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Engquist EN, Greco A, Joosten LAB, van Engelen BGM, Zammit PS, Banerji CRS. FSHD muscle shows perturbation in fibroadipogenic progenitor cells, mitochondrial function and alternative splicing independently of inflammation. Hum Mol Genet 2024; 33:182-197. [PMID: 37856562 PMCID: PMC10772042 DOI: 10.1093/hmg/ddad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy. FSHD is highly heterogeneous, with patients following a variety of clinical trajectories, complicating clinical trials. Skeletal muscle in FSHD undergoes fibrosis and fatty replacement that can be accelerated by inflammation, adding to heterogeneity. Well controlled molecular studies are thus essential to both categorize FSHD patients into distinct subtypes and understand pathomechanisms. Here, we further analyzed RNA-sequencing data from 24 FSHD patients, each of whom donated a biopsy from both a non-inflamed (TIRM-) and inflamed (TIRM+) muscle, and 15 FSHD patients who donated peripheral blood mononucleated cells (PBMCs), alongside non-affected control individuals. Differential gene expression analysis identified suppression of mitochondrial biogenesis and up-regulation of fibroadipogenic progenitor (FAP) gene expression in FSHD muscle, which was particularly marked on inflamed samples. PBMCs demonstrated suppression of antigen presentation in FSHD. Gene expression deconvolution revealed FAP expansion as a consistent feature of FSHD muscle, via meta-analysis of 7 independent transcriptomic datasets. Clustering of muscle biopsies separated patients in an unbiased manner into clinically mild and severe subtypes, independently of known disease modifiers (age, sex, D4Z4 repeat length). Lastly, the first genome-wide analysis of alternative splicing in FSHD muscle revealed perturbation of autophagy, BMP2 and HMGB1 signalling. Overall, our findings reveal molecular subtypes of FSHD with clinical relevance and identify novel pathomechanisms for this highly heterogeneous condition.
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Affiliation(s)
- Elise N Engquist
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
| | - Anna Greco
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, 400012, Cluj-Napoca, Romania
| | - Baziel G M van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
| | - Christopher R S Banerji
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
- The Alan Turing Institute, The British Library, 96 Euston Road, London NW1 2DB, United Kingdom
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Mousavi Khorshidi MS, Seeleuthner Y, Chavoshzadeh Z, Behfar M, Hamidieh AA, Alimadadi H, Sherkat R, Momen T, Behniafard N, Eskandarzadeh S, Mansouri M, Behnam M, Mahdavi M, Heydarazad Zadeh M, Shokri M, Alizadeh F, Movahedi M, Momenilandi M, Keramatipour M, Casanova JL, Cobat A, Abel L, Shahrooei M, Parvaneh N. Clinical, Immunological, and Genetic Findings in Iranian Patients with MHC-II Deficiency: Confirmation of c.162delG RFXANK Founder Mutation in the Iranian Population. J Clin Immunol 2023; 43:1941-1952. [PMID: 37584719 DOI: 10.1007/s10875-023-01562-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/30/2023] [Indexed: 08/17/2023]
Abstract
PURPOSE Major histocompatibility complex class II (MHC-II) deficiency is a rare inborn error of immunity (IEI). Impaired antigen presentation to CD4 + T cells results in combined immunodeficiency (CID). Patients typically present with severe respiratory and gastrointestinal tract infections at early ages. Hematopoietic stem cell transplantation (HSCT) is the only curative therapy. METHODS We describe the clinical, immunologic, and genetic features of eighteen unrelated Iranian patients with MHC-II deficiency. RESULTS Consanguinity was present in all affected families. The median age at the initial presentation was 5.5 months (range 7 days to 18 years). The main symptoms included failure to thrive, persistent diarrhea, and pneumonia. Autoimmune and neurologic features were also documented in about one-third of the patients, respectively. Thirteen patients carried RFXANK gene mutations, two carried RFX5 gene mutations, and three carried a RFXAP gene mutation. Six patients shared the same RFXANK founder mutation (c.162delG); limited to the Iranian population and dated to approximately 1296 years ago. Four of the patients underwent HSCT; three of them are alive. On the other hand, nine of the fourteen patients who did not undergo HSCT had a poor prognosis and died. CONCLUSION MHC-II deficiency is not rare in Iran, with a high rate of consanguinity. It should be considered in the differential diagnosis of CID at any age. With the limited access to HSCT and its variable results in MHC-II deficiency, implementing genetic counseling and family planning for the affected families are mandatory. We are better determined to study the c.162delG RFXANK heterozygous mutation frequency in the Iranian population.
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Affiliation(s)
- Mohadese Sadat Mousavi Khorshidi
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de La Santé Et de La Recherche Médicale (INSERM) U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University Paris Cité, Paris, France
| | - Zahra Chavoshzadeh
- Allergy and Immunology Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Behfar
- Pediatric Cell and Gene Therapy Research Center, Gene, Cell & Tissue Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children's Medical Center, Pediatric Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Ali Hamidieh
- Pediatric Cell and Gene Therapy Research Center, Gene, Cell & Tissue Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children's Medical Center, Pediatric Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hosein Alimadadi
- Division of Gastroenterology, Department of Pediatrics, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Roya Sherkat
- Immunodeficiency Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tooba Momen
- Department of Allergy and Clinical Immunology, Child Growth and Development Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nasrin Behniafard
- Children Growth Disorder Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Allergy and Clinical Immunology, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Shabnam Eskandarzadeh
- Allergy and Clinical Immunology Department, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahboubeh Mansouri
- Allergy and Immunology Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdiyeh Behnam
- Student Research Committee, Semnan University of Medical Sciences, Semnan, Iran
- Dr. Shahrooei Lab, 22 Bahman St., Ashrafi Esfahani Blvd, Tehran, Iran
| | - Mohadese Mahdavi
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Heydarazad Zadeh
- Allergy and Immunology Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Shokri
- Department of Pediatrics, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Fatemeh Alizadeh
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshid Movahedi
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mana Momenilandi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de La Santé Et de La Recherche Médicale (INSERM) U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University Paris Cité, Paris, France
| | - Mohammad Keramatipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de La Santé Et de La Recherche Médicale (INSERM) U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de La Santé Et de La Recherche Médicale (INSERM) U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de La Santé Et de La Recherche Médicale (INSERM) U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Mohammad Shahrooei
- Dr. Shahrooei Lab, 22 Bahman St., Ashrafi Esfahani Blvd, Tehran, Iran
- Clinical and Diagnostic Immunology, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Louvain, Belgium
| | - Nima Parvaneh
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
- Children's Medical Centre, No 62 Gharib St, Tehran, 1419733152, Iran.
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Wayman JA, Thomas A, Bejjani A, Katko A, Almanan M, Godarova A, Korinfskaya S, Cazares TA, Yukawa M, Kottyan LC, Barski A, Chougnet CA, Hildeman DA, Miraldi ER. An atlas of gene regulatory networks for memory CD4 + T cells in youth and old age. bioRxiv 2023:2023.03.07.531590. [PMID: 36945549 PMCID: PMC10028906 DOI: 10.1101/2023.03.07.531590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Aging profoundly affects immune-system function, promoting susceptibility to pathogens, cancers and chronic inflammation. We previously identified a population of IL-10-producing, T follicular helper-like cells (" Tfh10 "), linked to suppressed vaccine responses in aged mice. Here, we integrate single-cell ( sc )RNA-seq, scATAC-seq and genome-scale modeling to characterize Tfh10 - and the full CD4 + memory T cell ( CD4 + TM ) compartment - in young and old mice. We identified 13 CD4 + TM populations, which we validated through cross-comparison to prior scRNA-seq studies. We built gene regulatory networks ( GRNs ) that predict transcription-factor control of gene expression in each T-cell population and how these circuits change with age. Through integration with pan-cell aging atlases, we identified intercellular-signaling networks driving age-dependent changes in CD4 + TM. Our atlas of finely resolved CD4 + TM subsets, GRNs and cell-cell communication networks is a comprehensive resource of predicted regulatory mechanisms operative in memory T cells, presenting new opportunities to improve immune responses in the elderly.
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Chen S, Xu Y, Qian Y, Li Z, Dong M. Case Report: Novel splicing mutations in RFX5 causing MHC class II deficiency. Front Genet 2022; 13:978688. [DOI: 10.3389/fgene.2022.978688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Mutations of the Regulatory Factor X5 (RFX5) have been associated with the autosomal recessive major histocompatibility class II (MHC-II) deficiency, which is a severe immunodeficiency characterized by constitutive and interferon-gamma induced MHC II expression disorder and leads to the absence of cellular and humoral T-cell response to antigen challenge. The compound heterozygous splicing mutations of RFX5: c.353 + 6T>G (maternally inherited) and c.757 + 1G>A (paternally inherited) were identified in an infant diagnosed severe immunodeficiency. The mutation c.757 + 1G>A was classified as likely pathogenic while c.353 + 6T>G was classified as the variant of uncertain significance according to American College of Medical Genetics and Genomics (ACMG). To investigate the pathogenicity of RFX5: c.353 + 6T>G, reverse transcription PCR (RT-PCR) was conducted with the mother’s peripheral blood. An insertion of 191-bp intronic sequence (intron 6) was found in the transcripts, and this resulted in a frameshift and premature truncation of the protein, especially reduced the DNA-binding domain (DBD) of the RFX5 protein. Our data expanded the spectrum of pathogenic mutations in MHC-II deficiency and put new insights into the genetic counseling, prenatal diagnosis and preimplantation genetic testing (PGT) for the disease.
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Rodriguez-Marquez P, Calleja-Cervantes ME, Serrano G, Oliver-Caldes A, Palacios-Berraquero ML, Martin-Mallo A, Calviño C, Español-Rego M, Ceballos C, Lozano T, San Martin-Uriz P, Vilas-Zornoza A, Rodriguez-Diaz S, Martinez-Turrillas R, Jauregui P, Alignani D, Viguria MC, Redondo M, Pascal M, Martin-Antonio B, Juan M, Urbano-Ispizua A, Rodriguez-Otero P, Alfonso-Pierola A, Paiva B, Lasarte JJ, Inoges S, Lopez-Diaz de Cerio A, San-Miguel J, Fernandez de Larrea C, Hernaez M, Rodriguez-Madoz JR, Prosper F. CAR density influences antitumoral efficacy of BCMA CAR T cells and correlates with clinical outcome. Sci Adv 2022; 8:eabo0514. [PMID: 36179026 PMCID: PMC9524842 DOI: 10.1126/sciadv.abo0514] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 08/17/2022] [Indexed: 05/23/2023]
Abstract
Identification of new markers associated with long-term efficacy in patients treated with CAR T cells is a current medical need, particularly in diseases such as multiple myeloma. In this study, we address the impact of CAR density on the functionality of BCMA CAR T cells. Functional and transcriptional studies demonstrate that CAR T cells with high expression of the CAR construct show an increased tonic signaling with up-regulation of exhaustion markers and increased in vitro cytotoxicity but a decrease in in vivo BM infiltration. Characterization of gene regulatory networks using scRNA-seq identified regulons associated to activation and exhaustion up-regulated in CARHigh T cells, providing mechanistic insights behind differential functionality of these cells. Last, we demonstrate that patients treated with CAR T cell products enriched in CARHigh T cells show a significantly worse clinical response in several hematological malignancies. In summary, our work demonstrates that CAR density plays an important role in CAR T activity with notable impact on clinical response.
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Affiliation(s)
| | - Maria E. Calleja-Cervantes
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Computational Biology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Guillermo Serrano
- Computational Biology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Aina Oliver-Caldes
- Department of Hematology, Hospital Clinic de Barcelona, IDIBAPS, Universidad de Barcelona, Barcelona, Spain
| | | | - Angel Martin-Mallo
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Cristina Calviño
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
| | - Marta Español-Rego
- Department of Immunology, Hospital Clinic de Barcelona, IDIBAPS, Universidad de Barcelona, Barcelona, Spain
| | - Candela Ceballos
- Hematology Service, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Teresa Lozano
- Immunology and Immunotherapy Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | | | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Rebeca Martinez-Turrillas
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Patricia Jauregui
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
| | - Diego Alignani
- Flow Cytometry Core, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Maria C. Viguria
- Hematology Service, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Margarita Redondo
- Hematology Service, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Mariona Pascal
- Department of Immunology, Hospital Clinic de Barcelona, IDIBAPS, Universidad de Barcelona, Barcelona, Spain
| | - Beatriz Martin-Antonio
- Department of Hematology, Hospital Clinic de Barcelona, IDIBAPS, Universidad de Barcelona, Barcelona, Spain
| | - Manel Juan
- Department of Immunology, Hospital Clinic de Barcelona, IDIBAPS, Universidad de Barcelona, Barcelona, Spain
- Immunotherapy platform Hospital Sant Joan de Déu, Barcelona, Spain
| | - Alvaro Urbano-Ispizua
- Department of Hematology, Hospital Clinic de Barcelona, IDIBAPS, Universidad de Barcelona, Barcelona, Spain
| | - Paula Rodriguez-Otero
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
| | - Ana Alfonso-Pierola
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Bruno Paiva
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Flow Cytometry Core, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Juan J. Lasarte
- Immunology and Immunotherapy Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Susana Inoges
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Immunology and Immunotherapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
| | - Ascension Lopez-Diaz de Cerio
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Immunology and Immunotherapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
| | - Jesus San-Miguel
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Cancer Center Universidad de Navarra (CCUN), Pamplona, Spain
| | - Carlos Fernandez de Larrea
- Department of Hematology, Hospital Clinic de Barcelona, IDIBAPS, Universidad de Barcelona, Barcelona, Spain
| | - Mikel Hernaez
- Computational Biology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Data Science and Artificial Intelligence Institute (DATAI), Universidad de Navarra, Pamplona, Spain
| | - Juan R. Rodriguez-Madoz
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Felipe Prosper
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Hematology and Cell Therapy Department, Clínica Universidad de Navarra (CUN), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Cancer Center Universidad de Navarra (CCUN), Pamplona, Spain
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Spreng A, Brüll M, Leisner H, Suciu I, Leist M. Distinct and Dynamic Transcriptome Adaptations of iPSC-Generated Astrocytes after Cytokine Stimulation. Cells 2022; 11:2644. [PMID: 36078052 PMCID: PMC9455058 DOI: 10.3390/cells11172644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Astrocytes (ACs) do not only play a role in normal neurogenesis and brain homeostasis, but also in inflammatory and neurodevelopmental disorders. We studied here the different patterns of inflammatory activation triggered by cytokines in human induced pluripotent stem cell (iPSC)-derived ACs. An optimized differentiation protocol provided non-inflamed ACs. These cells reacted to TNFα with a rapid translocation of NFκB, while AC precursors showed little response. Transcriptome changes were quantified at seven time points (2–72 h) after stimulation with TNFα, IFNγ or TNFα plus IFNγ. TNFα triggered a strong response within 2 h. It peaked from 12–24 h and reverted towards the ground state after 72 h. Activation by IFNγ was also rapid, but the response pattern differed from that of TNFα. For instance, several chemokines up-regulated by TNFα were not affected by IFNγ. Instead, MHC-II-related antigen presentation was drastically enhanced. The combination of the two cytokines led to a stronger and more persistent response. For instance, TRIB3 up-regulation by the combination of TNFα plus IFNγ may have slowed NFκB inactivation. Additionally, highly synergistic regulation was observed for inflammation modifiers, such as CASP4, and for STAT1-controlled genes. The combination of the cytokines also increased oxidative stress markers (e.g., CHAC1), led to phenotypic changes in ACs and triggered markers related to cell death. In summary, these data demonstrate that there is a large bandwidth of pro-inflammatory AC states, and that single markers are not suitable to describe AC activation or their modulation in disease, development and therapy.
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Karimzadeh M, Hoffman MM. Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome. Genome Biol 2022; 23:126. [PMID: 35681170 PMCID: PMC9185870 DOI: 10.1186/s13059-022-02690-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
Existing methods for computational prediction of transcription factor (TF) binding sites evaluate genomic regions with similarity to known TF sequence preferences. Most TF binding sites, however, do not resemble known TF sequence motifs, and many TFs are not sequence-specific. We developed Virtual ChIP-seq, which predicts binding of individual TFs in new cell types, integrating learned associations with gene expression and binding, TF binding sites from other cell types, and chromatin accessibility data in the new cell type. This approach outperforms methods that predict TF binding solely based on sequence preference, predicting binding for 36 TFs (MCC>0.3).
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Affiliation(s)
- Mehran Karimzadeh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada.,Vector Institute, Toronto, ON, Canada
| | - Michael M Hoffman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .,Princess Margaret Cancer Centre, Toronto, ON, Canada. .,Vector Institute, Toronto, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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Chen J, Li X, Huang J, Wang Q, Wang S, Wei S, Qin Q, Yang M. The transcription factor RFX5 positively regulates expression of MHCIa in the red-spotted grouper (Epinephelus akaara). Fish Shellfish Immunol 2022; 121:370-379. [PMID: 35051562 DOI: 10.1016/j.fsi.2022.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Regulatory factor X 5 (RFX 5) is a member of the RFX family, and it forms the transcription factor complex RFX with RFXANK/B and RFXAP. The RFX complex can activate MHC expression by binding to the MHC promoter. However, the regulate mechanism of RFX in fish species is not been fully elucidated. In this study, we investigated the transcriptional regulation of Epinephelus akaara RFX5 (EaRFX5) on EaMHCI, and its effect on immune pathways. The genomic sequence of EaRFX5 was 35,774 bp and consisted of ten exons and nine introns. The length of EaRFX5 ORF sequence is 2,160 bp, encoding 719 amino acids. By qRT-PCR, EaRFX5 was detected constitutively expressed in twelve selected tissues, showing a wide range of expression. EaRFX5 expression parttern in response to poly (I:C), LPS, Zymosan A, SGIV, and NNV challenges showed that EaRFX5 plays a differentiated immunomodulatory role in response to various stimuli in different tissues, and EaRFX5 was most significantly upregulated in the kidney after challenge with SGIV. Subcellular localization assays showed that EaRFX5 is a typical nuclear protein. Based on the in vitro overexpression experiments, EaRFX5 appeared to promote the expression of EaMHCIa gene, interferon signalling pathway and inflammatory cytokine. Luciferase reporter assay showed that the -267 bp to +82 bp region of EaMHCIa promoter was the core region where EaRFX5 modulated. Additionally, point mutations and electrophoretic mobility shift assays indicating M3 is the EaRFX5 binding sites in the EaMHCIa promoter. These results contribute to elucidating the function of EaRFX5 in fish immune response, and provide the first evidence of positive regulation of MHCIa expression by RFX5 in fish.
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Affiliation(s)
- Jinpeng Chen
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xinshuai Li
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jianling Huang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qing Wang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shaowen Wang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shina Wei
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qiwei Qin
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, 519000, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
| | - Min Yang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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9
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Truong L, Matern BM, Groeneweg M, D'Orsogna L, Martinez P, Tilanus MGJ, De Santis D. Polymorphism clustering of the 21.5 kb DPA-promoter-DPB region reveals novel extended full-length haplotypes. HLA 2020; 96:299-311. [PMID: 32536006 DOI: 10.1111/tan.13975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 01/12/2023]
Abstract
DPB1 and DPA1 genes share the same promoter region. Single-nucleotide polymorphisms (SNPs) within the regulatory regions of DP have been reported. This study hypothesizes that by including the SNPs in the promoter region of DP, extended haplotypes are defined, and promoter polymorphism is more extensive than what is currently reported. To identify the SNPs in the region of interest, the DP region spanning 21.5 kb was amplified in three separate long-ranged polymerase chain reactions. A DNA panel consisting of 100 samples was selected to represent a broad range of DPB1 alleles. The panel was amplified and sequenced using a dual sequencing strategy. Binary alignment map (BAM) alignments were generated and the mapped sequence alignments were analyzed using Integrative Genomics Viewer. A total of 76 SNPs were identified, and SNPs were clustered into 12 SNP-linked haplotypes. Multiple sequence alignments of promoter sequences indicated four distinct lineages within the connective region (CR) between two genes. The relationship between DPA1, CR, DPB1, and amino acid motifs was found to be correlated with HV1 and HV6. Of the 12 promoter haplotypes, DPB1 alleles observed with ProDP-4 were in complete linkage with HV1/2/5/6, the rs9277534G SNP, and the highly immunogenic T-cell epitope group. Multiple extended haplotypes of different intronic subtypes of the same DPB1 alleles were also identified. This new view of the full DP haplotype shows the relation of polymorphism, genes, and alleles, and provides a basis for future functionality related nomenclature. The novel clustering of the DP-extended haplotype warrants future investigations of DP haplotype matching in the outcome of haematopoietic stem cell transplantation (HSCT).
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Affiliation(s)
- Linh Truong
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia.,School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Ben M Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Lloyd D'Orsogna
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia.,School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Patricia Martinez
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia.,School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Dianne De Santis
- Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia.,School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
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10
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Rajavel A, Heinrich F, Schmitt AO, Gültas M. Identifying Cattle Breed-Specific Partner Choice of Transcription Factors during the African Trypanosomiasis Disease Progression Using Bioinformatics Analysis. Vaccines (Basel) 2020; 8:E246. [PMID: 32456126 DOI: 10.3390/vaccines8020246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 12/18/2022] Open
Abstract
African Animal Trypanosomiasis (AAT) is a disease caused by pathogenic trypanosomes which affects millions of livestock every year causing huge economic losses in agricultural production especially in sub-Saharan Africa. The disease is spread by the tsetse fly which carries the parasite in its saliva. During the disease progression, the cattle are prominently subjected to anaemia, weight loss, intermittent fever, chills, neuronal degeneration, congestive heart failure, and finally death. According to their different genetic programs governing the level of tolerance to AAT, cattle breeds are classified as either resistant or susceptible. In this study, we focus on the cattle breeds N’Dama and Boran which are known to be resistant and susceptible to trypanosomiasis, respectively. Despite the rich literature on both breeds, the gene regulatory mechanisms of the underlying biological processes for their resistance and susceptibility have not been extensively studied. To address the limited knowledge about the tissue-specific transcription factor (TF) cooperations associated with trypanosomiasis, we investigated gene expression data from these cattle breeds computationally. Consequently, we identified significant cooperative TF pairs (especially DBP−PPARA and DBP−THAP1 in N’Dama and DBP−PAX8 in Boran liver tissue) which could help understand the underlying AAT tolerance/susceptibility mechanism in both cattle breeds.
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11
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Kwon HJ, Qing K, Ponnazhagan S, Wang XS, Markusic DM, Gupte S, Boye SE, Srivastava A. Adeno-Associated Virus D-Sequence-Mediated Suppression of Expression of a Human Major Histocompatibility Class II Gene: Implications in the Development of Adeno-Associated Virus Vectors for Modulating Humoral Immune Response. Hum Gene Ther 2020; 31:565-574. [PMID: 32220217 DOI: 10.1089/hum.2020.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A 20-nt long sequence, termed the D-sequence, in the adeno-associated virus (AAV) inverted terminal repeat was observed to share a partial sequence homology with the X-box in the regulatory region of the human leukocyte antigen DRA (HLA-DRA) promoter of the human major histocompatibility complex class II (MHC-II) genes. The D-sequence was also shown to specifically interact with the regulatory factor binding to the X-box (RFX), binding of which to the X-box is a critical step in the MHC-II gene expression, suggesting that D-sequence might compete for RFX transcription factor binding, thereby suppressing expression from the MHC-II promoter. In DNA-mediated transfection experiments, using a reporter gene under the control of the HLA-DRA promoter, D-sequence oligonucleotides were found to inhibit expression of the reporter gene expression in HeLa and 293 cells by ∼93% and 96%, respectively. No inhibition was observed when nonspecific synthetic oligonucleotides were used. D-sequence oligonucleotides had no effect on expression from the cytomegalovirus immediate-early gene promoter. Interferon-γ-mediated activation of MHC-II gene expression was also inhibited by D-sequence oligonucleotides as well as after infection with either the wild-type AAV or transduction with recombinant AAV vectors. These studies suggest that the D-sequence-mediated downregulation of the MHC-II gene expression may be exploited toward the development of novel AAV vectors capable of dampening the host humoral response, which has important implication in the optimal use of these vectors in human gene therapy.
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Affiliation(s)
- Hyung-Joo Kwon
- Department of Microbiology, Hallym University College of Medicine, Chuncheon, South Korea
| | - Keyun Qing
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA
| | | | | | - David M Markusic
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Siddhant Gupte
- Department of Ophthalmology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Shannon E Boye
- Department of Ophthalmology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Arun Srivastava
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama, USA.,Eli Lilly & Company, Indianapolis, Indiana, USA.,Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Ophthalmology, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, Florida, USA
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12
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Paramonova N, Trapina I, Dokane K, Kalnina J, Sjakste T, Sjakste N. An Intergenic rs9275596 Polymorphism on Chr. 6p21 Is Associated with Multiple Sclerosis in Latvians. Medicina (Kaunas) 2020; 56:medicina56040154. [PMID: 32244438 PMCID: PMC7230508 DOI: 10.3390/medicina56040154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 12/30/2022]
Abstract
Background and objectives: Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system, leading to demyelination of neurons and potentially debilitating physical and mental symptoms. The disease is more prevalent in women than in men. The major histocompatibility complex (MHC) region has been identified as a major genetic determinant for autoimmune diseases, and its role in some neurological disorders including MS was evaluated. An intergenic single-nucleotide polymorphism (SNP), rs9275596, located between the HLA-DQB1 and HLA-DQA2 genes, is in significant association with various autoimmune diseases according to genome-wide association studies (GWASs). A cumulative effect of this SNP with other polymorphisms from this region was revealed. The aim of the study was to verify the data on rs9275596 association in multiple sclerosis in a case/control study of the Latvian population and to evaluate eventual functional significance of allele substitutions. Materials and Methods: rs9275596 (chr6:32713854; GRCh38.p12) was genotyped in 273 MS patients and 208 controls on main and sex-specific associations. Eventual functional significance of allele substitutions was evaluated in silico using publicly available tools. Results: The rs9275596 rare alleles were identified as a disease susceptibility factor in association with the MS main group and in affected females (p < 0.001 and p < 0.01, respectively). Risk factor genotypes with rare alleles included were associated with the MS common cohort (p < 0.002) and female cohort (odds ratio, OR = 2.24) and were identified as disease susceptible in males (OR = 2.41). It was shown that structural changes of rs9275596 affect the secondary structure of DNA. Functional significance of allele substitutions was evaluated on the eventual sequence affinity to transcription factors (TFs) and splicing signals similarity. A possible impact of the particular polymorphisms on the transcription and splicing efficiency is discussed. Conclusions: Our results suggest susceptibility of rs9275596 to multiple sclerosis in Latvians.
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Affiliation(s)
- Natalia Paramonova
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, LV-1004 Riga, Latvia; (N.P.); (K.D.); (J.K.); (T.S.); (N.S.)
| | - Ilva Trapina
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, LV-1004 Riga, Latvia; (N.P.); (K.D.); (J.K.); (T.S.); (N.S.)
- Correspondence: ; Tel.: +371-29354786
| | - Kristine Dokane
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, LV-1004 Riga, Latvia; (N.P.); (K.D.); (J.K.); (T.S.); (N.S.)
| | - Jolanta Kalnina
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, LV-1004 Riga, Latvia; (N.P.); (K.D.); (J.K.); (T.S.); (N.S.)
| | - Tatjana Sjakste
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, LV-1004 Riga, Latvia; (N.P.); (K.D.); (J.K.); (T.S.); (N.S.)
| | - Nikolajs Sjakste
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, LV-1004 Riga, Latvia; (N.P.); (K.D.); (J.K.); (T.S.); (N.S.)
- Department of Medical Biochemistry of the University of Latvia, LV-1004 Riga, Latvia
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13
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Abstract
Perturbed diurnal rhythms are becoming increasingly evident as deleterious events in the pathology of metabolic diseases. Exercise is well characterized as a crucial intervention in the prevention and treatment of individuals with metabolic diseases. Little is known, however, regarding optimizing the timing of exercise bouts in order to maximize their health benefits. Furthermore, exercise is a potent modulator of skeletal muscle metabolism, and it is clear that skeletal muscle has a strong circadian profile. In humans, mitochondrial function peaks in the late afternoon, and the circadian clock might be inherently impaired in myotubes from patients with metabolic disease. Timing exercise bouts to coordinate with an individual's circadian rhythms might be an efficacious strategy to optimize the health benefits of exercise. The role of exercise as a Zeitgeber can also be used as a tool in combating metabolic disease. Shift work is known to induce acute insulin resistance, and appropriately timed exercise might improve health markers in shift workers who are at risk of metabolic disease. In this Review, we discuss the literature regarding diurnal skeletal muscle metabolism and the interaction with exercise bouts at different times of the day to combat metabolic disease.
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Affiliation(s)
- Brendan M Gabriel
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden.
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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14
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Dukler N, Booth GT, Huang YF, Tippens N, Waters CT, Danko CG, Lis JT, Siepel A. Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome Res 2017; 27:1816-1829. [PMID: 29025894 PMCID: PMC5668940 DOI: 10.1101/gr.222935.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022]
Abstract
Most studies of responses to transcriptional stimuli measure changes in cellular mRNA concentrations. By sequencing nascent RNA instead, it is possible to detect changes in transcription in minutes rather than hours and thereby distinguish primary from secondary responses to regulatory signals. Here, we describe the use of PRO-seq to characterize the immediate transcriptional response in human cells to celastrol, a compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory, and obesity-controlling effects. Celastrol is known to elicit a cellular stress response resembling the response to heat shock, but the transcriptional basis of this response remains unclear. Our analysis of PRO-seq data for K562 cells reveals dramatic transcriptional effects soon after celastrol treatment at a broad collection of both coding and noncoding transcription units. This transcriptional response occurred in two major waves, one within 10 min, and a second 40-60 min after treatment. Transcriptional activity was generally repressed by celastrol, but one distinct group of genes, enriched for roles in the heat shock response, displayed strong activation. Using a regression approach, we identified key transcription factors that appear to drive these transcriptional responses, including members of the E2F and RFX families. We also found sequence-based evidence that particular transcription factors drive the activation of enhancers. We observed increased polymerase pausing at both genes and enhancers, suggesting that pause release may be widely inhibited during the celastrol response. Our study demonstrates that a careful analysis of PRO-seq time-course data can disentangle key aspects of a complex transcriptional response, and it provides new insights into the activity of a powerful pharmacological agent.
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Affiliation(s)
- Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nathaniel Tippens
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Colin T Waters
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14850, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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15
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Maity SN. NF-Y (CBF) regulation in specific cell types and mouse models. Biochim Biophys Acta Gene Regul Mech 2016; 1860:598-603. [PMID: 27815195 DOI: 10.1016/j.bbagrm.2016.10.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/27/2016] [Accepted: 10/28/2016] [Indexed: 02/08/2023]
Abstract
The CCAAT-binding factor CBF/NF-Y is needed for cell proliferation and early embryonic development. NF-Y can regulate the expression of different cell type-specific genes that are activated by various physiological signaling pathways. Dysregulation of NF-Y was observed in pathogenic conditions in humans such as scleroderma, neurodegenerative disease, and cancer. Conditional inactivation of the NF-YA gene in mice demonstrated that NF-Y activity is essential for normal tissue homeostasis, survival, and metabolic function. Altogether, NF-Y is an essential transcription factor that plays a critical role in mammalian development, from the early stages to adulthood, and in human pathogenesis. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Sankar N Maity
- Department of Genitourinary Medical Oncology, David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.
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16
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Sachini N, Papamatheakis J. NF-Y and the immune response: Dissecting the complex regulation of MHC genes. Biochim Biophys Acta Gene Regul Mech 2017; 1860:537-42. [PMID: 27989934 DOI: 10.1016/j.bbagrm.2016.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/13/2022]
Abstract
Nuclear Factor Y (NF-Y) was first described as one of the CCAAT binding factors. Although CCAAT motifs were found to be present in various genes, NF-Y attracted a lot of interest early on, due to its role in Major Histocompatibility Complex (MHC) gene regulation. MHC genes are crucial in immune response and show peculiar expression patterns. Among other conserved elements on MHC promoters, an NF-Y binding CCAAT box was found to contribute to MHC transcriptional regulation. NF-Y along with other DNA binding factors assembles in a stereospecific manner to form a multiprotein scaffold, the MHC enhanceosome, which is necessary but not sufficient to drive transcription. Transcriptional activation is achieved by the recruitment of yet another factor, the class II transcriptional activator (CIITA). In this review, we briefly discuss basic findings on MHCII transcription regulation and we highlight NF-Y different modes of function in MHCII gene activation. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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17
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Zambelli F, Pavesi G. Genome wide features, distribution and correlations of NF-Y binding sites. Biochim Biophys Acta Gene Regul Mech 2016; 1860:581-589. [PMID: 27769808 DOI: 10.1016/j.bbagrm.2016.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 12/12/2022]
Abstract
NF-Y is a trimeric transcription factor that binds on DNA the CCAAT-box motif. In this article we reviewed and complemented with additional bioinformatic analysis existing data on genome-wide NF-Y binding characterization in human, reaching the following main conclusions: (1) about half of NF-Y binding sites are located at promoters, about 60-80 base pairs from transcription start sites; NF-Y binding to distal genomic regions takes place at inactive chromatin loci and/or DNA repetitive elements more often than active enhancers; (2) on almost half of its binding sites, regardless of their genomic localization (promoters or distal regions), NF-Y finds on DNA more than one CCAAT-box, and most of those multiple CCAAT binding loci present precise spacing and organization of the elements composing them; (3) there exists a well defined class of transcription factors that show genome-wide co-localization with NF-Y. Some of them lack their canonical binding site in binding regions overlapping with NF-Y, hence hinting at NF-Y mediated recruitment, while others show a precise positioning on DNA of their binding sites with respect to the CCAAT box bound by NF-Y. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Federico Zambelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy; Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Via Amendola 165/A, 70126, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy.
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18
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Dolfini D, Zambelli F, Pedrazzoli M, Mantovani R, Pavesi G. A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors. Nucleic Acids Res 2016; 44:4684-702. [PMID: 26896797 PMCID: PMC4889920 DOI: 10.1093/nar/gkw096] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/09/2016] [Indexed: 12/11/2022] Open
Abstract
NF-Y is a trimeric transcription factor (TF), binding the CCAAT box element, for which several results suggest a pioneering role in activation of transcription. In this work, we integrated 380 ENCODE ChIP-Seq experiments for 154 TFs and cofactors with sequence analysis, protein–protein interactions and RNA profiling data, in order to identify genome-wide regulatory modules resulting from the co-association of NF-Y with other TFs. We identified three main degrees of co-association with NF-Y for sequence-specific TFs. In the most relevant one, we found TFs having a significant overlap with NF-Y in their DNA binding loci, some with a precise spacing of binding sites with respect to the CCAAT box, others (FOS, Sp1/2, RFX5, IRF3, PBX3) mostly lacking their canonical binding site and bound to arrays of well spaced CCAAT boxes. As expected, NF-Y binding also correlates with RNA Pol II General TFs and with subunits of complexes involved in the control of H3K4 methylations. Co-association patterns are confirmed by protein–protein interactions, and correspond to specific functional categorizations and expression level changes of target genes following NF-Y inactivation. These data define genome-wide rules for the organization of NF-Y-centered regulatory modules, supporting a model of distinct categorization and synergy with well defined sets of TFs.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
| | - Federico Zambelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Via Amendola 165/A, 70126, Italy
| | - Maurizio Pedrazzoli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
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19
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Xu Z, Nayak DK, Benshoff N, Hachem R, Gelman AE, Mohanakumar T. De novo-developed antibodies to donor MHC antigens lead to dysregulation of microRNAs and induction of MHC class II. J Immunol 2015; 194:6133-43. [PMID: 25941328 DOI: 10.4049/jimmunol.1401848] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 04/03/2015] [Indexed: 01/09/2023]
Abstract
Immune responses to HLA and development of anti-donor HLA (DSA) were shown to play a role in chronic rejection following transplantation. We hypothesized that Abs to MHC change microRNAs (miRNAs), leading to chronic lung allograft rejection. Microarray analysis was performed in a murine model of anti-MHC-induced obliterative airway disease (OAD), a correlate of obliterative bronchiolitis. A unique profile of dysregulated miRNAs was detected in OAD mice on days 7 and 15 after Ab administration compared with control. Sixty-seven miRNAs were increased and 42 miRNAs were decreased in OAD mice on day 7. In addition, 15 miRNAs were overexpressed and 16 miRNAs were underexpressed in OAD mice on day 15. The expression of miR-16 and miR-195 was significantly decreased in lungs of OAD mice, as assessed by quantitative RT-PCR and in situ hybridization, with increases in H-2 Aa and H-2 Dma mRNA levels. Significant reductions in miR-16 and miR-195 levels were also noted in lung transplant (LTx) patients with DSA compared with LTx patients without DSA. Bioinformatic TargetScan and reporter assays identified the binding of miR-16 and miR-195 to the 3'-untranslated region of regulatory factor X 5. Quantitative PCR and immunohistochemistry indicated posttranscriptional increases in regulatory factor X 5 mRNA and protein expression in OAD mice, as well as in LTx recipients with DSA, which was associated with increased expression of HLA-DPA1, HLA-DQA1, and HLA-DRA mRNA. Therefore, our results demonstrated that miRNAs induced by alloimmunity may play important roles in chronic rejection after LTx.
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Affiliation(s)
- Zhongping Xu
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110
| | - Deepak K Nayak
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110
| | - Nicholas Benshoff
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110
| | - Ramsey Hachem
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Andrew E Gelman
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110
| | - Thalachallour Mohanakumar
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
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20
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Dashti HS, Smith CE, Lee YC, Parnell LD, Lai CQ, Arnett DK, Ordovás JM, Garaulet M. CRY1 circadian gene variant interacts with carbohydrate intake for insulin resistance in two independent populations: Mediterranean and North American. Chronobiol Int 2014; 31:660-7. [PMID: 24548145 DOI: 10.3109/07420528.2014.886587] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Dysregulation in the circadian system induced by variants of clock genes has been associated with type 2 diabetes. Evidence for the role of cryptochromes, core components of the system, in regulating glucose homeostasis is not supported by CRY1 candidate gene association studies for diabetes and insulin resistance in human, suggesting possible dietary influences. The purpose of this study was to test for interactions between a CRY1 polymorphism, rs2287161, and carbohydrate intake on insulin resistance in two independent populations: a Mediterranean (n = 728) and an European origin North American population (n = 820). Linear regression interaction models were performed in two populations to test for gene-diet interactions on fasting insulin and glucose and two insulin-related traits, homeostasis model assessment of insulin resistance (HOMA-IR) and quantitative insulin sensitivity check index (QUICKI). In addition, fixed effects meta-analyses for these interactions were performed. Cohort-specific interaction analyses showed significant interactions between the CRY1 variant and dietary carbohydrates for insulin resistance in both populations (p < 0.05). Findings from the meta-analyses of carbohydrate-single nucleotide polymorphism interactions indicated that an increase in carbohydrate intake (% of energy intake) was associated with a significant increase in HOMA-IR (p = 0.011), fasting insulin (p = 0.007) and a decrease in QUICKI (p = 0.028), only among individuals homozygous for the minor C allele. This novel finding supports the link between the circadian system and glucose metabolism and suggests the importance this CRY1 locus in developing personalized nutrition programs aimed at reducing insulin resistance and diabetes risk.
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Affiliation(s)
- Hassan S Dashti
- Nutrition and Genomics Laboratory, Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University , Boston, MA , USA
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Feng C, Zhang Y, Yin J, Li J, Abounader R, Zuo Z. Regulatory factor X1 is a new tumor suppressive transcription factor that acts via direct downregulation of CD44 in glioblastoma. Neuro Oncol 2014; 16:1078-85. [PMID: 24526308 DOI: 10.1093/neuonc/nou010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The biological functions of regulatory factor (RF)X1, a transcription factor, are not known. Since the RFX1 gene is often epigenetically silenced and clusters of differentiation (CD)44 proteins that regulate cancer cell biology are increased in human glioblastomas, we designed this study to determine whether RFX1 could regulate CD44 expression in glioblastoma. METHODS Regulatory factor X1 was overexpressed in 4 human glioblastoma cell lines. CD44 expression and cell proliferation, apoptosis, and invasion were assayed under in vitro conditions. In vivo growth of human glioblastoma xenografts was determined in mice. The expression of RFX1 and CD44 in human glioblastoma tissues was quantified. RESULTS A putative RFX1 binding sequence existed in the first exon of the human CD44 gene. The transcription activity of the DNA fragment containing this putative sequence was decreased in cells overexpressing RFX1. Regulatory factor X1 bound to the CD44 gene in glioblastoma cells. It reduced CD44 expression and activated Akt and extracellular signal-regulated kinase, signaling molecules downstream of CD44 to regulate cell proliferation and survival. Overexpression of RFX1 inhibited the survival, proliferation, and transwell invasion of glioblastoma cells and in vivo growth of human glioblastoma xenografts. CD44 overexpression reversed RFX1 effects on cell proliferation. Finally, CD44 protein levels were inversely correlated with RFX1 protein levels in human glioblastoma tissues. CONCLUSIONS These results suggest that RFX1 directly regulates CD44 expression. This mechanism may contribute to RFX1's effects on proliferation, survival, and invasion of glioblastoma cells. Our results provide initial evidence that RFX1 may be an important target/regulator of the malignancy of glioblastoma.
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Affiliation(s)
- Chenzhuo Feng
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA (C.F., J.Y., J.L., Z.Z.); Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA (Y.Z., R.A.); Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China (J.Y.); Department of Anesthesiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China (J.L.)
| | - Ying Zhang
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA (C.F., J.Y., J.L., Z.Z.); Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA (Y.Z., R.A.); Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China (J.Y.); Department of Anesthesiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China (J.L.)
| | - Jinbo Yin
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA (C.F., J.Y., J.L., Z.Z.); Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA (Y.Z., R.A.); Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China (J.Y.); Department of Anesthesiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China (J.L.)
| | - Jun Li
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA (C.F., J.Y., J.L., Z.Z.); Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA (Y.Z., R.A.); Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China (J.Y.); Department of Anesthesiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China (J.L.)
| | - Roger Abounader
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA (C.F., J.Y., J.L., Z.Z.); Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA (Y.Z., R.A.); Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China (J.Y.); Department of Anesthesiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China (J.L.)
| | - Zhiyi Zuo
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA (C.F., J.Y., J.L., Z.Z.); Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA (Y.Z., R.A.); Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China (J.Y.); Department of Anesthesiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China (J.L.)
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Abstract
Recent advances in technology have led to a dramatic increase in the number of available transcription factor ChIP-seq and ChIP-chip data sets. Understanding the motif content of these data sets is an important step in understanding the underlying mechanisms of regulation. Here we provide a systematic motif analysis for 427 human ChIP-seq data sets using motifs curated from the literature and also discovered de novo using five established motif discovery tools. We use a systematic pipeline for calculating motif enrichment in each data set, providing a principled way for choosing between motif variants found in the literature and for flagging potentially problematic data sets. Our analysis confirms the known specificity of 41 of the 56 analyzed factor groups and reveals motifs of potential cofactors. We also use cell type-specific binding to find factors active in specific conditions. The resource we provide is accessible both for browsing a small number of factors and for performing large-scale systematic analyses. We provide motif matrices, instances and enrichments in each of the ENCODE data sets. The motifs discovered here have been used in parallel studies to validate the specificity of antibodies, understand cooperativity between data sets and measure the variation of motif binding across individuals and species.
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Affiliation(s)
- Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA and Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02139, USA
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23
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Abstract
The CCAAT box promoter element and NF-Y, the transcription factor (TF) that binds to it, were among the first cis-elements and trans-acting factors identified; their interplay is required for transcriptional activation of a sizeable number of eukaryotic genes. NF-Y consists of three evolutionarily conserved subunits: a dimer of NF-YB and NF-YC which closely resembles a histone, and the "innovative" NF-YA. In this review, we will provide an update on the functional and biological features that make NF-Y a fundamental link between chromatin and transcription. The last 25 years have witnessed a spectacular increase in our knowledge of how genes are regulated: from the identification of cis-acting sequences in promoters and enhancers, and the biochemical characterization of the corresponding TFs, to the merging of chromatin studies with the investigation of enzymatic machines that regulate epigenetic states. Originally identified and studied in yeast and mammals, NF-Y - also termed CBF and CP1 - is composed of three subunits, NF-YA, NF-YB and NF-YC. The complex recognizes the CCAAT pentanucleotide and specific flanking nucleotides with high specificity (Dorn et al., 1997; Hatamochi et al., 1988; Hooft van Huijsduijnen et al, 1987; Kim & Sheffery, 1990). A compelling set of bioinformatics studies clarified that the NF-Y preferred binding site is one of the most frequent promoter elements (Suzuki et al., 2001, 2004; Elkon et al., 2003; Mariño-Ramírez et al., 2004; FitzGerald et al., 2004; Linhart et al., 2005; Zhu et al., 2005; Lee et al., 2007; Abnizova et al., 2007; Grskovic et al., 2007; Halperin et al., 2009; Häkkinen et al., 2011). The same consensus, as determined by mutagenesis and SELEX studies (Bi et al., 1997), was also retrieved in ChIP-on-chip analysis (Testa et al., 2005; Ceribelli et al., 2006; Ceribelli et al., 2008; Reed et al., 2008). Additional structural features of the CCAAT box - position, orientation, presence of multiple Transcriptional Start Sites - were previously reviewed (Dolfini et al., 2009) and will not be considered in detail here.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
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Lahat N, Bitterman H, Engelmayer-Goren M, Rosenzweig D, Weiss-Cerem L, Rahat MA. Reduced TIMP-2 in hypoxia enhances angiogenesis. Am J Physiol Cell Physiol 2010; 300:C557-66. [PMID: 21148412 DOI: 10.1152/ajpcell.00177.2010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hypoxia, which characterizes ischemia, trauma, inflammation, and solid tumors, recruits monocytes, immobilizes them, and alters their function, leading to an anti-inflammatory and proangiogenic phenotype. Monocyte extravasation from the circulation and their migration in tissues are partially mediated by the balance between matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs). The mechanisms evoked by hypoxia that regulate monocyte migration and activation are not entirely clear. Specifically, the effect of hypoxia on TIMPs in these cells has hardly been investigated. We show that hypoxia reduces TIMP-2 secretion from human primary monocytes and from the monocyte-like cell lines U937 and THP-1 by three- to fourfold (P < 0.01), by inhibiting TIMP-2 transcription through mechanisms that involve the transcription factor SP-1. Hypoxia also lowers TIMP-2 protein secretion from human endothelial cells (by 2-fold, P < 0.05). TIMP-2 levels do not influence the reduced migration of THP-1 cells in hypoxia; however, low TIMP-2 levels enhance endothelial cell migration/proliferation, their ability to form tubelike structures in vitro, and the appearance of mature blood vessels in a Matrigel plug assay in vivo. Thus we conclude that reduced TIMP-2 levels secreted from both hypoxic monocytes and endothelial cells are proangiogenic.
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Affiliation(s)
- Nitza Lahat
- Immunology Research Unit, Carmel Medical Ctr., 7 Michal St., Haifa 34362, Israel.
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25
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Laird KM, Briggs LL, Boss JM, Summers MF, Garvie CW. Solution structure of the heterotrimeric complex between the interaction domains of RFX5 and RFXAP from the RFX gene regulatory complex. J Mol Biol 2010; 403:40-51. [PMID: 20732328 DOI: 10.1016/j.jmb.2010.08.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/16/2010] [Accepted: 08/12/2010] [Indexed: 11/20/2022]
Abstract
The mammalian immune response is mediated by a heterotetrameric transcriptional control complex, called regulatory factor X (RFX), that regulates the expression of major histocompatibility complex class II genes. RFX comprises three proteins: RFX5 (two copies), RFXAP, and RFXB, and mutations and deletions that prevent the assembly of the RFX complex have been linked to a severe immunodeficiency disorder. Two RFX5 molecules and one RFXAP molecule assemble in the cytoplasm prior to nuclear localization, a process mediated by an N-terminal "dimerization domain" of RFX5 (RFX5(N)) and a C-terminal domain of RFXAP (RFXAP(C)). We previously presented evidence that RFXAP(C) is unstructured in the absence of RFX5(N) but adopts a regular structure in the RFX5(N)(2)-RFXAP(C) complex and that the RFX5(N)(2)-RFXAP(C) complex binds RFXB with high affinity. We now report the structure of the RFX5(N)(2)-RFXAP(C) complex, determined in solution by (15)N- and (13)C-edited NMR spectroscopy. RFX5(N) consists of a long central helix flanked by two shorter helices. The central helices of the two RFX5(N) molecules form an antiparallel coiled coil, and the flanking helices pack at the ends of the long helices in a perpendicular arrangement such that the RFX5(N) dimer is shaped like a staple. RFXAP(C) consists of two α-helices that form a V-shaped structure that packs within the RFX5(N)(2) staple. Leucine residues in the leucine-rich region of RFX5(N) (62-LYLYLQL-68) that are critical for major histocompatibility complex class II gene expression in vivo contribute to both the dimer (Leu64 and Leu68) and the RFX5(N)-RFXAP(C) interfaces (Leu62 and Leu66). The clustering of hydrophobic residues from different regions of RFXAP(C) suggests a potential binding site for RFXB.
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Chakraborty M, Sengupta A, Bhattacharya D, Banerjee S, Chakrabarti A. DNA binding domain of RFX5: interactions with X-box DNA and RFXANK. Biochim Biophys Acta 2010; 1804:2016-24. [PMID: 20637319 DOI: 10.1016/j.bbapap.2010.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 06/30/2010] [Accepted: 07/03/2010] [Indexed: 11/15/2022]
Abstract
Regulatory factor X (RFX) is a heterotrimeric protein complex having RFX5, RFXANK and RFXAP as its three subunits. It is involved in the regulation of the transcription of MHCII molecules in antigen presenting cells. The RFX complex binds to X-box DNA, using the DNA binding domain, present in RFX5. The DNA binding domain (DBD) of RFX5 (12kD) and intact RFXANK (35 kD) were subcloned, expressed and purified. The associations of RFX5DBD with the X-box DNA and between RFX5DBD and RFXANK were measured in this study. The interaction of RFX5DBD and X-box DNA was studied using steady state fluorescence quenching and circular dichroism. The binding dissociation constant (K(d)) of the DNA-protein complex was determined from fluorescence measurements. The van't Hoff plot was linear over the temperature range 10-25 degrees C and the binding was found to be entropy-driven and enthalpy-favorable. The effect of electrolytes in RFX5DBD-DNA association was also studied. Molecular association between RFX5DBD and RFXANK has been observed by fluorescence resonance energy transfer (FRET) measurements, changes in the ratio of the two vibronic intensities of pyrene labeled RFX5DBD in presence of RFXANK and chemical cross-linking followed by tandem mass spectrometry. Results showed that the two proteins could interact in the absence of the third subunit RFXAP, in vitro with an apparent dissociation constant (K(d)) of 128 nM.
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Affiliation(s)
- Madhumita Chakraborty
- Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
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27
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Yu FX, Luo Y. Tandem ChoRE and CCAAT motifs and associated factors regulate Txnip expression in response to glucose or adenosine-containing molecules. PLoS One 2009; 4:e8397. [PMID: 20027290 PMCID: PMC2791861 DOI: 10.1371/journal.pone.0008397] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 11/30/2009] [Indexed: 12/18/2022] Open
Abstract
Background Thioredoxin interacting protein (Txnip) is a multifunctional protein involved in regulation of cell cycle events and cellular metabolism. The expression of Txnip is known to be induced by glucose, adenosine-containing molecules, and other physiological cues; however, the underlying regulatory mechanisms remain elusive. Methodology/Principal Findings In this study, using promoter reporter, electrophoresis mobility shift (EMSA), and chromatin immuno-precipitation (ChIP) assays, we have identified an additional carbohydrate response element (ChoRE) on the promoter of Txnip gene, which functions cooperatively with the earlier identified ChoRE to mediate optimal Txnip expression. However, these two ChoREs are not sufficient to mediate the induction of Txnip expression by glucose or adenosine-containing molecules; and two CCAAT boxes, both of which can recruit nuclear factor Y (NF-Y) to the Txnip promoter, are also required for the induction. Accordingly, we have found that the function of ChoREs and associated factors is contingent on tandem CCAAT boxes, in that occupancy of the Txnip promoter by NF-Y is a prerequisite for efficacious recruitment of Mondo/MLX to ChoREs under glucose stimulation. Conclusions/Significance Our findings suggest a synergy between the tandem CCAAT and ChoRE motifs and associated NF-Y and Mondo/MLX transcription factors in enhancing transcription from the Txnip promoter. This piece of information will be helpful for future dissection of molecular mechanisms governing the transcriptional regulation of Txnip, a glucose responsive gene.
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Affiliation(s)
- Fa-Xing Yu
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Yan Luo
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
- * E-mail:
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28
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Briggs L, Laird K, Boss JM, Garvie CW. Formation of the RFX gene regulatory complex induces folding of the interaction domain of RFXAP. Proteins 2009; 76:655-64. [PMID: 19274739 DOI: 10.1002/prot.22379] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Major histocompatibility complex class II (MHCII) molecules have a central role in the mammalian adaptive immune response against infection. The level of the immune response is directly related to the concentration of MHCII molecules in the cell, which have a central role in initiating the immune response. MHCII molecules are therefore a potential target for the development of immunosuppressant drugs for the treatment of organ transplant rejection and autoimmune disease. The expression of MHCII molecules is regulated by a cell specific multiprotein complex. The RFX complex is the key DNA binding component of this complex. The RFX complex is composed of three proteins-RFX5, RFXAP, and RFXB-all of which are required for activation of expression of the MHCII genes. Little is currently known about the precise regions of the RFX proteins that are required for complex formation, or their structure. We have therefore identified the key regions of RFX5, RFXAP, and RFXB, which are required to form the RFX complex and have characterized the individual domains and the complexes they form using NMR and circular dichroism spectroscopy and isothermal titration calorimetry. Our results support a model for the assembly of the RFX complex in which the interaction between RFX5 and RFXAP promote folding of a poorly structured region ofRFXAP, which is required for high affinity binding of RFXB to the RFX5.RFXAP complex.
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Affiliation(s)
- LaTese Briggs
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141, USA
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29
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Abstract
Pathogenic bacteria and their hosts have had a two-way conversation for millions of years. This interaction has led to many measure/counter-measure responses by the host and bacteria. The host immune response has developed many mechanisms to neutralize and remove pathogen bacteria. In turn pathogenic bacteria have developed mechanisms to alter and evade the host immune response. We will review some of the mechanisms utilized by bacteria to accomplish this goal. We will also examine the current state of understanding of Francisella tularensis mediated immune evasion.
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Affiliation(s)
- Matthew D Woolard
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7290, USA
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30
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Aftab S, Semenec L, Chu JSC, Chen N. Identification and characterization of novel human tissue-specific RFX transcription factors. BMC Evol Biol 2008; 8:226. [PMID: 18673564 PMCID: PMC2533330 DOI: 10.1186/1471-2148-8-226] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 08/01/2008] [Indexed: 02/06/2023] Open
Abstract
Background Five regulatory factor X (RFX) transcription factors (TFs)–RFX1-5–have been previously characterized in the human genome, which have been demonstrated to be critical for development and are associated with an expanding list of serious human disease conditions including major histocompatibility (MHC) class II deficiency and ciliaophathies. Results In this study, we have identified two additional RFX genes–RFX6 and RFX7–in the current human genome sequences. Both RFX6 and RFX7 are demonstrated to be winged-helix TFs and have well conserved RFX DNA binding domains (DBDs), which are also found in winged-helix TFs RFX1-5. Phylogenetic analysis suggests that the RFX family in the human genome has undergone at least three gene duplications in evolution and the seven human RFX genes can be clearly categorized into three subgroups: (1) RFX1-3, (2) RFX4 and RFX6, and (3) RFX5 and RFX7. Our functional genomics analysis suggests that RFX6 and RFX7 have distinct expression profiles. RFX6 is expressed almost exclusively in the pancreatic islets, while RFX7 has high ubiquitous expression in nearly all tissues examined, particularly in various brain tissues. Conclusion The identification and further characterization of these two novel RFX genes hold promise for gaining critical insight into development and many disease conditions in mammals, potentially leading to identification of disease genes and biomarkers.
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Affiliation(s)
- Syed Aftab
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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31
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vanWert JM, Wolfe SA, Grimes SR. Binding of RFX2 and NF-Y to the testis-specific histone H1t promoter may be required for transcriptional activation in primary spermatocytes. J Cell Biochem 2008; 104:1087-101. [DOI: 10.1002/jcb.21694] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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32
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Krawczyk M, Leimgruber E, Seguín-Estévez Q, Dunand-Sauthier I, Barras E, Reith W. Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes. Nucleic Acids Res 2006; 35:595-605. [PMID: 17175541 PMCID: PMC1802633 DOI: 10.1093/nar/gkl980] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The small GTPase RAB4 regulates endocytic recycling, a process that contributes to Major Histocompatibility Complex (MHC)-mediated antigen presentation by specialized antigen presenting cells (APC) of the immune system. The gene encoding the RAB4B isoform of RAB4 was singled out by two complementary genome-wide screens. One of these consisted of a computer scan to identify genes containing characteristic MHC class II-related regulatory sequences. The second was the use of chromatin immunoprecipitation coupled to microarrays (ChIP-on-chip) to identify novel targets of a transcriptional co-activator called the MHC class II transactivator (CIITA). We show that the RAB4B gene is regulated by a typical MHC class II-like enhancer that is controlled directly by both CIITA and the multiprotein transcription factor complex known as the MHC class II enhanceosome. RAB4B expression is thus activated by the same regulatory machinery that is known to be essential for the expression of MHC class II genes. This molecular link between the transcriptional activation of RAB4B and MHC class II genes implies that APC boost their antigen presentation capacity by increasing RAB4-mediated endocytic recycling.
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Affiliation(s)
| | | | | | | | | | - Walter Reith
- To whom correspondence should be addressed. Tel: +41 22 379 56 66; Fax: +41 22 379 57 46;
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Ben-Naim O, Eshed R, Parnis A, Teper-Bamnolker P, Shalit A, Coupland G, Samach A, Lifschitz E. The CCAAT binding factor can mediate interactions between CONSTANS-like proteins and DNA. Plant J 2006; 46:462-76. [PMID: 16623906 DOI: 10.1111/j.1365-313x.2006.02706.x] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
CONSTANS-Like (COL) proteins are plant-specific nuclear regulators of gene expression but do not contain a known DNA-binding motif. We tested whether a common DNA-binding protein can deliver these proteins to specific cis-acting elements. We screened for proteins that interact with two members of a subgroup of COL proteins. These COL proteins were Tomato COL1 (TCOL1), which does not seem to be involved in the control of flowering time, and the Arabidopsis thaliana CONSTANS (AtCO) protein which mediates photoperiodic induction of flowering. We show that the C-terminal plant-specific CCT (CO, CO-like, TIMING OF CAB EXPRESSION 1) domain of both proteins binds the trimeric CCAAT binding factor (CBF) via its HAP5/NF-YC component. Chromatin immunoprecipitation demonstrated that TCOL is recruited to the CCAAT motifs of the yeast CYC1 and HEM1 promoters by HAP5. In Arabidopsis, each of the three CBF components is encoded by several different genes that are highly transcribed. Under warm long days, high levels of expression of a tomato HAP5 (THAP5a) gene can reduce the flowering time of Arabidopsis. A mutation in the CCT domain of TCOL1 disrupts the interaction with THAP5 and the analogous mutation in AtCO impairs its function and delays flowering. CBFs are therefore likely to recruit COL proteins to their DNA target motifs in planta.
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Affiliation(s)
- Orna Ben-Naim
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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34
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Niesen MI, Osborne AR, Yang H, Rastogi S, Chellappan S, Cheng JQ, Boss JM, Blanck G. Activation of a methylated promoter mediated by a sequence-specific DNA-binding protein, RFX. J Biol Chem 2005; 280:38914-22. [PMID: 16166088 DOI: 10.1074/jbc.m504633200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The roles of eukaryotic DNA methylation in the repression of mRNA transcription and in the formation of heterochromatin have been extensively elucidated over the past several years. However, the role of DNA methylation in transcriptional activation remains a mystery. In particular, it is not known whether the transcriptional activation of methylated DNA is promoter-specific, depends directly on sequence-specific DNA-binding proteins, or is facilitated by the methylation. Here we report that the sequence-specific DNA-binding protein, RFX, previously shown to mediate the transition from an inactive to an active chromatin structure, activates a methylated promoter. RFX is capable of mediating enhanceosome formation on a methylated promoter, thereby mediating a transition from a methylation-dependent repression of the promoter to a methylation-dependent activation of the promoter. These results indicate novel roles for DNA methylation and sequence-specific DNA-binding proteins in transcriptional activation.
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Affiliation(s)
- Melissa I Niesen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Florida, Tampa, Florida 33612, USA
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Kabe Y, Yamada J, Uga H, Yamaguchi Y, Wada T, Handa H. NF-Y is essential for the recruitment of RNA polymerase II and inducible transcription of several CCAAT box-containing genes. Mol Cell Biol 2005; 25:512-22. [PMID: 15601870 PMCID: PMC538762 DOI: 10.1128/mcb.25.1.512-522.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Osteoclast differentiation factor (ODF)/receptor activator of NF-kappaB ligand is essential for inducing the differentiation of mature osteoclasts. We find that nuclear factor Y (NF-Y) binds to the CCAAT box on the ODF promoter and regulates its basal transcriptional activity. The CCAAT box on the ODF gene is required for its transcriptional induction by vitamin D3, suggesting that NF-Y coregulates this promoter along with VDR. Chromatin immunoprecipitation analysis reveals that NF-Y is required for the recruitment of RNA polymerase II (RNAPII) and TATA box binding protein on the ODF promoter. Stimulation with vitamin D3 facilitates the recruitment of VDR and p300 onto the ODF promoter, resulting in acetylation of histone H4 in an NF-Y-independent manner. ODF gene induction by parathyroid hormone or prostaglandin E is also dependent on NF-Y. Furthermore, NF-Y is essential for the recruitment of RNAPII onto other CCAAT box-containing promoters, such as those of osteopontin, CYP24, and E2F1. These results suggest that NF-Y recruits RNAPII and general transcription factors onto various CCAAT box-containing promoters in response to various inductions to permit strong transcriptional activation independently of histone modifications.
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Affiliation(s)
- Yasuaki Kabe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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Hjerrild M, Stensballe A, Rasmussen TE, Kofoed CB, Blom N, Sicheritz-Ponten T, Larsen MR, Brunak S, Jensen ON, Gammeltoft S. Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. J Proteome Res 2004; 3:426-33. [PMID: 15253423 DOI: 10.1021/pr0341033] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation plays a key role in cell regulation and identification of phosphorylation sites is important for understanding their functional significance. Here, we present an artificial neural network algorithm: NetPhosK (http://www.cbs.dtu.dk/services/NetPhosK/) that predicts protein kinase A (PKA) phosphorylation sites. The neural network was trained with a positive set of 258 experimentally verified PKA phosphorylation sites. The predictions by NetPhosK were validated using four novel PKA substrates: Necdin, RFX5, En-2, and Wee 1. The four proteins were phosphorylated by PKA in vitro and 13 PKA phosphorylation sites were identified by mass spectrometry. NetPhosK was 100% sensitive and 41% specific in predicting PKA sites in the four proteins. These results demonstrate the potential of using integrated computational and experimental methods for detailed investigations of the phosphoproteome.
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Affiliation(s)
- Majbrit Hjerrild
- Department of Clinical Biochemistry, Glostrup Hospital, Nordre Ringvej 57, DK-2600 Glostrup, Denmark.
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37
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Abstract
Major histocompatibility complex (MHC) class II deficiency is a primary immunodeficiency. Lentiviral vectors are used for gene therapy in a mouse model of this disease. In addition, by a direct genetic correction approach, a diagnostic test to determine which of the four MHC II genes is defective in new MHC II-deficiency patients has been optimized.
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Affiliation(s)
- Franck Matheux
- Immunology and Transplant Unit, Division of Immunology and Allergology, Geneva University Hospital, 1211 Geneva 4, Switzerland
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Challacombe JF, Rechtsteiner A, Gottardo R, Rocha LM, Browne EP, Shenk T, Altherr MR, Brettin TS. Evaluation of the host transcriptional response to human cytomegalovirus infection. Physiol Genomics 2004; 18:51-62. [PMID: 15069167 DOI: 10.1152/physiolgenomics.00155.2003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gene expression data from human cytomegalovirus (HCMV)-infected cells were analyzed using DNA-Chip Analyzer (dChip) followed by singular value decomposition (SVD) and compared with a previous analysis of the same data that employed GeneChip software and a fold change filtering approach. dChip and SVD analysis revealed two clusters of coexpressed human genes responding differently to HCMV infection: one containing some genes identified previously, and another that was largely unique to this analysis. Annotating these genes, we identified several functional categories important to host cell responses to HCMV infection. These categories included genes involved in transcriptional regulation, oncogenesis, and cell cycle regulation, which were more prevalent in cluster 1, and genes involved in immune system regulation, signal transduction, and cell adhesion, which were more prevalent in cluster 2. Within these categories, we found genes involved in the host response to HCMV infection (mainly in cluster 1), as well as genes targeted by HCMV’s immune evasion strategies (mainly in cluster 2). As the second group of genes identified by the dChip and SVD approach was statistically and biologically significant, our results point out the advantages of using different methods to analyze gene expression data.
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Affiliation(s)
- Jean F Challacombe
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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39
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Osborne AR, Zhang H, Fejer G, Palubin KM, Niesen MI, Blanck G. Oct-1 maintains an intermediate, stable state of HLA-DRA promoter repression in Rb-defective cells: an Oct-1-containing repressosome that prevents NF-Y binding to the HLA-DRA promoter. J Biol Chem 2004; 279:28911-9. [PMID: 15105429 DOI: 10.1074/jbc.m403118200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cell surface HLA-DR molecule binds foreign peptide antigen and forms an intercellular complex with the T cell receptor in the course of the development of an immune response against or immune tolerance to the antigen represented by the bound peptide. The HLA-DR molecule also functions as a receptor that mediates cell signaling pathways, including as yet poorly characterized pathway(s) leading to apoptosis. Expression of HLA-DR mRNA and protein is ordinarily inducible by interferon-gamma but is not inducible in tumor cells defective for the retinoblastoma tumor suppressor protein (Rb). In the case of the HLA-DRA gene, which encodes the HLA-DR heavy chain, previous work has indicated that this loss of inducibility is attributable to Oct-1 binding to the HLA-DRA promoter. In this report, we used Oct-1 antisense transformants to determine that Oct-1 represses the interferon-gamma response of the endogenous HLA-DRA gene. This determination is consistent with results from a chromatin immunoprecipitation assay, indicating that Oct-1 occupies the endogenous HLA-DRA promoter when the HLA-DRA promoter is inactive in Rb-defective cells but not when the promoter is converted to a previously defined, transcriptionally competent state, induced by treatment of the Rb-defective cells with the HDAC inhibitor, trichostatin A. In vitro DNA-protein binding analyses indicated that Oct-1 prevents HLA-DRA promoter activation by mediating the formation of a complex of proteins, termed DRAN (DRA negative), that blocks NF-Y access to the promoter.
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Affiliation(s)
- Aaron R Osborne
- Department of Biochemistry, College of Medicine, University of South Florida, Tampa, FL 33612, USA
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40
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Matheux F, Ikinciogullari A, Zapata DA, Barras E, Zufferey M, Dogu F, Regueiro JR, Reith W, Villard J. Direct genetic correction as a new method for diagnosis and molecular characterization of MHC class II deficiency. Mol Ther 2002; 6:824-9. [PMID: 12498778 DOI: 10.1006/mthe.2002.0804] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Major histocompatibility complex class II (MHCII) deficiency is a primary immunodeficiency resulting from defects in one of four different MHCII-specific transcription factors-CIITA, RFX5, RFXAP, and RFXANK. Despite this genetic heterogeneity, the phenotypical manifestations are homogeneous. It is frequently difficult to establish a definitive diagnosis of the disease on the basis of clinical and immunological criteria. Moreover, the phenotypical homogeneity precludes unambiguous identification of the regulatory gene that is affected. Identification of the four genes mutated in the disease has now allowed us to develop a rapid and straightforward diagnostic test for new MHCII-deficiency patients. This test is based on direct correction of the genetic defect by transduction of cells from patients with lentiviral vectors encoding CIITA, RFXANK, RFX5, or RFXAP. We have validated this approach by defining the molecular defects in two new patients. The RFXANK vector restored MHCII expression in a T cell line from one patient. The RFXAP vector corrected primary cells (PBL) from a second patient. Molecular analysis confirmed the presence of homozygous mutations in the RFXANK and RFXAP genes, respectively. Direct genetic correction represents a valuable tool for the diagnosis and classification of new MHCII-deficiency patients.
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Affiliation(s)
- Franck Matheux
- Department of Genetics and Microbiology, University of Geneva Medical School, Geneva, Switzerland
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41
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Nekrep N, Jabrane-Ferrat N, Wolf HM, Eibl MM, Geyer M, Peterlin BM. Mutation in a winged-helix DNA-binding motif causes atypical bare lymphocyte syndrome. Nat Immunol 2002; 3:1075-81. [PMID: 12368908 DOI: 10.1038/ni840] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2002] [Accepted: 08/26/2002] [Indexed: 11/08/2022]
Abstract
Bare lymphocyte syndrome (BLS) is an autosomal recessive severe-combined immunodeficiency that can result from mutations in four different transcription factors that regulate the expression of major histocompatibility complex (MHC) class II genes. We have identified here the defective gene that is responsible for the phenotype of the putative fifth BLS complementation group. The mutation was found in the regulatory factor that binds X-box 5 (RFX5) and was mapped to one of the arginines in a DNA-binding surface of this protein. Its wild-type counterpart restored binding of the RFX complex to DNA, transcription of all MHC class II genes and the appearance of these determinants on the surface of BLS cells.
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Affiliation(s)
- Nada Nekrep
- Department of Medicine, Rosalind Russell Medical Research Center, University of California, San Francisco, CA 94143-0703, USA
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Caruso ML, Litzka O, Martic G, Lottspeich F, Brakhage AA. Novel basic-region helix-loop-helix transcription factor (AnBH1) of Aspergillus nidulans counteracts the CCAAT-binding complex AnCF in the promoter of a penicillin biosynthesis gene. J Mol Biol 2002; 323:425-39. [PMID: 12381299 DOI: 10.1016/s0022-2836(02)00965-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cis-acting CCAAT elements are found frequently in eukaryotic promoter regions. Many of the genes containing such elements in their promoters are regulated by a conserved multimeric CCAAT-binding complex. In the fungus Emericella (Aspergillus) nidulans, this complex was designated AnCF (A.nidulans CCAAT-binding factor). AnCF regulates several genes, including the penicillin biosynthesis genes ipnA and aatA. Since it is estimated that the CCAAT-binding complex regulates more than 200 genes, an important question concerns the regulation mechanism that allows so many genes to be regulated by a single complex in a gene-specific manner. One of the answers to this question appears to lie in the interaction of AnCF with other transcription factors. Here, a novel transcription factor designated AnBH1 was isolated. The corresponding anbH1 gene was cloned and found to be located on chromosome IV. The deduced AnBH1 protein belongs to the family of basic-region helix-loop-helix (bHLH) transcription factors. AnBH1 binds in vitro as a homodimer to an, not previously described, asymmetric E-box within the aatA promoter that overlaps with the AnCF-binding site. This is the first report demonstrating that the CCAAT-binding complex and a bHLH transcription factor bind to overlapping sites. Since deletion of anbH1 appears to be lethal, the anbH1 gene was replaced by a regulatable alcAp-anbH1 gene fusion. The analysis of aatAp-lacZ expression in such a strain indicated that AnBH1 acts as a repressor of aatA gene expression and therefore counteracts the positive action of AnCF.
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Affiliation(s)
- Maria Louise Caruso
- Institut für Mikrobiologie, Universität Hannover, Schneiderberg 50, 30167 Hannover, Germany
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43
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Abstract
The class II transactivator (CIITA) is a potent and critical transcriptional regulator. It activates genes necessary for antigen presentation function. It also regulates cytokine gene expression in CD4 T cells. We recently found that CIITA prevents cell death by inhibiting Fas ligand (FasL) gene expression. Thus, CIITA regulates multiple immune responses. The activation and the repression function of CIITA are mediated by its interaction with other transcription factors. To activate the target gene, CIITA interacts with DNA binding proteins and recruits the coactivator CBP/p300 to the promoter forming an enhanceosome necessary for transcription. In addition, CIITA interacts with self. Inter- and intramolecular interactions of CIITA are essential for transactivation function. Each domain of CIITA has a distinct role and all domains are required for CIITA activity. However, the regulatory mechanisms of CIITA interaction with self and other proteins are poorly understood and remain to be investigated.
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Affiliation(s)
- Cheong-Hee Chang
- Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor 48109-0620, USA.
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44
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Jabrane-Ferrat N, Nekrep N, Tosi G, Esserman LJ, Peterlin BM. Major histocompatibility complex class II transcriptional platform: assembly of nuclear factor Y and regulatory factor X (RFX) on DNA requires RFX5 dimers. Mol Cell Biol 2002; 22:5616-25. [PMID: 12101253 PMCID: PMC133954 DOI: 10.1128/mcb.22.15.5616-5625.2002] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major histocompatibility complex class II (MHC-II) genes are regulated in a B-cell-specific and gamma interferon-inducible manner. Conserved upstream sequences (CUS) in their compact promoters bind nuclear factor Y (NFY) and regulatory factor X (RFX) complexes. These DNA-bound proteins form a platform that attracts the class II transactivator, which initiates and elongates MHC-II transcription. In this report, we analyzed the complex assembly of these DNA-bound proteins. First, we found that NFY can interact with RFX in cells. In particular, NFYA and NFYC bound RFXANK/B in vitro. Next, RFX5 formed dimers in vivo and in vitro. Within a leucine-rich stretch N-terminal to the DNA-binding domain in RFX5, the leucine at position 66 was found to be critical for this self-association. Mutant RFX5 proteins that could not form dimers also did not support the formation of higher-order DNA-protein complexes on CUS in vitro or MHC-II transcription in vivo. We conclude that the MHC-II transcriptional platform begins to assemble off CUS and then binds DNA via multiple, spatially constrained interactions. These findings offer one explanation of why in the Bare Lymphocyte Syndrome, which is a congenital severe combined immunodeficiency, MHC-II promoters are bare when any subunit of RFX is mutated or missing.
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Affiliation(s)
- Nabila Jabrane-Ferrat
- Department of Surgery, University of California-San Francisco, San Francisco, CA 94115-0703, USA
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45
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Abstract
The transcription start site of the collagen alpha2(1) gene (COL1A2) has a sequence-specific binding site for a DNA methylation-responsive binding protein called regulatory factor for X-box 1 (RFX1) (Sengupta, P. K., Erhlich, M., and Smith, B. D. (1999) J. Biol. Chem. 274, 36649-36655). In this report, we demonstrate that RFX1 forms homodimers as well as heterodimers with RFX2 spanning the collagen transcription start site. Methylation at +7 on the coding strand increases RFX1 complex formation in gel shift assays. Methylation on the template strand, however, does not increase RFX1 complex formation. DNA from human fibroblasts contains minimal methylation on the coding strand (<4%) with variable methylation on the template strand. RFX1 acts as a repressor of collagen transcription as judged by in vitro transcription and co-transfection assays with an unmethylated collagen promoter-reporter construct. In addition, an RFX5 complex present in human fibroblasts interacts with the collagen RFX site, which is not sensitive to methylation. This is the first demonstration of RFX5 complex formation on a gene other than major histocompatibility complex (MHC) promoters. Also, RFX5 represses transcription of a collagen promoter-reporter construct in rat fibroblasts that have no detectable RFX5 complex formation or protein. RFX5 complex activates MHC II transcription by interacting with an interferon-gamma (IFN-gamma)-inducible protein, major histocompatibility class II trans-activator (CIITA). Collagen transcription is repressed by IFN-gamma in a dose-dependent manner in human but not in rat fibroblasts. IFN-gamma enhances RFX5 binding activity, and CIITA is present in the RFX5 complex of IFN-gamma-treated human fibroblasts. CIITA repressed collagen gene transcription more effectively in human fibroblasts than in rat fibroblasts, suggesting that the RFX5 complex may, in part, recruit CIITA protein to the collagen transcription start site. Thus the RFX family may be important repressors of collagen gene transcription through a RFX binding site spanning the transcription start site.
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Affiliation(s)
- Pritam K Sengupta
- Department of Biochemistry, Boston University School of Medicine, Massachusetts 02118, USA
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46
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Affiliation(s)
- Ling Shao
- Division of Clinical Immunology, Mount Sinai School of Medicine, New York, New York 10029, USA
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47
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Morotomi-Yano K, Yano KI, Saito H, Sun Z, Iwama A, Miki Y. Human regulatory factor X 4 (RFX4) is a testis-specific dimeric DNA-binding protein that cooperates with other human RFX members. J Biol Chem 2002; 277:836-42. [PMID: 11682486 DOI: 10.1074/jbc.m108638200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Regulatory factor X (RFX) members are evolutionarily conserved transcription factors that share a highly conserved winged helix DNA-binding domain. Human RFX4 has been isolated from breast cancer as a partial cDNA encoding a short RFX-type DNA-binding domain fused to the estrogen receptor, but the entire structure of RFX4 has been unknown. Here, we report the molecular cloning and characterization of human RFX4. RFX4 contains evolutionarily conserved regions, including a RFX-type DNA-binding domain, a dimerization domain, and other conserved regions, and is closely related to RFX1, RFX2, and RFX3 in structure. The expression of RFX4 is restricted to testis. In vitro synthesized RFX4 protein bound to typical RFX binding sites in a sequence-dependent manner. Immunoprecipitation analyses showed that RFX4 interacts physically with RFX2, RFX3, and RFX4 itself but not with RFX1. In contrast to other mammalian RFX members that form dimers, RFX4 is revealed to have no distinct transcriptional activation domains. By using a chimeric protein of RFX1 and RFX4, the C-terminal domain of RFX4 was shown to be a possible transcriptional repression domain. Taken together, these results indicate that RFX4 is the first mammalian member of RFX family without transcriptional activation capacity and might function through selective interactions with other RFX members in transcriptional regulation.
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Affiliation(s)
- Keiko Morotomi-Yano
- Department of Molecular Diagnosis, Cancer Institute, Japanese Foundation for Cancer Research, 1-37-1 Kami-ikebukuro, Toshima-ku, Tokyo 170-8455, Japan
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48
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Liberati C, Cera MR, Secco P, Santoro C, Mantovani R, Ottolenghi S, Ronchi A. Cooperation and competition between the binding of COUP-TFII and NF-Y on human epsilon- and gamma-globin gene promoters. J Biol Chem 2001; 276:41700-9. [PMID: 11544252 DOI: 10.1074/jbc.m102987200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The nuclear receptor COUP-TFII was recently shown to bind to the promoter of the epsilon- and gamma-globin genes and was identified as the nuclear factor NF-E3. Transgenic experiments and genetic evidence from humans affected with hereditary persistence of fetal hemoglobin suggest that NF-E3 may be a repressor of adult epsilon and gamma expression. We show that, on the epsilon-promoter, recombinant COUP-TFII binds to two sites, the more downstream of which overlaps with an NF-Y binding CCAAT box. Binding occurs efficiently to either the 5' or the 3' COUP-TFII site but not to both sites simultaneously. However, adding recombinant NF-Y induces the formation of a stable COUP-TFII.NF-Y-promoter complex at concentrations of COUP-TFII that would not give significant binding in the absence of NF-Y. Mutations of the promoter indicate that COUP-TFII cooperates with NF-Y when bound to the 5' site, whereas binding at the 3' site is mutually exclusive. Likewise, in the gamma-promoter, COUP-TFII binds to a site overlapping the distal member of a duplicated CCAAT box, competing with NF-Y binding. Transfections in K562 cells show that both the mutation of the 5' COUP-TFII or of the NF-Y site on the epsilon-promoter decrease the activity of a luciferase reporter; the mutation of the 3' COUP-TFII site has little effect. These results, together with transgenic experiments suggesting a repressive activity of COUP-TFII on the epsilon-promoter and the observation that, on the 3' site, COUP-TFII and NF-Y binding is mutually exclusive, suggest that COUP-TFII may exert different effects on epsilon transcription depending on whether it binds to the 5' or to the 3' site. At the 5' site, COUP-TFII might cooperate with NF-Y, forming a stable complex, and stimulate transcription; at the 3' site, COUP-TFII might compete for binding with NF-Y and, directly or indirectly, decrease gene activity.
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Affiliation(s)
- C Liberati
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy
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49
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Affiliation(s)
- J Villard
- Immunology and Transplant Unit, Division of Immunology and Allergology, Geneva University Hospital, Geneva, Switzerland.
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50
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Gobin SJ, van Zutphen M, Westerheide SD, Boss JM, van den Elsen PJ. The MHC-specific enhanceosome and its role in MHC class I and beta(2)-microglobulin gene transactivation. J Immunol 2001; 167:5175-84. [PMID: 11673530 DOI: 10.4049/jimmunol.167.9.5175] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The promoter regions of MHC class I and beta(2)-microglobulin (beta(2)m) genes possess a regulatory module consisting of S, X, and Y boxes, which is shared by MHC class II and its accessory genes. In this study we show that, similar to MHC class II, the SXY module in MHC class I and beta(2)m promoters is cooperatively bound by a multiprotein complex containing regulatory factor X, CREB/activating transcription factor, and nuclear factor Y. Together with the coactivator class II transactivator this multiprotein complex drives transactivation of these genes. In contrast to MHC class II, the multiprotein complex has an additional function in the constitutive transactivation of MHC class I and beta(2)m genes. The requirement for all transcription factors in the complex and correct spacing of the binding sites within the SXY regulatory module for complex formation and functioning of this multiprotein complex strongly suggests that this complex can be regarded as a bona fide enhanceosome. The general coactivators CREB binding protein, p300, general control nonderepressible-5, and p300/CREB binding protein-associated factor exert an ancillary function in MHC class I and beta(2)m transactivation, but exclusively through the class II transactivator component of this enhanceosome. Thus, the SXY module is the basis for a specific enhanceosome important for the constitutive and inducible transactivation of MHC class I and beta(2)m genes.
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Affiliation(s)
- S J Gobin
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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