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Moyroud E, Minguet EG, Ott F, Yant L, Posé D, Monniaux M, Blanchet S, Bastien O, Thévenon E, Weigel D, Schmid M, Parcy F. Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. THE PLANT CELL 2011; 23:1293-306. [PMID: 21515819 PMCID: PMC3101549 DOI: 10.1105/tpc.111.083329] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/22/2011] [Accepted: 04/01/2011] [Indexed: 05/18/2023]
Abstract
Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Applying the model to other plant species, we could follow the evolution of the regulatory relationship between LFY and the AGAMOUS (AG) subfamily of MADS box genes and show that this link predates the divergence between monocots and eudicots. Remarkably, our model succeeds in detecting the connection between LFY and AG homologs despite extensive variation in binding sites. This demonstrates that the cis-element fluidity recently observed in animals also exists in plants, but the challenges it poses can be overcome with predictions grounded in a biophysical model. Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences.
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Affiliation(s)
- Edwige Moyroud
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Eugenio Gómez Minguet
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Felix Ott
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - Levi Yant
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - David Posé
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - Marie Monniaux
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Sandrine Blanchet
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Olivier Bastien
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Emmanuel Thévenon
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - Markus Schmid
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - François Parcy
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
- Address correspondence to
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409
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Lee EK, Lee MJ, Abdelmohsen K, Kim W, Kim MM, Srikantan S, Martindale JL, Hutchison ER, Kim HH, Marasa BS, Selimyan R, Egan JM, Smith SR, Fried SK, Gorospe M. miR-130 suppresses adipogenesis by inhibiting peroxisome proliferator-activated receptor gamma expression. Mol Cell Biol 2011; 31:626-38. [PMID: 21135128 PMCID: PMC3028659 DOI: 10.1128/mcb.00894-10] [Citation(s) in RCA: 282] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/01/2010] [Accepted: 11/18/2010] [Indexed: 01/04/2023] Open
Abstract
Adipose tissue development is tightly regulated by altering gene expression. MicroRNAs are strong posttranscriptional regulators of mammalian differentiation. We hypothesized that microRNAs might influence human adipogenesis by targeting specific adipogenic factors. We identified microRNAs that showed varying abundance during the differentiation of human preadipocytes into adipocytes. Among them, miR-130 strongly affected adipocyte differentiation, as overexpressing miR-130 impaired adipogenesis and reducing miR-130 enhanced adipogenesis. A key effector of miR-130 actions was the protein peroxisome proliferator-activated receptor γ (PPARγ), a major regulator of adipogenesis. Interestingly, miR-130 potently repressed PPARγ expression by targeting both the PPARγ mRNA coding and 3' untranslated regions. Adipose tissue from obese women contained significantly lower miR-130 and higher PPARγ mRNA levels than that from nonobese women. Our findings reveal that miR-130 reduces adipogenesis by repressing PPARγ biosynthesis and suggest that perturbations in this regulation is linked to human obesity.
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Affiliation(s)
- Eun Kyung Lee
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Mi Jeong Lee
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Kotb Abdelmohsen
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Wook Kim
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Mihee M. Kim
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Subramanya Srikantan
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Jennifer L. Martindale
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Emmette R. Hutchison
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Hyeon Ho Kim
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Bernard S. Marasa
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Roza Selimyan
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Josephine M. Egan
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Steven R. Smith
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Susan K. Fried
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
| | - Myriam Gorospe
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, Laboratory of Clinical Investigation, NIA-IRP, NIH, Baltimore, Maryland 21224, Laboratory of Neurosciences, NIA-IRP, NIH, Baltimore, Maryland 21224, Translational Research Institute, Florida Hospital-Burnham Institute, Winter Park, Florida 32789
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412
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Yu CY, Mayba O, Lee JV, Tran J, Harris C, Speed TP, Wang JC. Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis. PLoS One 2010; 5:e15188. [PMID: 21187916 PMCID: PMC3004788 DOI: 10.1371/journal.pone.0015188] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/28/2010] [Indexed: 01/19/2023] Open
Abstract
Glucocorticoids play important roles in the regulation of distinct aspects of adipocyte biology. Excess glucocorticoids in adipocytes are associated with metabolic disorders, including central obesity, insulin resistance and dyslipidemia. To understand the mechanisms underlying the glucocorticoid action in adipocytes, we used chromatin immunoprecipitation sequencing to isolate genome-wide glucocorticoid receptor (GR) binding regions (GBRs) in 3T3-L1 adipocytes. Furthermore, gene expression analyses were used to identify genes that were regulated by glucocorticoids. Overall, 274 glucocorticoid-regulated genes contain or locate nearby GBR. We found that many GBRs were located in or nearby genes involved in triglyceride (TG) synthesis (Scd-1, 2, 3, GPAT3, GPAT4, Agpat2, Lpin1), lipolysis (Lipe, Mgll), lipid transport (Cd36, Lrp-1, Vldlr, Slc27a2) and storage (S3-12). Gene expression analysis showed that except for Scd-3, the other 13 genes were induced in mouse inguinal fat upon 4-day glucocorticoid treatment. Reporter gene assays showed that except Agpat2, the other 12 glucocorticoid-regulated genes contain at least one GBR that can mediate hormone response. In agreement with the fact that glucocorticoids activated genes in both TG biosynthetic and lipolytic pathways, we confirmed that 4-day glucocorticoid treatment increased TG synthesis and lipolysis concomitantly in inguinal fat. Notably, we found that 9 of these 12 genes were induced in transgenic mice that have constant elevated plasma glucocorticoid levels. These results suggested that a similar mechanism was used to regulate TG homeostasis during chronic glucocorticoid treatment. In summary, our studies have identified molecular components in a glucocorticoid-controlled gene network involved in the regulation of TG homeostasis in adipocytes. Understanding the regulation of this gene network should provide important insight for future therapeutic developments for metabolic diseases.
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Affiliation(s)
- Chi-Yi Yu
- Department of Nutritional Science & Toxicology, University of California, Berkeley, California, United States of America
| | - Oleg Mayba
- Department of Statistics, University of California, Berkeley, California, United States of America
| | - Joyce V. Lee
- Department of Nutritional Science & Toxicology, University of California, Berkeley, California, United States of America
| | - Joanna Tran
- Department of Nutritional Science & Toxicology, University of California, Berkeley, California, United States of America
| | - Charlie Harris
- Department of Medicine, Gladstone Institute of Cardiovascular Disease, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Terence P. Speed
- Department of Statistics, University of California, Berkeley, California, United States of America
| | - Jen-Chywan Wang
- Department of Nutritional Science & Toxicology, University of California, Berkeley, California, United States of America
- Department of Medicine, Gladstone Institute of Cardiovascular Disease, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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