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Al-Jaberi FAH, Kongsbak-Wismann M, Aguayo-Orozco A, Krogh N, Buus TB, Lopez DV, Rode AKO, Gravesen E, Olgaard K, Brunak S, Woetmann A, Ødum N, Bonefeld CM, Geisler C. Impaired Vitamin D Signaling in T Cells From a Family With Hereditary Vitamin D Resistant Rickets. Front Immunol 2021; 12:684015. [PMID: 34093587 PMCID: PMC8170129 DOI: 10.3389/fimmu.2021.684015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022] Open
Abstract
The active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), mediates its immunomodulatory effects by binding to the vitamin D receptor (VDR). Here, we describe a new point mutation in the DNA-binding domain of the VDR and its consequences for 1,25(OH)2D3 signaling in T cells from heterozygous and homozygous carriers of the mutation. The mutation did not affect the overall structure or the ability of the VDR to bind 1,25(OH)2D3 and the retinoid X receptor. However, the subcellular localization of the VDR was strongly affected and the transcriptional activity was abolished by the mutation. In heterozygous carriers of the mutation, 1,25(OH)2D3-induced gene regulation was reduced by ~ 50% indicating that the expression level of wild-type VDR determines 1,25(OH)2D3 responsiveness in T cells. We show that vitamin D-mediated suppression of vitamin A-induced gene regulation depends on an intact ability of the VDR to bind DNA. Furthermore, we demonstrate that vitamin A inhibits 1,25(OH)2D3-induced translocation of the VDR to the nucleus and 1,25(OH)2D3-induced up-regulation of CYP24A1. Taken together, this study unravels novel aspects of vitamin D signaling and function of the VDR in human T cells.
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Affiliation(s)
- Fatima A H Al-Jaberi
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Martin Kongsbak-Wismann
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Alejandro Aguayo-Orozco
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Nicolai Krogh
- RNA and Gene Medicine Program, Department of Cellular and Molecular Medicine, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Terkild B Buus
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Daniel V Lopez
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Anna K O Rode
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Eva Gravesen
- Department of Nephrology, University of Copenhagen, Rigshospitalet and Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Klaus Olgaard
- Department of Nephrology, University of Copenhagen, Rigshospitalet and Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Anders Woetmann
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Niels Ødum
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Charlotte M Bonefeld
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Carsten Geisler
- The LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
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2
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Tsai SY, Catts VS, Fullerton JM, Corley SM, Fillman SG, Weickert CS. Nuclear Receptors and Neuroinflammation in Schizophrenia. MOLECULAR NEUROPSYCHIATRY 2018; 3:181-191. [PMID: 29888229 DOI: 10.1159/000485565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/21/2017] [Indexed: 01/23/2023]
Abstract
Introduction Several nuclear receptor family members have been associated with schizophrenia and inflammation. Vitamins A and D exert anti-inflammatory actions, but their receptors (mainly nuclear receptors) have not been extensively studied in either schizophrenia brains or in association with neuroinflammation. We examined the expression of vitamin A (RARs and RXRs) and vitamin D and protein disulphide-isomerase A3 (PDIA3) receptors, as well as nuclear orphan receptors (NR4As), in the context of elevated cytokine expression in the dorsolateral prefrontal cortex (DLPFC). Methods mRNA levels of nuclear receptors were measured in DLPFC tissues via RT-qPCR. ANCOVAs comparing high inflammation schizophrenia, low inflammation schizophrenia and low inflammation control groups were performed. Results RARG, RXRB, NR4A1 and NR4A3 transcripts showed significant differential expression across the three groups (ANCOVA p = 0.02-0.001). Post hoc testing revealed significant reductions in RARG expression in schizophrenia with low inflammation compared to schizophrenia with high inflammation and to controls, and RXRB mRNA was significantly reduced in schizophrenia with low inflammation compared to controls. NR4A1 and NR4A3 mRNAs were decreased in schizophrenia with high inflammation compared to schizophrenia with low inflammation, with NR4A1 also significantly different to controls. Conclusion In schizophrenia, changes in nuclear receptor mRNA levels involved with mediating actions of vitamin A derivatives vary according to the inflammatory state of brains.
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Affiliation(s)
- Shan-Yuan Tsai
- Schizophrenia Research Institute, Sydney, New South Wales, Australia.,Neuroscience Research Australia, Sydney, New South Wales, Australia.,School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Vibeke S Catts
- Schizophrenia Research Institute, Sydney, New South Wales, Australia.,Neuroscience Research Australia, Sydney, New South Wales, Australia.,School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Janice M Fullerton
- Schizophrenia Research Institute, Sydney, New South Wales, Australia.,Neuroscience Research Australia, Sydney, New South Wales, Australia.,School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Susan M Corley
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Stuart G Fillman
- Schizophrenia Research Institute, Sydney, New South Wales, Australia.,Neuroscience Research Australia, Sydney, New South Wales, Australia.,School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Cynthia Shannon Weickert
- Schizophrenia Research Institute, Sydney, New South Wales, Australia.,Neuroscience Research Australia, Sydney, New South Wales, Australia.,School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
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Gallone G, Haerty W, Disanto G, Ramagopalan SV, Ponting CP, Berlanga-Taylor AJ. Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease. Hum Mol Genet 2017; 26:2164-2176. [PMID: 28335003 PMCID: PMC5886188 DOI: 10.1093/hmg/ddx092] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 02/28/2017] [Accepted: 03/07/2017] [Indexed: 01/24/2023] Open
Abstract
Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies. Nevertheless, few underlying molecular mechanisms of complex disease are currently known. We investigated whether variation in binding of a transcription factor, the vitamin D receptor (VDR), whose activating ligand vitamin D has been proposed as a modifiable factor in multiple disorders, could explain any of these associations. VDR modifies gene expression by binding DNA as a heterodimer with the Retinoid X receptor (RXR). We identified 43,332 genetic variants significantly associated with altered VDR binding affinity (VDR-BVs) using a high-resolution (ChIP-exo) genome-wide analysis of 27 HapMap lymphoblastoid cell lines. VDR-BVs are enriched in consensus RXR::VDR binding motifs, yet most fell outside of these motifs, implying that genetic variation often affects the binding affinity only indirectly. Finally, we compared 341 VDR-BVs replicating by position in multiple individuals against background sets of variants lying within VDR-binding regions that had been matched in allele frequency and were independent with respect to linkage disequilibrium. In this stringent test, these replicated VDR-BVs were significantly (q < 0.1) and substantially (>2-fold) enriched in genomic intervals associated with autoimmune and other diseases, including inflammatory bowel disease, Crohn's disease and rheumatoid arthritis. The approach's validity is underscored by RXR::VDR motif sequence being predictive of binding strength and being evolutionarily constrained. Our findings are consistent with altered RXR::VDR binding contributing to immunity-related diseases. Replicated VDR-BVs associated with these disorders could represent causal disease risk alleles whose effect may be modifiable by vitamin D levels.
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Affiliation(s)
- Giuseppe Gallone
- MRC Functional Genomics Unit
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Wilfried Haerty
- MRC Functional Genomics Unit
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - Giulio Disanto
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | | | - Chris P. Ponting
- MRC Functional Genomics Unit
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Antonio J. Berlanga-Taylor
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK
- CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
- MRC-PHE Centre for Environment and Health, Department of Epidemiology & Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, St Mary’s Campus, Norfolk Place, London W2 1PG, UK
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Liu S, Han SJ, Smith CL. Cooperative activation of gene expression by agonists and antagonists mediated by estrogen receptor heteroligand dimer complexes. Mol Pharmacol 2013; 83:1066-77. [PMID: 23462505 DOI: 10.1124/mol.112.084228] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Estrogen receptor (ER) antagonists are generally thought to inhibit estrogen action through competitive inhibition, resulting in receptor binding to antagonist rather than agonist. However, microarray analyses reveal a group of genes for which ER agonist and antagonist cooperatively regulate expression, suggesting additional models of combined agonist/antagonist action must exist. In conjunction with a chimeric reporter gene and two modified ERs, one [ERα(GSCKV)] with a mutation in the DNA-binding domain and the other (ERα-G521R) with a ligand-binding specificity mutation, we herein demonstrate that ER agonist and antagonist cooperatively activate gene expression through an ER heteroligand dimer complex (ER-HLD) consisting of one subunit of the receptor dimer bound to agonist and another occupied by antagonist. Coimmunoprecipitation experiments confirmed interaction between the agonist-bound and antagonist-bound receptors. This cooperative activation of gene expression was enhanced by steroid receptor coactivator 3 coactivator, and required each ligand-bound subunit of the dimer to bind to DNA, as well as both activation function 1 domains for maximal transcriptional activity. Ligand combinations able to induce ER-HLD transcriptional activity include the agonists 17β-estradiol or conjugated estrogens with the antagonists tamoxifen, raloxifene, bazedoxifene, or fulvestrant. Moreover, ER-HLD can activate transcription in the context of a natural promoter. Taken together, these findings broaden our understanding of the complex relationship between ER agonist and antagonist, and suggest a novel model by which cell and tissue selective effects of antiestrogens may be achieved.
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Affiliation(s)
- Shuang Liu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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5
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Giardina C, Madigan JP, Tierney CAG, Brenner BM, Rosenberg DW. Vitamin D resistance and colon cancer prevention. Carcinogenesis 2011; 33:475-82. [PMID: 22180570 DOI: 10.1093/carcin/bgr301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Observational studies have been largely consistent in showing an inverse association between vitamin D and an individual's risk of developing colorectal cancer. Vitamin D protection is further supported by a range of preclinical colon cancer models, including carcinogen, genetic and dietary models. A large number of mechanistic studies in both humans and rodents point to vitamin D preventing cancer by regulating cell proliferation. Counterbalancing this mostly positive data are the results of human intervention studies in which supplemental vitamin D was found to be ineffective for reducing colon cancer risk. One explanation for these discrepancies is the timing of vitamin D intervention. It is possible that colon lesions may progress to a stage where they become unresponsive to vitamin D. Such a somatic loss in vitamin D responsiveness bears the hallmarks of an epigenetic change. Here, we review data supporting the chemopreventive effectiveness of vitamin D and discuss how gene silencing and other molecular changes somatically acquired during colon cancer development may limit the protection that may otherwise be afforded by vitamin D via dietary intervention. Finally, we discuss how understanding the mechanisms by which vitamin D protection is lost might be used to devise strategies to enhance its chemopreventive actions.
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Affiliation(s)
- Charles Giardina
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, U3215, Storrs, CT 06269, USA.
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Tse AKW, Zhu GY, Wan CK, Shen XL, Yu ZL, Fong WF. 1α,25-Dihydroxyvitamin D3 inhibits transcriptional potential of nuclear factor kappa B in breast cancer cells. Mol Immunol 2010; 47:1728-38. [DOI: 10.1016/j.molimm.2010.03.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 02/28/2010] [Accepted: 03/04/2010] [Indexed: 11/16/2022]
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Bastie JN, Balitrand N, Guillemot I, Chomienne C, Delva L. Cooperative action of 1α,25-dihydroxyvitamin D3 and retinoic acid in NB4 acute promyelocytic leukemia cell differentiation is transcriptionally controlled. Exp Cell Res 2005; 310:319-30. [PMID: 16181625 DOI: 10.1016/j.yexcr.2005.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 08/01/2005] [Accepted: 08/03/2005] [Indexed: 11/23/2022]
Abstract
All-trans-retinoic acid (RA) and 1alpha,25-dihydroxyvitamin D3 (1,25D3) are involved in the control of hematopoiesis and have been suggested to play a role in cellular differentiation and are as such potent inducers of differentiation of myeloid leukemia cells. In this study, we show that, in promyelocytic NB4 cells, addition of 1,25D3 enhances terminal granulocytic RA-dependent differentiation concomitant with the enhanced activation of the RA transcriptional activity through an RARbeta promoter. By EMSA and ChIP assays, we further demonstrate that, while both VDR and RAR are bound to the RARbeta promoter in NB4 cells, addition of 1,25D3 increases VDR binding to this promoter, while that of RA induces the release of VDR and increases the binding of RAR. Thus, contrary to normal myeloid cells, 1,25D3 does not act as a transrepressor of RA transcriptional activity in leukemic cells, suggesting that transcriptional regulation of RA-target genes may be modified in malignant cells. In promyelocytic leukemic cells, the combination of 1,25D3 and RA results in both enhanced transactivation and differentiation.
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Affiliation(s)
- Jean-Noël Bastie
- Inserm U718, Laboratoire de Biologie Cellulaire Hématopoïétique, Institut Universitaire d'Hématologie, Paris 7, Hôpital Saint-Louis, Paris, France
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8
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Mamo S, Ponsuksili S, Wimmers K, Gilles M, Schellander K. Expression of retinoid X receptor transcripts and their significance for developmental competence in in vitro-produced pre-implantation-stage bovine embryos. Reprod Domest Anim 2005; 40:177-83. [PMID: 15819971 DOI: 10.1111/j.1439-0531.2005.00579.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Retinoid X receptors are frequently implicated in their role in embryonic development. However, there is no report regarding their expression in embryos with different qualities. In this study, expression pattern and levels of retinoid X receptor transcripts in different qualities and stages of in vitro-produced pre-implantation bovine embryos were examined using real-time polymerase chain reaction (PCR) techniques. Four independent cDNA pools per sample were prepared from mRNAs isolated from different developmental-stage embryos, after classifying them to be of good and bad quality. Primers were also designed to amplify products with PCR. Based on analysis, except retinoid X receptor gamma (RXRG) transcripts, the remaining two types (alpha and beta forms) were expressed in all samples with significantly higher (p < or = 0.05) levels until the eight-cell stage compared with the stages thereafter. However, the transcript levels for bad-quality embryos were consistently lower in all cases in comparison with good-quality embryos. RXRG was identified in 39% of the samples, but all in the pre-embryonic genome activation development stage. Therefore, strong expression patterns of these transcripts in earlier stages indicates their possible role during the maternal phase of embryo development, and the variations of copy number in embryos with different qualities substantiates their possible candidacy as potential quality markers. Moreover, identifying the transcript variations in different qualities and expression of RXRG at these stages is a novel input to the pre-implantation-stage knowledge.
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Affiliation(s)
- S Mamo
- Institute of Animal Breeding Sciences, University of Bonn, Bonn, Germany.
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Voss TC, Demarco IA, Booker CF, Day RN. Functional interactions with Pit-1 reorganize co-repressor complexes in the living cell nucleus. J Cell Sci 2005; 118:3277-88. [PMID: 16030140 PMCID: PMC2910337 DOI: 10.1242/jcs.02450] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The co-repressor proteins SMRT and NCoR concentrate in specific subnuclear compartments and function with DNA-binding factors to inhibit transcription. To provide detailed mechanistic understanding of these activities, this study tested the hypothesis that functional interactions with transcription factors, such as the pituitary-gland-specific Pit-1 homeodomain protein, direct the subnuclear organization and activity of co-repressor complexes. Both SMRT and NCoR repressed Pit-1-dependent transcription, and NCoR was co-immunoprecipitated with Pit-1. Immunofluorescence experiments confirmed that endogenous NCoR is concentrated in small focal bodies and that incremental increases in fluorescent-protein-tagged NCoR expression lead to progressive increases in the size of these structures. In pituitary cells, the endogenous NCoR localized with endogenous Pit-1 and the co-expression of a fluorescent-protein-labeled Pit-1 redistributed both NCoR and SMRT into diffuse nucleoplasmic compartments that also contained histone deacetylase and chromatin. Automated image-analysis methods were applied to cell populations to characterize the reorganization of co-repressor proteins by Pit-1 and mutation analysis showed that Pit-1 DNA-binding activity was necessary for the reorganization of co-repressor proteins. These data support the hypothesis that spherical foci serve as co-repressor storage compartments, whereas Pit-1/co-repressor complexes interact with target genes in more widely dispersed subnuclear domains. The redistribution of co-repressor complexes by Pit-1 might represent an important mechanism by which transcription factors direct changes in cell-specific gene expression.
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10
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Scsucova S, Palacios D, Savignac M, Mellström B, Naranjo JR, Aranda A. The repressor DREAM acts as a transcriptional activator on Vitamin D and retinoic acid response elements. Nucleic Acids Res 2005; 33:2269-79. [PMID: 15849313 PMCID: PMC1084319 DOI: 10.1093/nar/gki503] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2005] [Revised: 03/22/2005] [Accepted: 03/22/2005] [Indexed: 12/22/2022] Open
Abstract
DREAM (downstream regulatory element antagonist modulator) is a transcriptional repressor, which binds DREs (downstream response elements) in a Ca2+-regulated manner. The DREs consist of core GTCA motifs, very similar to binding motifs for non-steroid nuclear receptors. In this work, we find that DREAM stimulates basal and ligand-dependent activation of promoters containing vitamin D and retinoic acid response elements (VDREs and RAREs), consisting of direct repeats of the sequence AGT/GTCA spaced by 3 or 5 nt, respectively. Stimulation occurs when the element is located upstream, but not downstream, the transcription initiation site. Activation requires both Ca2+ binding to the EF-hands and the leucine-charged domains (LCDs), analogous to those responsible for the interaction of the nuclear receptors with coregulators. Further more, DREAM can bind both 'in vitro' and in chromatin immunoprecipitation assays to these elements. Importantly, 'in vivo' binding is only observed in vitamin D- or RA-treated cells. These results show that DREAM can function as an activator of transcription on certain promoters and demonstrate a novel role for DREAM acting as a potential modulator of genes containing binding sites for nuclear receptors.
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Affiliation(s)
- Sona Scsucova
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de MadridArturo Duperier 4, 28029 Madrid, Spain
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de MadridArturo Duperier 4, 28029 Madrid, Spain
| | - Daniela Palacios
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de MadridArturo Duperier 4, 28029 Madrid, Spain
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de MadridArturo Duperier 4, 28029 Madrid, Spain
| | - Magali Savignac
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de MadridArturo Duperier 4, 28029 Madrid, Spain
| | - Britt Mellström
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de MadridArturo Duperier 4, 28029 Madrid, Spain
| | - Jose Ramon Naranjo
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de MadridArturo Duperier 4, 28029 Madrid, Spain
| | - Ana Aranda
- To whom correspondence should be addressed. Tel: +34 91 5854453; Fax: +34 91 5854401;
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Bi C, Rogan PK. Bipartite pattern discovery by entropy minimization-based multiple local alignment. Nucleic Acids Res 2004; 32:4979-91. [PMID: 15388800 PMCID: PMC521645 DOI: 10.1093/nar/gkh825] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Revised: 08/11/2004] [Accepted: 08/26/2004] [Indexed: 11/14/2022] Open
Abstract
Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel bipartite algorithm, bipartite pattern discovery (Bipad), which produces a mathematical model based on information maximization or Shannon's entropy minimization principle, for discovery of bipartite sequence patterns. Bipad is a C++ program that applies greedy methods to search the bipartite alignment space and examines the upstream or downstream regions of co-regulated genes, looking for cis-regulatory bipartite patterns. An input sequence file with zero or one site per locus is required, and the left and right motif widths and a range of possible gap lengths must be specified. Bipad can run in either single-block or bipartite pattern search modes, and it is capable of comprehensively searching all four orientations of half-site patterns. Simulation studies showed that the accuracy of this motif discovery algorithm depends on sample size and motif conservation level, but results were independent of background composition. Bipad performed equivalent with or better than other pattern search algorithms in correctly identifying Escherichia coli cyclic AMP receptor protein and Bacillus subtilis sigma factor binding site sequences based on experimentally defined benchmarks. Finally, a new bipartite information weight matrix for vitamin D3 receptor/retinoid X receptor alpha (VDR/RXRalpha) binding sites was derived that comprehensively models the natural variability inherent in these sequence elements.
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Affiliation(s)
- Chengpeng Bi
- Laboratory of Human Molecular Genetics, Children's Mercy Hospital & Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA
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Keeton EK, Fletcher TM, Baumann CT, Hager GL, Smith CL. Glucocorticoid receptor domain requirements for chromatin remodeling and transcriptional activation of the mouse mammary tumor virus promoter in different nucleoprotein contexts. J Biol Chem 2002; 277:28247-55. [PMID: 12029095 DOI: 10.1074/jbc.m203898200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The glucocorticoid receptor (GR) contains several activation domains, tau1 (AF-1), tau2, and AF-2, which were initially defined using transiently transfected reporter constructs. Using domain mutations in the context of full-length GR, this study defines those domains required for activation of the mouse mammary tumor virus (MMTV) promoter in two distinct nucleoprotein configurations. A transiently transfected MMTV template with a disorganized, accessible chromatin structure was largely dependent on the AF-2 domain for activation. In contrast, activation of an MMTV template in organized, replicated chromatin requires both domains but has a relatively larger dependence on the tau1 domain. Domain requirements for GR-induced chromatin remodeling of the latter template were also investigated. Mutation of the AF-2 helix 12 domain partially inhibits the induction of nuclease hypersensitivity, but the inhibition was relieved in the absence of tau1, suggesting the occurrence of an important interaction between the two domains. Further mutational analysis indicates that GR-induced chromatin remodeling requires the ligand-binding domain in the region of helix 3. Our study shows that the GR activation surfaces required for transcriptional modulation of a target promoter were determined in part by its chromatin structure. Within a particular cellular environment the GR appears to possess a significant degree of versatility in the mechanism by which it activates a target promoter.
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MESH Headings
- Alanine
- Amino Acid Substitution
- Animals
- Base Sequence
- Binding Sites
- Chromatin/physiology
- Chromatin/ultrastructure
- Cloning, Molecular
- Dexamethasone/pharmacology
- Mammary Tumor Virus, Mouse/genetics
- Mice
- Models, Molecular
- Mutagenesis, Site-Directed
- Nuclear Proteins/metabolism
- Nucleoproteins/metabolism
- Oligodeoxyribonucleotides
- Promoter Regions, Genetic
- Protein Structure, Secondary
- Receptors, Glucocorticoid/chemistry
- Receptors, Glucocorticoid/genetics
- Receptors, Glucocorticoid/metabolism
- Receptors, Interferon/metabolism
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/metabolism
- Serine
- Templates, Genetic
- Transfection
- Tumor Cells, Cultured
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Ylikomi T, Laaksi I, Lou YR, Martikainen P, Miettinen S, Pennanen P, Purmonen S, Syvälä H, Vienonen A, Tuohimaa P. Antiproliferative action of vitamin D. VITAMINS AND HORMONES 2002; 64:357-406. [PMID: 11898396 DOI: 10.1016/s0083-6729(02)64010-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the past few years, it has become apparent that vitamin D may play an important role in malignant transformation. Epidemiological studies suggest that low vitamin D serum concentration increases especially the risk of hormone-related cancers. Experimentally, vitamin D suppresses the proliferation of normal and malignant cells and induces differentiation and apoptosis. In the present review we discuss the mechanisms whereby vitamin D regulates cell proliferation and whether it could be used in prevention and treatment of hyperproliferative disorders like cancers.
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Affiliation(s)
- Timo Ylikomi
- Graduate School of Biomedicine, Department of Cell Biology, 33014 University of Tampere, Finland
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14
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Abstract
The nuclear hormone receptor superfamily includes receptors for thyroid and steroid hormones, retinoids and vitamin D, as well as different "orphan" receptors of unknown ligand. Ligands for some of these receptors have been recently identified, showing that products of lipid metabolism such as fatty acids, prostaglandins, or cholesterol derivatives can regulate gene expression by binding to nuclear receptors. Nuclear receptors act as ligand-inducible transcription factors by directly interacting as monomers, homodimers, or heterodimers with the retinoid X receptor with DNA response elements of target genes, as well as by "cross-talking" to other signaling pathways. The effects of nuclear receptors on transcription are mediated through recruitment of coregulators. A subset of receptors binds corepressor factors and actively represses target gene expression in the absence of ligand. Corepressors are found within multicomponent complexes that contain histone deacetylase activity. Deacetylation leads to chromatin compactation and transcriptional repression. Upon ligand binding, the receptors undergo a conformational change that allows the recruitment of multiple coactivator complexes. Some of these proteins are chromatin remodeling factors or possess histone acetylase activity, whereas others may interact directly with the basic transcriptional machinery. Recruitment of coactivator complexes to the target promoter causes chromatin decompactation and transcriptional activation. The characterization of corepressor and coactivator complexes, in concert with the identification of the specific interaction motifs in the receptors, has demonstrated the existence of a general molecular mechanism by which different receptors elicit their transcriptional responses in target genes.
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Affiliation(s)
- A Aranda
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain.
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15
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Mathur M, Tucker PW, Samuels HH. PSF is a novel corepressor that mediates its effect through Sin3A and the DNA binding domain of nuclear hormone receptors. Mol Cell Biol 2001; 21:2298-311. [PMID: 11259580 PMCID: PMC86864 DOI: 10.1128/mcb.21.7.2298-2311.2001] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2000] [Accepted: 01/08/2001] [Indexed: 11/20/2022] Open
Abstract
Members of the type II nuclear hormone receptor subfamily (e.g., thyroid hormone receptors [TRs], retinoic acid receptors, retinoid X receptors [RXRs], vitamin D receptor, and the peroxisome proliferator-activated receptors) bind to their response sequences with or without ligand. In the absence of ligand, these DNA-bound receptors mediate different degrees of repression or silencing of gene expression which is thought to result from the association of their ligand binding domains (LBDs) with corepressors. Two related corepressors, N-CoR and SMRT, interact to various degrees with the LBDs of these type II receptors in the absence of their cognate ligands. N-CoR and SMRT have been proposed to act by recruiting class I histone deacetylases (HDAC I) through an association with Sin3, although they have also been shown to recruit class II HDACs through a Sin3-independent mechanism. In this study, we used a biochemical approach to identify novel nuclear factors that interact with unliganded full-length TR and RXR. We found that the DNA binding domains (DBDs) of TR and RXR associate with two proteins which we identified as PSF (polypyrimidine tract-binding protein-associated splicing factor) and NonO/p54(nrb). Our studies indicate that PSF is a novel repressor which interacts with Sin3A and mediates silencing through the recruitment of HDACs to the receptor DBD. In vivo studies with TR showed that although N-CoR fully dissociates in the presence of ligand, the levels of TR-bound PSF and Sin3A appear to remain unchanged, indicating that Sin3A can be recruited to the receptor independent of N-CoR or SMRT. RXR was not detected to bind N-CoR although it bound PSF and Sin3A as effectively as TR, and this association with RXR did not change with ligand. Our studies point to a novel PSF/Sin3-mediated pathway for nuclear hormone receptors, and possibly other transcription factors, which may fine-tune the transcriptional response as well as play an important role in mediating the repressive effects of those type II receptors which only weakly interact with N-CoR and SMRT.
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Affiliation(s)
- M Mathur
- Division of Clinical and Molecular Endocrinology, Department of Medicine, New York University School of Medicine, New York, New York 10016, USA
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16
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Tolón RM, Castillo AI, Jiménez-Lara AM, Aranda A. Association with Ets-1 causes ligand- and AF2-independent activation of nuclear receptors. Mol Cell Biol 2000; 20:8793-802. [PMID: 11073980 PMCID: PMC86515 DOI: 10.1128/mcb.20.23.8793-8802.2000] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vitamin D receptor (VDR) normally functions as a ligand-dependent transcriptional activator. Here we show that, in the presence of Ets-1, VDR stimulates the prolactin promoter in a ligand-independent manner, behaving as a constitutive activator. Mutations in the AF2 domain abolish vitamin D-dependent transactivation but do not affect constitutive activation by Ets-1. Therefore, in contrast with the actions of vitamin D, activation by Ets-1 is independent of the AF2 domain. Ets-1 also conferred a ligand-independent activation to the estrogen receptor and to peroxisome proliferator-activated receptor alpha. In addition, Ets-1 cooperated with the unliganded receptors to stimulate the activity of reporter constructs containing consensus response elements fused to the thymidine kinase promoter. There is a direct interaction of the receptors with Ets-1 which requires the DNA binding domains of both proteins. Interaction with Ets-1 induces a conformational change in VDR which can be detected by an increased resistance to proteolytic digestion. Furthermore, a retinoid X receptor-VDR heterodimer in which both receptors lack the core C-terminal AF2 domain can recruit coactivators in the presence, but not in the absence, of Ets-1. This suggests that Ets-1 induces a conformational change in the receptor which creates an active interaction surface with coactivators even in the AF2-defective mutants. These results demonstrate the existence of a novel mechanism, alternative to ligand binding, which can convert an unliganded receptor from an inactive state into a competent transcriptional activator.
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Affiliation(s)
- R M Tolón
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28029 Madrid, Spain
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17
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Pérez-Juste G, García-Silva S, Aranda A. An element in the region responsible for premature termination of transcription mediates repression of c-myc gene expression by thyroid hormone in neuroblastoma cells. J Biol Chem 2000; 275:1307-14. [PMID: 10625678 DOI: 10.1074/jbc.275.2.1307] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The thyroid hormone (T3) blocks proliferation and induces differentiation of neuroblastoma N2a-beta cells that express the thyroid hormone receptor (TR) beta1 isoform. c-Myc is required for cell cycle progression, and this study shows that T3-induced neuronal differentiation is preceded by a rapid decrease of c-myc gene expression. A negative T3 responsive element (TRE), arranged as an inverted palindrome spaced by three nucleotides, has been identified within the first exon between nucleotides +237 and +268. The TRE is adjacent to the binding site for the transcriptional repressor CCCTC binding factor and maps precisely within the region of RNA polymerase II pausing and release, suggesting a direct implication of TR on premature termination of transcription. Furthermore, the TRE confers repression by T3 to an heterologous promoter only when inserted downstream of the transcription initiation site. Binding of CCCTC binding factor and TR to their cognate sites in the region of transcriptional attenuation, as well as direct interactions between both factors, could facilitate the formation of a repressor complex and the inhibition of c-myc gene expression. These studies provide insight into mechanisms by which TR mediate transcriptional repression and contribute to the understanding of the important effects of thyroid hormones on growth and differentiation of neuronal cells.
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Affiliation(s)
- G Pérez-Juste
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas and Universidad Aut-noma de Madrid, 28029 Madrid, Spain
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