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Betzler AC, Brunner C. The Role of the Transcriptional Coactivator BOB.1/OBF.1 in Adaptive Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:53-77. [PMID: 39017839 DOI: 10.1007/978-3-031-62731-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
BOB.1/OBF.1 is a transcriptional coactivator involved in octamer-dependent transcription. Thereby, BOB.1/OBF.1 is involved in the transcriptional regulation of genes important for lymphocyte physiology. BOB.1/OBF.1-deficient mice reveal multiple B- and T-cell developmental defects. The most prominent defect of these mice is the complete absence of germinal centers (GCs) resulting in severely impaired T-cell-dependent immune responses. In humans, BOB.1/OBF.1 is associated with several autoimmune and inflammatory diseases but also linked to liquid and solid tumors. Although its role for B-cell development is relatively well understood, its exact role for the GC reaction and T-cell biology has long been unclear. Here, the contribution of BOB.1/OBF.1 for B-cell maturation is summarized, and recent findings regarding its function in GC B- as well as in various T-cell populations are discussed. Finally, a detailed perspective on how BOB.1/OBF.1 contributes to different pathologies is provided.
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Affiliation(s)
- Annika C Betzler
- Department of Oto-Rhino-Larnygology, Ulm University Medical Center, Ulm, Germany
- Core Facility Immune Monitoring, Ulm University, Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Larnygology, Ulm University Medical Center, Ulm, Germany.
- Core Facility Immune Monitoring, Ulm University, Ulm, Germany.
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2
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Kind L, Raasakka A, Molnes J, Aukrust I, Bjørkhaug L, Njølstad PR, Kursula P, Arnesen T. Structural and biophysical characterization of transcription factor HNF-1A as a tool to study MODY3 diabetes variants. J Biol Chem 2022; 298:101803. [PMID: 35257744 PMCID: PMC8988010 DOI: 10.1016/j.jbc.2022.101803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 11/05/2022] Open
Abstract
Hepatocyte nuclear factor 1A (HNF-1A) is a transcription factor expressed in several embryonic and adult tissues, modulating the expression of numerous target genes. Pathogenic variants in the HNF1A gene are known to cause maturity-onset diabetes of the young 3 (MODY3 or HNF1A MODY), a disease characterized by dominant inheritance, age of onset before 25 to 35 years of age, and pancreatic β-cell dysfunction. A precise diagnosis can alter management of this disease, as insulin can be exchanged with sulfonylurea tablets and genetic counseling differs from polygenic forms of diabetes. Therefore, more knowledge on the mechanisms of HNF-1A function and the level of pathogenicity of the numerous HNF1A variants is required for precise diagnostics. Here, we structurally and biophysically characterized an HNF-1A protein containing both the DNA-binding domain and the dimerization domain, and determined the folding and DNA-binding capacity of two established MODY3 HNF-1A variant proteins (P112L, R263C) and one variant of unknown significance (N266S). All three variants showed reduced functionality compared to the WT protein. Furthermore, while the R263C and N266S variants displayed reduced binding to an HNF-1A target promoter, we found the P112L variant was unstable in vitro and in cells. Our results support and mechanistically explain disease causality for these investigated variants and present a novel approach for the dissection of structurally unstable and DNA-binding defective variants. This study indicates that structural and biochemical investigation of HNF-1A is a valuable tool in reliable variant classification needed for precision diabetes diagnostics and management.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Janne Molnes
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Lise Bjørkhaug
- Department of Safety, Chemistry, and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Pål Rasmus Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway; Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Biological Sciences, University of Bergen, Bergen, Norway; Department of Surgery, Haukeland University Hospital, Bergen, Norway.
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3
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Yeremenko N, Danger R, Baeten D, Tomilin A, Brouard S. Transcriptional regulator BOB.1: Molecular mechanisms and emerging role in chronic inflammation and autoimmunity. Autoimmun Rev 2021; 20:102833. [PMID: 33864944 DOI: 10.1016/j.autrev.2021.102833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 11/19/2022]
Abstract
Lymphocytes constitute an essential and potent effector compartment of the immune system. Therefore, their development and functions must be strictly regulated to avoid inappropriate immune responses, such as autoimmune reactions. Several lines of evidence from genetics (e.g. association with multiple sclerosis and primary biliary cirrhosis), human expression studies (e.g. increased expression in target tissues and draining lymph nodes of patients with autoimmune diseases), animal models (e.g. loss of functional protein protects animals from the development of collagen-induced arthritis, experimental autoimmune encephalomyelitis, type 1 diabetes, bleomycin-induced fibrosis) strongly support a causal link between the aberrant expression of the lymphocyte-restricted transcriptional regulator BOB.1 and the development of autoimmune diseases. In this review, we summarize the current knowledge of unusual structural and functional plasticity of BOB.1, stringent regulation of its expression, and the pivotal role that BOB.1 plays in shaping B- and T-cell responses. We discuss recent developments highlighting the significant contribution of BOB.1 to the pathogenesis of autoimmune diseases and how to leverage our knowledge to target this regulator to treat autoimmune tissue inflammation.
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Affiliation(s)
- Nataliya Yeremenko
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France; Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology and Rheumatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.
| | - Richard Danger
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Dominique Baeten
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology and Rheumatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Alexey Tomilin
- Institute of Cytology, Russian Academy of Sciences, St-Petersburg, Russian Federation
| | - Sophie Brouard
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
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Snijders Blok L, Kleefstra T, Venselaar H, Maas S, Kroes HY, Lachmeijer AMA, van Gassen KLI, Firth HV, Tomkins S, Bodek S, Õunap K, Wojcik MH, Cunniff C, Bergstrom K, Powis Z, Tang S, Shinde DN, Au C, Iglesias AD, Izumi K, Leonard J, Abou Tayoun A, Baker SW, Tartaglia M, Niceta M, Dentici ML, Okamoto N, Miyake N, Matsumoto N, Vitobello A, Faivre L, Philippe C, Gilissen C, Wiel L, Pfundt R, Deriziotis P, Brunner HG, Fisher SE. De Novo Variants Disturbing the Transactivation Capacity of POU3F3 Cause a Characteristic Neurodevelopmental Disorder. Am J Hum Genet 2019; 105:403-412. [PMID: 31303265 PMCID: PMC6698880 DOI: 10.1016/j.ajhg.2019.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/07/2019] [Indexed: 01/22/2023] Open
Abstract
POU3F3, also referred to as Brain-1, is a well-known transcription factor involved in the development of the central nervous system, but it has not previously been associated with a neurodevelopmental disorder. Here, we report the identification of 19 individuals with heterozygous POU3F3 disruptions, most of which are de novo variants. All individuals had developmental delays and/or intellectual disability and impairments in speech and language skills. Thirteen individuals had characteristic low-set, prominent, and/or cupped ears. Brain abnormalities were observed in seven of eleven MRI reports. POU3F3 is an intronless gene, insensitive to nonsense-mediated decay, and 13 individuals carried protein-truncating variants. All truncating variants that we tested in cellular models led to aberrant subcellular localization of the encoded protein. Luciferase assays demonstrated negative effects of these alleles on transcriptional activation of a reporter with a FOXP2-derived binding motif. In addition to the loss-of-function variants, five individuals had missense variants that clustered at specific positions within the functional domains, and one small in-frame deletion was identified. Two missense variants showed reduced transactivation capacity in our assays, whereas one variant displayed gain-of-function effects, suggesting a distinct pathophysiological mechanism. In bioluminescence resonance energy transfer (BRET) interaction assays, all the truncated POU3F3 versions that we tested had significantly impaired dimerization capacities, whereas all missense variants showed unaffected dimerization with wild-type POU3F3. Taken together, our identification and functional cell-based analyses of pathogenic variants in POU3F3, coupled with a clinical characterization, implicate disruptions of this gene in a characteristic neurodevelopmental disorder.
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Affiliation(s)
- Lot Snijders Blok
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, PO Box 310, 6500AH Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, PO Box 9104, 6500HE Nijmegen, the Netherlands.
| | - Tjitske Kleefstra
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, PO Box 9104, 6500HE Nijmegen, the Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands
| | - Saskia Maas
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Meibergdreef 9, 1105AZ Amsterdam, the Netherlands
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, PO Box 85090, 3508AB Utrecht, the Netherlands
| | - Augusta M A Lachmeijer
- Department of Genetics, University Medical Center Utrecht, PO Box 85090, 3508AB Utrecht, the Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, PO Box 85090, 3508AB Utrecht, the Netherlands
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Susan Tomkins
- Clinical Genetics Service, University Hospitals Bristol National Health Service Foundation Trust, Bristol BS2 8HW, UK
| | - Simon Bodek
- Clinical Genetics Service, University Hospitals Bristol National Health Service Foundation Trust, Bristol BS2 8HW, UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu 51014, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu 51014, Estonia
| | - Monica H Wojcik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Newborn Medicine, Division of Genetics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher Cunniff
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zoë Powis
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sha Tang
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | | | - Catherine Au
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY 10032, USA
| | - Alejandro D Iglesias
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY 10032, USA
| | - Kosuke Izumi
- Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jacqueline Leonard
- Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ahmad Abou Tayoun
- Division of Genomic Diagnostics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Samuel W Baker
- Division of Genomic Diagnostics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00146 Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00146 Rome, Italy
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00146 Rome, Italy
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Antonio Vitobello
- UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire Dijon Bourgogne, 21000 Dijon, France; INSERM UMR1231 Génétique des Anomalies du Développement, F-21000 Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 Génétique des Anomalies du Développement, F-21000 Dijon, France; Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Centre de Génétique, Hôpital d'Enfants, Fédération Hospitalo-Universitaire Médecine TRANSLationnelle et Anomalies du Développement, Centre Hospitalier Universitaire Dijon Bourgogne, 21000 Dijon, France
| | - Christophe Philippe
- UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire Dijon Bourgogne, 21000 Dijon, France; INSERM UMR1231 Génétique des Anomalies du Développement, F-21000 Dijon, France
| | - Christian Gilissen
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands
| | - Laurens Wiel
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands
| | - Rolph Pfundt
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands
| | - Pelagia Deriziotis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, PO Box 310, 6500AH Nijmegen, the Netherlands
| | - Han G Brunner
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, PO Box 9104, 6500HE Nijmegen, the Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6202AZ Maastricht, the Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, PO Box 310, 6500AH Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, PO Box 9104, 6500HE Nijmegen, the Netherlands.
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5
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Agarwal S, Cho TY. Biochemical and structural characterization of a novel cooperative binding mode by Pit-1 with CATT repeats in the macrophage migration inhibitory factor promoter. Nucleic Acids Res 2019; 46:929-941. [PMID: 29186613 PMCID: PMC5778499 DOI: 10.1093/nar/gkx1183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/14/2017] [Indexed: 12/25/2022] Open
Abstract
Overexpression of the proinflammatory cytokine macrophage migration inhibitory factor (MIF) is linked to a number of autoimmune diseases and cancer. MIF production has been correlated to the number of CATT repeats in a microsatellite region upstream of the MIF gene. We have characterized the interaction of pituitary-specific positive transcription factor 1 (Pit-1) with a portion of the MIF promoter region flanking a microsatellite polymorphism (-794 CATT5-8). Using fluorescence anisotropy, we quantified tight complex formation between Pit-1 and an oligonucleotide consisting of eight consecutive CATT repeats (8xCATT) with an apparent Kd of 35 nM. Using competition experiments we found a 23 base pair oligonucleotide with 4xCATT repeats to be the minimum DNA sequence necessary for high affinity interaction with Pit-1. The stoichiometry of the Pit-1 DNA interaction was determined to be 2:1 and binding is cooperative in nature. We subsequently structurally characterized the complex and discovered a completely novel binding mode for Pit-1 in contrast to previously described Pit-1 complex structures. The affinity of Pit-1 for the CATT target sequence was found to be highly dependent on cooperativity. This work lays the groundwork for understanding transcriptional regulation of MIF and pursuing Pit-1 as a therapeutic target to treat MIF-mediated inflammatory disorders.
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Affiliation(s)
- Sorabh Agarwal
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Thomas Yoonsang Cho
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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6
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Malik V, Zimmer D, Jauch R. Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming. Cell Mol Life Sci 2018; 75:1587-1612. [PMID: 29335749 PMCID: PMC11105716 DOI: 10.1007/s00018-018-2748-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Abstract
The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. The fundamental importance of POU TFs to orchestrate embryonic development and to direct cellular fate decisions is well established, but the molecular basis for this activity is insufficiently understood. POU TFs possess a bipartite 'two-in-one' DNA binding domain consisting of two independently folding structural units connected by a poorly conserved and flexible linker. Therefore, they represent a paradigmatic example to study the molecular basis for the functional versatility of TFs. Their modular architecture endows POU TFs with the capacity to accommodate alternative composite DNA sequences by adopting different quaternary structures. Moreover, associations with partner proteins crucially influence the selection of their DNA binding sites. The plentitude of DNA binding modes confers the ability to POU TFs to regulate distinct genes in the context of different cellular environments. Likewise, different binding modes of POU proteins to DNA could trigger alternative regulatory responses in the context of different genomic locations of the same cell. Prominent POU TFs such as Oct4, Brn2, Oct6 and Brn4 are not only essential regulators of development but have also been successfully employed to reprogram somatic cells to pluripotency and neural lineages. Here we review biochemical, structural, genomic and cellular reprogramming studies to examine how the ability of POU TFs to select regulatory DNA, alone or with partner factors, is tied to their capacity to epigenetically remodel chromatin and drive specific regulatory programs that give cells their identities.
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Affiliation(s)
- Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Dennis Zimmer
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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Chin SO, Hwang JK, Rhee SY, Chon S, Oh S, Lee M, Pellegata NS, Kim SW. Acromegaly due to a Macroinvasive Plurihormonal Pituitary Adenoma and a Rectal Carcinoid Tumor. Endocrinol Metab (Seoul) 2015; 30:389-94. [PMID: 25559714 PMCID: PMC4595365 DOI: 10.3803/enm.2015.30.3.389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/24/2014] [Accepted: 11/06/2014] [Indexed: 11/28/2022] Open
Abstract
A macroinvasive pituitary adenoma with plurihormonality usually causes acromegaly and hyperprolactinemia, and also accompanies with neurologic symptoms such as visual disturbances. However, its concurrent presentation with a rectal carcinoid tumor is rarely observed. This study reports the history, biochemical, colonoscopic and immunohistochemical results of a 48-year-old female with acromegaly and hyperprolactinemia. Despite the large size and invasive nature of the pituitary adenoma to adjacent anatomical structures, she did not complain of any neurologic symptoms such as visual disturbance or headache. Immunohistochemical staining of the surgical specimen from the pituitary adenoma revealed that the tumor cells were positive for growth hormone (GH), prolactin (PRL), and thyroid stimulating hormone (TSH). Staining for pituitary-specific transcription factor-1 (Pit-1) was shown to be strongly positive, which could have been possibly contributing to the plurihormonality of this adenoma. Colonoscopy found a rectal polyp that was identified to be a carcinoid tumor using immunohistochemical staining. A macroinvasive pituitary adenoma with concomitant rectal carcinoid tumor was secreting GH, PRL, and TSH, which were believed to be in association with over-expression of Pit-1. This is the first case report of double primary tumors comprising a plurihormonal pituitary macroadenoma and rectal carcinoid tumor.
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Affiliation(s)
- Sang Ouk Chin
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Jin Kyung Hwang
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Sang Youl Rhee
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Suk Chon
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Seungjoon Oh
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Misu Lee
- Institute of Pathology, Helmholtz Zentrum Munchen, Neuherberg, Germany
| | | | - Sung Woon Kim
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea.
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8
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Bentrari F, Chantôme A, Knights A, Jeannin JF, Pance A. Oct-2 forms a complex with Oct-1 on the iNOS promoter and represses transcription by interfering with recruitment of RNA PolII by Oct-1. Nucleic Acids Res 2015; 43:9757-65. [PMID: 26271992 PMCID: PMC4787767 DOI: 10.1093/nar/gkv829] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 08/04/2015] [Indexed: 01/09/2023] Open
Abstract
Oct-1 (POU2f1) and Oct-2 (POU2f2) are members of the POU family of transcription factors. They recognize the same DNA sequence but fulfil distinct functions: Oct-1 is ubiquitous and regulates a variety of genes while Oct-2 is restricted to B-cells and neurones. Here we examine the interplay and regulatory mechanisms of these factors to control the inducible nitric oxide synthase (iNOS, NOS2). Using two breast cancer cell lines as a comparative model, we found that MCF-7 express iNOS upon cytokine stimulation while MDA-MB-231 do not. Oct-1 is present in both cell lines but MDA-MB-231also express high levels of Oct-2. Manipulation of Oct-2 expression in these cell lines demonstrates that it is directly responsible for the repression of iNOS in MDA-MB-231. In MCF-7 cells Oct-1 binds the iNOS promoter, recruits RNA PolII and triggers initiation of transcription. In MDA-MB-231 cells, both Oct-1 and Oct-2 bind the iNOS promoter, forming a higher-order complex which fails to recruit RNA PolII, and as a consequence iNOS transcription does not proceed. Unravelling the mechanisms of transcription factor activity is paramount to the understanding of gene expression patterns that determine cell behaviour.
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Affiliation(s)
- Fatima Bentrari
- EPHE Laboratory, Faculty of Medicine, University of Bourgogne, 7 Boulevard Jeanne D'Arc, 21033 Dijon, France
| | - Aurelie Chantôme
- EPHE Laboratory, Faculty of Medicine, University of Bourgogne, 7 Boulevard Jeanne D'Arc, 21033 Dijon, France
| | - Andrew Knights
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jean-François Jeannin
- EPHE Laboratory, Faculty of Medicine, University of Bourgogne, 7 Boulevard Jeanne D'Arc, 21033 Dijon, France
| | - Alena Pance
- EPHE Laboratory, Faculty of Medicine, University of Bourgogne, 7 Boulevard Jeanne D'Arc, 21033 Dijon, France The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Towers ER, Kelly JJ, Sud R, Gale JE, Dawson SJ. Caprin-1 is a target of the deafness gene Pou4f3 and is recruited to stress granules in cochlear hair cells in response to ototoxic damage. J Cell Sci 2011; 124:1145-55. [PMID: 21402877 DOI: 10.1242/jcs.076141] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The POU4 family of transcription factors are required for survival of specific cell types in different sensory systems. Pou4f3 is essential for the survival of auditory sensory hair cells and several mutations in human POU4F3 cause hearing loss. Thus, genes regulated by Pou4f3 are likely to be essential for hair cell survival. We performed a subtractive hybridisation screen in an inner-ear-derived cell line to find genes with differential expression in response to changes in Pou4f3 levels. The screen identified the stress-granule-associated protein Caprin-1 as being downregulated by Pou4f3. We demonstrated that this regulation occurs through the direct interaction of Pou4f3 with binding sites in the Caprin-1 5' flanking sequence, and describe the expression pattern of Caprin-1 mRNA and protein in the cochlea. Moreover, we found Caprin-1-containing stress granules are induced in cochlear hair cells following aminoglycoside-induced damage. This is the first report of stress granule formation in mammalian hair cells and suggests that the formation of Caprin-1-containing stress granules is a key damage response to a clinically relevant ototoxic agent. Our results have implications for the understanding of aminoglycoside-induced hearing loss and provide further evidence that stress granule formation is a fundamental cellular stress response.
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Affiliation(s)
- Emily R Towers
- UCL Ear Institute, 332 Gray's Inn Road, London WC1X 8EE, UK
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Boissonnet A, Dupouy C, Millard P, Durrieu MP, Tarrat N, Escudier JM. α,β-D-CNA featuring canonical and noncanonical α/β torsional angles behaviours within oligonucleotides. NEW J CHEM 2011. [DOI: 10.1039/c1nj20086k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
The last decade has seen an incredible breakthrough in technologies that allow histones, transcription factors (TFs), and RNA polymerases to be precisely mapped throughout the genome. From this research, it is clear that there is a complex interaction between the chromatin landscape and the general transcriptional machinery and that the dynamic control of this interface is central to gene regulation. However, the chromatin remodeling enzymes and general TFs cannot, on their own, recognize and stably bind to promoter or enhancer regions. Rather, they are recruited to cis regulatory regions through interaction with site-specific DNA binding TFs and/or proteins that recognize epigenetic marks such as methylated cytosines or specifically modified amino acids in histones. These "recruitment" factors are modular in structure, reflecting their ability to interact with the genome via one region of the protein and to simultaneously bind to other regulatory proteins via "effector" domains. In this chapter, we provide examples of common effector domains that can function in transcriptional regulation via their ability to (a) interact with the basal transcriptional machinery and general co-activators, (b) interact with other TFs to allow cooperative binding, and (c) directly or indirectly recruit histone and chromatin modifying enzymes.
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Affiliation(s)
- Seth Frietze
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA,
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12
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Jauch R, Choo SH, Ng CKL, Kolatkar PR. Crystal structure of the dimeric Oct6 (POU3f1) POU domain bound to palindromic MORE DNA. Proteins 2010; 79:674-7. [DOI: 10.1002/prot.22916] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Hofmann E, Reichart U, Gausterer C, Guelly C, Meijer D, Müller M, Strobl B. Octamer-binding factor 6 (Oct-6/Pou3f1) is induced by interferon and contributes to dsRNA-mediated transcriptional responses. BMC Cell Biol 2010; 11:61. [PMID: 20687925 PMCID: PMC2924845 DOI: 10.1186/1471-2121-11-61] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 08/05/2010] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Octamer-binding factor 6 (Oct-6, Pou3f1, SCIP, Tst-1) is a transcription factor of the Pit-Oct-Unc (POU) family. POU proteins regulate key developmental processes and have been identified from a diverse range of species. Oct-6 expression is described to be confined to the developing brain, Schwann cells, oligodendrocyte precursors, testes, and skin. Its function is primarily characterised in Schwann cells, where it is required for correctly timed transition to the myelinating state. In the present study, we report that Oct-6 is an interferon (IFN)-inducible protein and show for the first time expression in murine fibroblasts and macrophages. RESULTS Oct-6 was induced by type I and type II IFN, but not by interleukin-6. Induction of Oct-6 after IFNbeta treatment was mainly dependent on signal transducer and activator of transcription 1 (Stat1) and partially on tyrosine kinase 2 (Tyk2). Chromatin immunopreciptitation experiments revealed binding of Stat1 to the Oct-6 promoter in a region around 500 bp upstream of the transcription start site, a region different from the downstream regulatory element involved in Schwann cell-specific Oct-6 expression. Oct-6 was also induced by dsRNA treatment and during viral infections, in both cases via autocrine/paracrine actions of IFNalpha/beta. Using microarray and RT-qPCR, we furthermore show that Oct-6 is involved in the regulation of transcriptional responses to dsRNA, in particular in the gene regulation of serine/threonine protein kinase 40 (Stk40) and U7 snRNA-associated Sm-like protein Lsm10 (Lsm10). CONCLUSION Our data show that Oct-6 expression is not as restricted as previously assumed. Induction of Oct-6 by IFNs and viruses in at least two different cell types, and involvement of Oct-6 in gene regulation after dsRNA treatment, suggest novel functions of Oct-6 in innate immune responses.
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Affiliation(s)
- Elisabeth Hofmann
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
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14
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Jariwala U, Cogan JP, Jia L, Frenkel B, Coetzee GA. Inhibition of AR-mediated transcription by binding of Oct1 to a motif enriched in AR-occupied regions. Prostate 2009; 69:392-400. [PMID: 19058140 PMCID: PMC2743387 DOI: 10.1002/pros.20893] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The androgen receptor (AR) plays roles in prostate development and cancer (PCa). In response to androgens, the AR binds to androgen-response elements (AREs) to modulate gene transcription. The responses of such genes are dependent on the cellular milieu and on sequences around the AREs, which attract other transcription factors. Previously, bioinformatic analysis of 62 AR-occupied regions (ARORs) in PCa cells revealed enrichment for both AREs and a TTGGCAAATA-like motif. We undertook the present study to investigate the significance of the TTGGCAAATA-like motif. METHODS Prostate cancer cell lines, LNCaP and C4-2B, were analyzed by transient transfections of wild-type and mutant reporter constructs, electro-mobility shift assays (EMSAs), and RT-qPCR analysis of endogenous genes. RESULTS In two of six tested ARORs, point mutations in the TTGGCAAATA-like motif resulted in inhibition of DHT-mediated enhancer activity. EMSA revealed that Oct1 bound the motif, and that the mutations that abolished DHT responsiveness in the transfection assays augmented Oct1 binding. These results suggest a role for Oct1 as a context-dependent negative coregulator of AR. Consistent with this, siRNA knockdown of Oct1 increased the DHT-mediated enhancer activity of transfected reporters as well as an endogenous AR target gene, transglutaminase 2. CONCLUSIONS Oct1 negatively regulates DHT-mediated enhancer activity in a subset of ARORs. The enrichment of ARORs for the Oct-binding, TTGGCAAATA-like motif may reflect a mechanism that utilizes Oct1 to keep AR activity in check at some ARORs, while augmenting AR activity in other ARORs. Therefore, Oct1 may have regulatory functions in prostate development and cancer progression.
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Affiliation(s)
- Unnati Jariwala
- Department of Biochemistry & Molecular Biology, USC Keck School of Medicine, Los Angeles, CA
- Institute for Genetic Medicine, USC Keck School of Medicine, Los Angeles, CA
| | - Jon P. Cogan
- Department of Biochemistry & Molecular Biology, USC Keck School of Medicine, Los Angeles, CA
- Institute for Genetic Medicine, USC Keck School of Medicine, Los Angeles, CA
| | - Li Jia
- Department of Urology, USC Keck School of Medicine, Los Angeles, CA
- Norris Cancer Center, USC Keck School of Medicine, Los Angeles, CA
| | - Baruch Frenkel
- Department of Biochemistry & Molecular Biology, USC Keck School of Medicine, Los Angeles, CA
- Department of Orthopaedic Surgery, USC Keck School of Medicine, Los Angeles, CA
- Institute for Genetic Medicine, USC Keck School of Medicine, Los Angeles, CA
| | - Gerhard A. Coetzee
- Department of Urology, USC Keck School of Medicine, Los Angeles, CA
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA
- Norris Cancer Center, USC Keck School of Medicine, Los Angeles, CA
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15
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Malhas AN, Lee CF, Vaux DJ. Lamin B1 controls oxidative stress responses via Oct-1. J Cell Biol 2009; 184:45-55. [PMID: 19139261 PMCID: PMC2615091 DOI: 10.1083/jcb.200804155] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 12/11/2008] [Indexed: 12/14/2022] Open
Abstract
Interaction of lamins with chromatin and transcription factors regulate transcription. Oct-1 has previously been shown to colocalize partly with B-type lamins and is essential for transcriptional regulation of oxidative stress response genes. Using sequential extraction, co-immunoprecipitation (IP), fluorescence loss in photobleaching, and fluorescence resonance energy transfer, we confirm Oct-1-lamin B1 association at the nuclear periphery and show that this association is lost in Lmnb1(Delta/Delta) cells. We show that several Oct-1-dependent genes, including a subset involved in oxidative stress response, are dysregulated in Lmnb1(Delta/Delta) cells. Electrophoretic mobility shift assay and chromatin IP reveal that Oct-1 binds to the putative octamer-binding sequences of the dysregulated genes and that this activity is increased in cells lacking functional lamin B1. Like Oct1(-/-) cells, Lmnb1(Delta/Delta) cells have elevated levels of reactive oxygen species and are more susceptible to oxidative stress. Sequestration of Oct-1 at the nuclear periphery by lamin B1 may be a mechanism by which the nuclear envelope can regulate gene expression and contribute to the cellular response to stress, development, and aging.
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Affiliation(s)
- Ashraf N Malhas
- Department of Physics, Sir William Dunn School of Pathology, University of Oxford, Oxford, England, UK
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Lu P, Rha GB, Chi YI. Structural basis of disease-causing mutations in hepatocyte nuclear factor 1beta. Biochemistry 2007; 46:12071-80. [PMID: 17924661 PMCID: PMC2367142 DOI: 10.1021/bi7010527] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
HNF1beta is an atypical POU transcription factor that participates in a hierarchical network of transcription factors controlling the development and proper function of vital organs such as liver, pancreas, and kidney. Many inheritable mutations on HNF1beta are the monogenic causes of diabetes and several kidney diseases. To elucidate the molecular mechanism of its function and the structural basis of mutations, we have determined the crystal structure of human HNF1beta DNA binding domain in complex with a high-affinity promoter. Disease-causing mutations have been mapped to our structure, and their predicted effects have been tested by a set of biochemical/ functional studies. These findings together with earlier findings with a homologous protein HNF1alpha, help us to understand the structural basis of promoter recognition by these atypical POU transcription factors and the site-specific functional disruption by disease-causing mutations.
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Affiliation(s)
- Peng Lu
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
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17
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Abstract
Flavin-containing monooxygenases (FMOs) are important oxidative drug metabolizing enzymes. FMO3 is the primary human adult liver FMO enzyme, but is developmentally regulated. FMO3 promoter characterization using in vitro DNA binding assays with HepG2 cell and fetal and adult liver nuclear protein, as well as FMO3/reporter construct transient expression in HepG2 cells, provided evidence for specific mechanisms contributing to both developmental and constitutive adult regulation. NFY, USF1, an unidentified GC box binding protein, and YY1 appear to play major roles regulating constitutive FMO3 transcription, while Pbx(2) as a heterodimer with an unidentified Hox isoform also may contribute to FMO3 developmental expression.
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Affiliation(s)
- David E Klick
- Department of Pediatrics, and The Children's Research Institute, Medical College of Wisconsin, and Children's Hospital and Health System, Milwaukee, Wisconsin 53226, USA
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18
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Abnizova I, Subhankulova T, Gilks WR. Recent computational approaches to understand gene regulation: mining gene regulation in silico. Curr Genomics 2007; 8:79-91. [PMID: 18660846 PMCID: PMC2435357 DOI: 10.2174/138920207780368150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 12/13/2006] [Accepted: 12/15/2006] [Indexed: 01/03/2023] Open
Abstract
This paper reviews recent computational approaches to the understanding of gene regulation in eukaryotes. Cis-regulation of gene expression by the binding of transcription factors is a critical component of cellular physiology. In eukaryotes, a number of transcription factors often work together in a combinatorial fashion to enable cells to respond to a wide spectrum of environmental and developmental signals. Integration of genome sequences and/or Chromatin Immunoprecipitation on chip data with gene-expression data has facilitated in silico discovery of how the combinatorics and positioning of transcription factors binding sites underlie gene activation in a variety of cellular processes.The process of gene regulation is extremely complex and intriguing, therefore all possible points of view and related links should be carefully considered. Here we attempt to collect an inventory, not claiming it to be comprehensive and complete, of related computational biological topics covering gene regulation, which may en-lighten the process, and briefly review what is currently occurring in these areas.We will consider the following computational areas:o gene regulatory network construction;o evolution of regulatory DNA;o studies of its structural and statistical informational properties;o and finally, regulatory RNA.
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Affiliation(s)
| | - T Subhankulova
- Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, Cambridge, UK
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Malone CS, Kuraishy AI, Fike FM, Loya RG, Mikkili MR, Teitell MA, Wall R. B29 gene silencing in pituitary cells is regulated by its 3' enhancer. J Mol Biol 2006; 362:173-83. [PMID: 16920149 PMCID: PMC2104784 DOI: 10.1016/j.jmb.2006.07.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 07/21/2006] [Indexed: 12/26/2022]
Abstract
B cell-specific B29 (Igbeta, CD79b) genes in rat, mouse, and human are situated between the 5' growth hormone (GH) locus control region and the 3' GH gene cluster. The entire GH genomic region is DNase 1 hypersensitive in GH-expressing pituitary cells, which predicts an "open" chromatin configuration, and yet B29 is not expressed. The B29 promoter and enhancers exhibit histone deacetylation in pituitary cells, but histone deacetylase inhibition failed to activate B29 expression. The B29 promoter and a 3' enhancer showed local dense DNA methylation in both pituitary and non-lymphoid cells consistent with gene silencing. However, DNA methyltransferase inhibition did not activate B29 expression either. B29 promoter constructs were minimally activated in transfected pituitary cells. Co-transfection of the B cell-specific octamer transcriptional co-activator Bob1 with the B29 promoter construct resulted in high level promoter activity in pituitary cells comparable to B29 promoter activity in transfected B cells. Unexpectedly, inclusion of the B29 3' enhancer in B29 promoter constructs strongly inhibited B29 transcriptional activity even when pituitary cells were co-transfected with Bob1. Both Oct-1 and Pit-1 bind the B29 3' enhancer in in vitro electrophoretic mobility shift assay and in in vivo chromatin immunoprecipitation analyses. These data indicate that the GH locus-embedded, tissue-specific B29 gene is silenced in GH-expressing pituitary cells by epigenetic mechanisms, the lack of a B cell-specific transcription factor, and likely by the B29 3' enhancer acting as a powerful silencer in a context and tissue-specific manner.
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Affiliation(s)
- Cindy S Malone
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA.
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Malin S, Linderson Y, Almqvist J, Ernberg I, Tallone T, Pettersson S. DNA-dependent conversion of Oct-1 and Oct-2 into transcriptional repressors by Groucho/TLE. Nucleic Acids Res 2005; 33:4618-25. [PMID: 16103132 PMCID: PMC1187819 DOI: 10.1093/nar/gki744] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
POU domain proteins contain a bipartite DNA-binding element that can confer allosteric control of coactivator recruitment. Dimerization of Oct-1 and Oct-2 on palindromic response elements results in the conformational dependent inclusion or exclusion of the transcriptional coactivator OBF-1. In this paper, we demonstrate that Oct-1 and Oct-2 can function as transcriptional repressors by recruiting and physically interacting with members of the Grg/TLE family of corepressors. In accordance with a model of DNA induced cofactor assembly, and analogous to the recruitment of the OBF-1 coactivator, the different Grg/TLE members can discriminate between both Oct-1 and Oct-2, and the monomeric or dimeric nature of the POU/DNA complex.
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Affiliation(s)
| | | | | | | | | | - Sven Pettersson
- To whom correspondence should be addressed. Tel: +46 8 524 86686; Fax: +46 8 331547;
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Makeev VJ, Lifanov AP, Nazina AG, Papatsenko DA. Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res 2004; 31:6016-26. [PMID: 14530449 PMCID: PMC219477 DOI: 10.1093/nar/gkg799] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We explored distance preferences in the arrangement of binding motifs for five transcription factors (Bicoid, Krüppel, Hunchback, Knirps and Caudal) in a large set of Drosophila cis-regulatory modules (CRMs). Analysis of non-overlapping binding motifs revealed the presence of periodic signals specific to particular combinations of binding motifs. The most striking periodic signals (10 bp for Bicoid and 11 bp for Hunchback) suggest preferential positioning of some binding site combinations on the same side of the DNA helix. We also analyzed distance preferences in arrangements of highly correlated overlapping binding motifs, such as Bicoid and Krüppel. Based on the distance analysis, we extracted preferential binding site arrangements and proposed models for potential composite elements (CEs) and antagonistic motif pairs involved in the function of developmental CRMs. Our results suggest that there are distinct hierarchical levels in the organization of transcription regulatory information. We discuss the role of the hierarchy in understanding transcriptional regulation and in detection of transcription regulatory regions in genomes.
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Duval DL, Jean A, Gutierrez-Hartmann A. Ras signaling and transcriptional synergy at a flexible Ets-1/Pit-1 composite DNA element is defined by the assembly of selective activation domains. J Biol Chem 2003; 278:39684-96. [PMID: 12902343 DOI: 10.1074/jbc.m302433200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pit-1 and Ets-1 binding to a composite element synergistically activates and targets Ras-mitogen-activated protein kinase signaling to the rat prolactin promoter. These transcriptional responses appear to depend on three molecular features: organization of the Ets-1/Pit-1 composite element, physical interaction of these two factors via the Pit-1 homeodomain (amino acids 199-291) and the Ets-1 regulatory III domain (amino acids 190-257), and assembly of their transcriptional activation domains (TADs). Here we show that the organization of the Ets-1/Pit-1 composite element tolerates significant flexibility with regard to Ras stimulation and synergy. Specifically, the putative monomeric Pit-1 binding site can be substituted with bona fide binding sites for either a Pit-1 monomer or dimer, and these sites tolerated a separation of 28 bp. Additionally, we show that the physical interaction of Ets-1 and Pit-1 is not required for Ras responsiveness or synergy because block mutations of the Pit-1 interaction surface in Ets-1, which reduced Ets-1/Pit-1 binding in vitro, did not significantly affect Ets-1 stimulation of Ras responsiveness or synergy. We also show differential use of distinct TAD subtypes and Pit-1 TAD subregions to mediate either synergy or Ras responsiveness. Specifically, TADs from Gal4, VP16, or Ets-2 regulatory III domain linked to Ets-1 DNA binding domain constructs restored synergy to these TAD/Ets-1 DNA binding domain fusions. Conversely, deletion of the defined Pit-1 TAD (amino acids 2-80) retained synergy, but not Ras responsiveness. Consequently, we further defined the Pit-1 amino-terminal TAD into region 1 (R1, amino acids 2-45) and region 2 (R2, amino acids 46-80). R1 appears to regulate basal and synergistic responses, whereas the Ras response was mapped to R2. In summary, Ras responsiveness and Pit-1/Ets-1 synergy are mediated through the assembly of distinct TADs at a flexible composite element, indicating that different mechanisms underlie these two transcriptional responses and that the Pit-1 R2 subregion represents a novel, tissue-specific Ras-responsive TAD.
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Affiliation(s)
- Dawn L Duval
- Department of Medicine, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA.
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Reményi A, Lins K, Nissen LJ, Reinbold R, Schöler HR, Wilmanns M. Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes Dev 2003; 17:2048-59. [PMID: 12923055 PMCID: PMC196258 DOI: 10.1101/gad.269303] [Citation(s) in RCA: 283] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Accepted: 06/11/2003] [Indexed: 11/24/2022]
Abstract
Members of the POU and SOX transcription factor families exemplify the partnerships established between various transcriptional regulators during early embryonic development. Although functional cooperativity between key regulator proteins is pivotal for milestone decisions in mammalian development, little is known about the underlying molecular mechanisms. In this study, we focus on two transcription factors, Oct4 and Sox2, as their combination on DNA is considered to direct the establishment of the first three lineages in the mammalian embryo. Using experimental high-resolution structure determination, followed by model building and experimental validation, we found that Oct4 and Sox2 were able to dimerize onto DNA in distinct conformational arrangements. We demonstrate that the DNA enhancer region of their target genes is responsible for the correct spatial alignment of glue-like interaction domains on their surface. Interestingly, these surfaces frequently have redundant functions and are instrumental in recruiting various interacting protein partners.
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Affiliation(s)
- Attila Reményi
- Gene Expression Program, EMBL, 69117 Heidelberg, Germany.
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