, Nucleic Acids Res..

[11]  J. Stephens The Fat Controller: Adipocyte Development , 2012, PLoS biology.

[12]  D. Green,et al.  c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells , 2012, Cell.

[13]  David Z. Chen,et al.  Architecture of the human regulatory network derived from ENCODE data , 2012, Nature.

[14]  William Stafford Noble,et al.  Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors , 2012, Genome research.

[15]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[16]  T. Mikkelsen,et al.  Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO. , 2012, Molecular cell.

[17]  P. Seale,et al.  An Evi1-C/EBPβ Complex Controls Peroxisome Proliferator-Activated Receptor γ2 Gene Expression To Initiate White Fat Cell Differentiation , 2012, Molecular and Cellular Biology.

[18]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[19]  M. Winnefeld,et al.  Identification of New Genes Involved in Human Adipogenesis and Fat Storage , 2012, PloS one.

[20]  G. Berx,et al.  Evolutionary functional analysis and molecular regulation of the ZEB transcription factors , 2012, Cellular and Molecular Life Sciences.

[21]  S. Mandrup,et al.  Transcriptional networks and chromatin remodeling controlling adipogenesis , 2012, Trends in Endocrinology & Metabolism.

[22]  O. MacDougald,et al.  Adipose tissue stem cells meet preadipocyte commitment: going back to the future[S] , 2012, Journal of Lipid Research.

[23]  Chris T. A. Evelo,et al.  WikiPathways: building research communities on biological pathways , 2011, Nucleic Acids Res..

[24]  D. van der A,et al.  Trend in Obesity Prevalence in European Adult Cohort Populations during Follow-up since 1996 and Their Predictions to 2015 , 2011, PloS one.

[25]  Aedín C. Culhane,et al.  Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments , 2011, Nucleic Acids Res..

[26]  D. Gašperíková,et al.  Adipogenesis and insulin sensitivity in obesity are regulated by retinoid-related orphan receptor gamma , 2011, EMBO molecular medicine.

[27]  Tanya M. Teslovich,et al.  Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution , 2011, Nature Genetics.

[28]  H. Aburatani,et al.  Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation , 2011, PLoS genetics.

[29]  Jacques Rougemont,et al.  GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR , 2011, Database J. Biol. Databases Curation.

[30]  M. Lazar,et al.  Repressor transcription factor 7-like 1 promotes adipogenic competency in precursor cells , 2011, Proceedings of the National Academy of Sciences.

[31]  A. Griffith,et al.  A Noncoding Point Mutation of Zeb1 Causes Multiple Developmental Malformations and Obesity in Twirler Mice , 2011, PLoS genetics.

[32]  S. Mandrup,et al.  Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis , 2011, The EMBO journal.

[33]  A. Hevener,et al.  TLE3 is a dual-function transcriptional coregulator of adipogenesis. , 2011, Cell metabolism.

[34]  L. Coin,et al.  Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads , 2011, Genome Biology.

[35]  Thomas Meitinger,et al.  Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution , 2010, Nature Genetics.

[36]  Eric S. Lander,et al.  Comparative Epigenomic Analysis of Murine and Human Adipogenesis , 2010, Cell.

[37]  M. Ronaghi,et al.  Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data , 2010, PloS one.

[38]  M. Shibamori,et al.  DNA binding - dependent glucocorticoid receptor activity promotes adipogenesis via krüppel-like factor 15 gene expression , 2010, Laboratory Investigation.

[39]  Hedi Peterson,et al.  Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development , 2010, Genome Biology.

[40]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[41]  Jonathan Schug,et al.  Propagation of adipogenic signals through an epigenomic transition state. , 2010, Genes & development.

[42]  R. Kauppinen,et al.  Inhibitor of DNA Binding 4 (ID4) Regulation of Adipocyte Differentiation and Adipose Tissue Formation in Mice* , 2010, The Journal of Biological Chemistry.

[43]  Feng Lin,et al.  A signal-noise model for significance analysis of ChIP-seq with negative control , 2010, Bioinform..

[44]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[45]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[46]  B. Spiegelman,et al.  Transcriptional Control of Preadipocyte Determination by Zfp423 , 2010, Nature.

[47]  M. Cleary,et al.  The ZEB1 Transcription Factor Is a Novel Repressor of Adiposity in Female Mice , 2009, PloS one.

[48]  G. Berx,et al.  The role of the ZEB family of transcription factors in development and disease , 2009, Cellular and Molecular Life Sciences.

[49]  M. Neville,et al.  Markers of de novo lipogenesis in adipose tissue: associations with small adipocytes and insulin sensitivity in humans , 2009, Diabetologia.

[50]  H. Stunnenberg,et al.  Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. , 2008, Genes & development.

[51]  Chris T. A. Evelo,et al.  Presenting and exploring biological pathways with PathVisio , 2008, BMC Bioinformatics.

[52]  J. Friedman,et al.  Transcriptional regulation of adipogenesis by KLF4. , 2008, Cell metabolism.

[53]  P. A. Pérez-Mancera,et al.  Adipose tissue mass is modulated by SLUG (SNAI2). , 2007, Human molecular genetics.

[54]  Ole Winther,et al.  JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update , 2007, Nucleic Acids Res..

[55]  D. Trono,et al.  Production and Titration of Lentiviral Vectors , 2007, Current protocols in human genetics.

[56]  William Stafford Noble,et al.  Quantifying similarity between motifs , 2007, Genome Biology.

[57]  O. MacDougald,et al.  Adipocyte differentiation from the inside out , 2006, Nature Reviews Molecular Cell Biology.

[58]  M. Sigvardsson,et al.  Critical Role for Ebf1 and Ebf2 in the Adipogenic Transcriptional Cascade , 2006, Molecular and Cellular Biology.

[59]  S. Farmer Transcriptional control of adipocyte formation. , 2006, Cell metabolism.

[60]  D. Trono,et al.  Production and Titration of Lentiviral Vectors , 2006, Current protocols in neuroscience.

[61]  Herbert Tilg,et al.  Adipocytokines: mediators linking adipose tissue, inflammation and immunity , 2006, Nature Reviews Immunology.

[62]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[63]  Hisato Kondoh,et al.  δEF1 Mediates TGF-β Signaling in Vascular Smooth Muscle Cell Differentiation , 2006 .

[64]  O. Danos,et al.  Efficient control of gene expression in the hematopoietic system using a single Tet-on inducible lentiviral vector. , 2006, Molecular therapy : the journal of the American Society of Gene Therapy.

[65]  Y. Matsuki,et al.  Role of Krüppel-like Factor 15 (KLF15) in Transcriptional Regulation of Adipogenesis* , 2005, Journal of Biological Chemistry.

[66]  M. Lane,et al.  Commitment of C3H10T1/2 pluripotent stem cells to the adipocyte lineage. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Su‐Li Cheng,et al.  Msx2 Promotes Osteogenesis and Suppresses Adipogenic Differentiation of Multipotent Mesenchymal Progenitors* , 2003, Journal of Biological Chemistry.

[68]  R. Urrutia KRAB-containing zinc-finger repressor proteins , 2003, Genome Biology.

[69]  J. Stephens,et al.  STAT5A promotes adipogenesis in nonprecursor cells and associates with the glucocorticoid receptor during adipocyte differentiation. , 2003, Diabetes.

[70]  M. Lane,et al.  Mitotic clonal expansion: A synchronous process required for adipogenesis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[71]  K. Kristiansen,et al.  The retinoblastoma-histone deacetylase 3 complex inhibits PPARgamma and adipocyte differentiation. , 2002, Developmental cell.

[72]  P. Pitha,et al.  Interferon Regulatory Factors , 2002 .

[73]  Barbara D. Saatkamp,et al.  Distinct Transcriptional Profiles of Adipogenesisin Vivo and in Vitro * , 2001, The Journal of Biological Chemistry.

[74]  Q. Tong,et al.  Function of GATA transcription factors in preadipocyte-adipocyte transition. , 2000, Science.

[75]  P. Puigserver,et al.  Transcriptional regulation of adipogenesis. , 2000, Genes & development.

[76]  B. Spiegelman,et al.  Cross-Regulation of C/EBPα and PPARγ Controls the Transcriptional Pathway of Adipogenesis and Insulin Sensitivity , 1999 .

[77]  K. Clément,et al.  A genome-wide scan for human obesity genes reveals a major susceptibility locus on chromosome 10 , 1998, Nature Genetics.

[78]  B. Spiegelman,et al.  ADD1/SREBP1 activates PPARγ through the production of endogenous ligand , 1998 .

[79]  E. Nicodemou-Lena,et al.  De novo adipogenesis in mice at the site of injection of basement membrane and basic fibroblast growth factor. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[80]  J. Auwerx,et al.  The Organization, Promoter Analysis, and Expression of the Human PPARγ Gene* , 1997, The Journal of Biological Chemistry.

[81]  H. Kikutani,et al.  Impairment of  T Cell Development in δ EF1 Mutant Mice , 1997, The Journal of experimental medicine.

[82]  B. Spiegelman,et al.  mPPAR gamma 2: tissue-specific regulator of an adipocyte enhancer. , 1994, Genes & development.

[83]  Hisato Kondoh,et al.  Identification of nuclear factor delta EF1 and its binding site essential for lens-specific activity of the delta 1-crystallin enhancer , 1991, Nucleic Acids Res..

[84]  C. Emerson,et al.  10T1/2 cells: an in vitro model for molecular genetic analysis of mesodermal determination and differentiation. , 1989, Environmental health perspectives.

[85]  H. Green,et al.  Formation of normally differentiated subcutaneous fat pads by an established preadipose cell line , 1979, Journal of cellular physiology.

[86]  H. Green,et al.  Spontaneous heritable changes leading to increased adipose conversion in 3T3 cells , 1976, Cell.

[87]  H. Green,et al.  An established preadipose cell line and its differentiation in culture II. Factors affecting the adipose conversion , 1975, Cell.

[88]  H. Green,et al.  An established pre-adipose cell line and its differentiation in culture. , 1974, Cell.

[89]  Petra C. Schwalie,et al.  Data from: Identification of ZEB1 as a central component of the adipogenic gene regulatory network , 2014 .

[90]  M. Lane,et al.  Adipogenesis: from stem cell to adipocyte. , 2012, Annual review of biochemistry.

[91]  S. Raghav,et al.  Genome-wide profiling of DNA-binding proteins using barcode-based multiplex Solexa sequencing. , 2012, Methods in molecular biology.

[92]  S. Mandrup,et al.  Transcriptional networks controlling adipocyte differentiation. , 2011, Cold Spring Harbor symposia on quantitative biology.

[93]  Michael Q. Zhang,et al.  Interferon regulatory factors are transcriptional regulators of adipogenesis. , 2008, Cell metabolism.

[94]  D. Trono,et al.  Production and Titration of Lentiviral , 2007 .

[95]  S. Akira,et al.  Krüppel-like transcription factor KLF5 is a key regulator of adipocyte differentiation. , 2005, Cell metabolism.

[96]  B. Spiegelman,et al.  Molecular regulation of adipogenesis. , 2000, Annual review of cell and developmental biology.

[97]  B. Spiegelman,et al.  Cross-regulation of C/EBP alpha and PPAR gamma controls the transcriptional pathway of adipogenesis and insulin sensitivity. , 1999, Molecular cell.

[98]  B. Spiegelman,et al.  ADD1/SREBP1 activates PPARgamma through the production of endogenous ligand. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[99]  M. Lindberg,et al.  Adipose Tissue , 2018 .