1
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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2
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Säisä-Borreill S, Davidson G, Kleiber T, Thevenot A, Martin E, Mondot S, Blottière H, Helleux A, Mengus G, Plateroti M, Duluc I, Davidson I, Freund JN. General transcription factor TAF4 antagonizes epigenetic silencing by Polycomb to maintain intestine stem cell functions. Cell Death Differ 2023; 30:839-853. [PMID: 36639541 PMCID: PMC9984434 DOI: 10.1038/s41418-022-01109-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Taf4 (TATA-box binding protein-associated factor 4) is a subunit of the general transcription factor TFIID, a component of the RNA polymerase II pre-initiation complex that interacts with tissue-specific transcription factors to regulate gene expression. Properly regulated gene expression is particularly important in the intestinal epithelium that is constantly renewed from stem cells. Tissue-specific inactivation of Taf4 in murine intestinal epithelium during embryogenesis compromised gut morphogenesis and the emergence of adult-type stem cells. In adults, Taf4 loss impacted the stem cell compartment and associated Paneth cells in the stem cell niche, epithelial turnover and differentiation of mature cells, thus exacerbating the response to inflammatory challenge. Taf4 inactivation ex vivo in enteroids prevented budding formation and maintenance and caused broad chromatin remodeling and a strong reduction in the numbers of stem and progenitor cells with a concomitant increase in an undifferentiated cell population that displayed high activity of the Ezh2 and Suz12 components of Polycomb Repressive Complex 2 (PRC2). Treatment of Taf4-mutant enteroids with a specific Ezh2 inhibitor restored buddings, cell proliferation and the stem/progenitor compartment. Taf4 loss also led to increased PRC2 activity in cells of adult crypts associated with modification of the immune/inflammatory microenvironment that potentiated Apc-driven tumorigenesis. Our results reveal a novel function of Taf4 in antagonizing PRC2-mediated repression of the stem cell gene expression program to assure normal development, homeostasis, and immune-microenvironment of the intestinal epithelium.
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Affiliation(s)
- Susanna Säisä-Borreill
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Thomas Kleiber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
- Orphazyme, Ole Maaloes 3, 2200, Copenhagen, Denmark
| | - Andréa Thevenot
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Elisabeth Martin
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Stanislas Mondot
- University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Hervé Blottière
- University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Alexandra Helleux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Michelina Plateroti
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Isabelle Duluc
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Jean-Noel Freund
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France.
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3
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Florentin J, Zhao J, Tai YY, Sun W, Ohayon LL, O'Neil SP, Arunkumar A, Zhang X, Zhu J, Al Aaraj Y, Watson A, Sembrat J, Rojas M, Chan SY, Dutta P. Loss of Amphiregulin drives inflammation and endothelial apoptosis in pulmonary hypertension. Life Sci Alliance 2022; 5:5/11/e202101264. [PMID: 35732465 PMCID: PMC9218345 DOI: 10.26508/lsa.202101264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 12/15/2022] Open
Abstract
Pulmonary hypertension (PH) is a vascular disease characterized by elevated pulmonary arterial pressure, leading to right ventricular failure and death. Pathogenic features of PH include endothelial apoptosis and vascular inflammation, which drive vascular remodeling and increased pulmonary arterial pressure. Re-analysis of the whole transcriptome sequencing comparing human pulmonary arterial endothelial cells (PAECs) isolated from PH and control patients identified AREG, which encodes Amphiregulin, as a key endothelial survival factor. PAECs from PH patients and mice exhibited down-regulation of AREG and its receptor epidermal growth factor receptor (EGFR). Moreover, the deficiency of AREG and EGFR in ECs in vivo and in vitro heightened inflammatory leukocyte recruitment, cytokine production, and endothelial apoptosis, as well as diminished angiogenesis. Correspondingly, hypoxic mice lacking Egfr in ECs (cdh5 cre/+ Egfr fl/fl) displayed elevated RVSP and pulmonary remodeling. Computational analysis identified NCOA6, PHB2, and RRP1B as putative genes regulating AREG in endothelial cells. The master transcription factor of hypoxia HIF-1⍺ binds to the promoter regions of these genes and up-regulates their expression in hypoxia. Silencing of these genes in cultured PAECs decreased inflammation and apoptosis, and increased angiogenesis in hypoxic conditions. Our pathway analysis and gene silencing experiments revealed that BCL2-associated agonist of cell death (BAD) is a downstream mediator of AREG BAD silencing in ECs lacking AREG mitigated inflammation and apoptosis, and suppressed tube formation. In conclusion, loss of Amphiregulin and its receptor EGFR in PH is a crucial step in the pathogenesis of PH, promoting pulmonary endothelial cell death, influx of inflammatory myeloid cells, and vascular remodeling.
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Affiliation(s)
- Jonathan Florentin
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jingsi Zhao
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yi-Yin Tai
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Wei Sun
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lee L Ohayon
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Scott P O'Neil
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Anagha Arunkumar
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Xinyi Zhang
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jianhui Zhu
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yassmin Al Aaraj
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Annie Watson
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen Y Chan
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Partha Dutta
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA .,Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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4
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Scheer E, Luo J, Bernardini A, Ruffenach F, Garnier JM, Kolb-Cheynel I, Gupta K, Berger I, Ranish J, Tora L. TAF8 regions important for TFIID lobe B assembly or for TAF2 interactions are required for embryonic stem cell survival. J Biol Chem 2021; 297:101288. [PMID: 34634302 PMCID: PMC8564675 DOI: 10.1016/j.jbc.2021.101288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 11/25/2022] Open
Abstract
The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. TFIID is composed of three lobes, named A, B, and C. A 5TAF core complex can be assembled in vitro constituting a building block for the further assembly of either lobe A or B in TFIID. Structural studies showed that TAF8 forms a histone fold pair with TAF10 in lobe B and participates in connecting lobe B to lobe C. To better understand the role of TAF8 in TFIID, we have investigated the requirement of the different regions of TAF8 for the in vitro assembly of lobe B and C and the importance of certain TAF8 regions for mouse embryonic stem cell (ESC) viability. We have identified a region of TAF8 distinct from the histone fold domain important for assembling with the 5TAF core complex in lobe B. We also delineated four more regions of TAF8 each individually required for interacting with TAF2 in lobe C. Moreover, CRISPR/Cas9-mediated gene editing indicated that the 5TAF core-interacting TAF8 domain and the proline-rich domain of TAF8 that interacts with TAF2 are both required for mouse embryonic stem cell survival. Thus, our study defines distinct TAF8 regions involved in connecting TFIID lobe B to lobe C that appear crucial for TFIID function and consequent ESC survival.
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Affiliation(s)
- Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
| | - Jie Luo
- Institute for Systems Biology (ISB), Seattle, Washington, USA
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
| | - Frank Ruffenach
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
| | - Jean-Marie Garnier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
| | - Isabelle Kolb-Cheynel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
| | - Kapil Gupta
- School of Biochemistry and Bristol Research Centre for Synthetic Biology BrisSynBio, University of Bristol, Bristol, UK
| | - Imre Berger
- School of Biochemistry and Bristol Research Centre for Synthetic Biology BrisSynBio, University of Bristol, Bristol, UK
| | - Jeff Ranish
- Institute for Systems Biology (ISB), Seattle, Washington, USA
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France.
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5
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Kleiber T, Davidson G, Mengus G, Martianov I, Davidson I. Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4. Cell Death Dis 2021; 12:790. [PMID: 34385420 PMCID: PMC8361202 DOI: 10.1038/s41419-021-04067-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022]
Abstract
Regulation of gene expression involves a complex and dynamic dialogue between transcription factors, chromatin remodelling and modification complexes and the basal transcription machinery. To address the function of the Taf4 subunit of general transcription factor TFIID in the regulation of insulin signalling, it was inactivated in adult murine pancreatic beta cells. Taf4 inactivation impacted the expression of critical genes involved in beta-cell function leading to increased glycaemia, lowered plasma insulin levels and defective glucose-stimulated insulin secretion. One week after Taf4-loss, single-cell RNA-seq revealed cells with mixed beta cell, alpha and/or delta cell identities as well as a beta cell population trans-differentiating into alpha-like cells. Computational analysis of single-cell RNA-seq defines how known critical beta cell and alpha cell determinants may act in combination with additional transcription factors and the NuRF chromatin remodelling complex to promote beta cell trans-differentiation.
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Affiliation(s)
- Thomas Kleiber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Orphazyme, Ole Malloes Vej 3, 2200, Copenhagen, Danmark
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Igor Martianov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Equipe Labélisée Ligue National contre le Cancer, Alsace, France.
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6
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El-Saafin F, Curry C, Ye T, Garnier JM, Kolb-Cheynel I, Stierle M, Downer NL, Dixon MP, Negroni L, Berger I, Thomas T, Voss AK, Dobyns W, Devys D, Tora L. Homozygous TAF8 mutation in a patient with intellectual disability results in undetectable TAF8 protein, but preserved RNA polymerase II transcription. Hum Mol Genet 2018; 27:2171-2186. [PMID: 29648665 PMCID: PMC5985725 DOI: 10.1093/hmg/ddy126] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/21/2023] Open
Abstract
The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. In a child with intellectual disability, mild microcephaly, corpus callosum agenesis and poor growth, we identified a homozygous splice-site mutation in TAF8 (NM_138572.2: c.781-1G > A). Our data indicate that the patient's mutation generates a frame shift and an unstable TAF8 mutant protein with an unrelated C-terminus. The mutant TAF8 protein could not be detected in extracts from the patient's fibroblasts, indicating a loss of TAF8 function and that the mutation is most likely causative. Moreover, our immunoprecipitation and proteomic analyses show that in patient cells only partial TAF complexes exist and that the formation of the canonical TFIID is impaired. In contrast, loss of TAF8 in mouse embryonic stem cells and blastocysts leads to cell death and to a global decrease in Pol II transcription. Astonishingly however, in human TAF8 patient cells, we could not detect any cellular phenotype, significant changes in genome-wide Pol II occupancy and pre-mRNA transcription. Thus, the disorganization of the essential holo-TFIID complex did not affect global Pol II transcription in the patient's fibroblasts. Our observations further suggest that partial TAF complexes, and/or an altered TFIID containing a mutated TAF8, could support human development and thus, the absence of holo-TFIID is less deleterious for transcription than originally predicted.
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Affiliation(s)
- Farrah El-Saafin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Cynthia Curry
- University of California, San Francisco, San Francisco, CA, USA
- Genetic Medicine, University Pediatric Specialists, Fresno, CA 93701, USA
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Jean-Marie Garnier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Isabelle Kolb-Cheynel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Matthieu Stierle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Natalie L Downer
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Mathew P Dixon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Imre Berger
- School of Biochemistry and Bristol Research Centre for Synthetic Biology BrisSynBio, University of Bristol, Bristol BS8 1TD, UK
| | - Tim Thomas
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - William Dobyns
- Departments of Pediatrics and Neurology, University of Washington, Seattle, WA 98101, USA
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
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7
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Kazantseva J, Sadam H, Neuman T, Palm K. Targeted alternative splicing of TAF4: a new strategy for cell reprogramming. Sci Rep 2016; 6:30852. [PMID: 27499390 PMCID: PMC4976350 DOI: 10.1038/srep30852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/08/2016] [Indexed: 12/20/2022] Open
Abstract
Reprogramming of somatic cells has become a versatile tool for biomedical research and for regenerative medicine. In the current study, we show that manipulating alternative splicing (AS) is a highly potent strategy to produce cells for therapeutic applications. We demonstrate that silencing of hTAF4-TAFH activity of TAF4 converts human facial dermal fibroblasts to melanocyte-like (iMel) cells. iMel cells produce melanin and express microphthalmia-associated transcription factor (MITF) and its target genes at levels comparable to normal melanocytes. Reprogramming of melanoma cells by manipulation with hTAF4-TAFH activity upon TAFH RNAi enforces cell differentiation towards chondrogenic pathway, whereas ectoptic expression of TAF4 results in enhanced multipotency and neural crest-like features in melanoma cells. In both cell states, iMels and cancer cells, hTAF4-TAFH activity controls migration by supporting E- to N-cadherin switches. From our data, we conclude that targeted splicing of hTAF4-TAFH coordinates AS of other TFIID subunits, underscoring the role of TAF4 in synchronised changes of Pol II complex composition essential for efficient cellular reprogramming. Taken together, targeted AS of TAF4 provides a unique strategy for generation of iMels and recapitulating stages of melanoma progression.
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Affiliation(s)
| | - Helle Sadam
- Protobios LLC, Tallinn, Estonia.,The Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | | | - Kaia Palm
- Protobios LLC, Tallinn, Estonia.,The Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
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8
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The role of barrier genes in epidermal malignancy. Oncogene 2016; 35:5705-5712. [PMID: 27041586 DOI: 10.1038/onc.2016.84] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/17/2016] [Accepted: 02/18/2016] [Indexed: 12/24/2022]
Abstract
The outermost layer of the mammalian skin, the epidermis, forms a protective barrier against pathogenic microbes and tissue dehydration. This barrier is formed and maintained by complex genetic networks that connect cellular differentiation processes, enzymatic activities and cellular junctions. Disruption in these networks affects the balance between keratinocyte proliferation and differentiation resulting in barrier function impairment, epidermal hyperproliferation and in some cases, squamous cell carcinoma (SCC). Recent studies in wound-induced inflammation-mediated cancers in mice have identified dysregulation of core barrier components as tumor drivers. We therefore propose a hypothesis in which loss of key barrier genes, induce barrier dysfunction, and promote inflammation-driven epidermal hyperplasia and carcinogenesis over time. This emerging vision suggests that under specific genetic circumstances, localized barrier impairment could be considered as a hallmark of initiating lesions in epidermal SCC.
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9
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Langer D, Martianov I, Alpern D, Rhinn M, Keime C, Dollé P, Mengus G, Davidson I. Essential role of the TFIID subunit TAF4 in murine embryogenesis and embryonic stem cell differentiation. Nat Commun 2016; 7:11063. [PMID: 27026076 PMCID: PMC4820908 DOI: 10.1038/ncomms11063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/17/2016] [Indexed: 12/15/2022] Open
Abstract
TAF4 (TATA-binding protein-associated factor 4) and its paralogue TAF4b are components of the TFIID core module. We inactivated the murine Taf4a gene to address Taf4 function during embryogenesis. Here we show that Taf4a−/− embryos survive until E9.5 where primary germ layers and many embryonic structures are identified showing Taf4 is dispensable for their specification. In contrast, Taf4 is required for correct patterning of the trunk and anterior structures, ventral morphogenesis and proper heart positioning. Overlapping expression of Taf4a and Taf4b during embryogenesis suggests their redundancy at early stages. In agreement with this, Taf4a−/− embryonic stem cells (ESCs) are viable and comprise Taf4b-containing TFIID. Nevertheless, Taf4a−/− ESCs do not complete differentiation into glutamatergic neurons and cardiomyocytes in vitro due to impaired preinitiation complex formation at the promoters of critical differentiation genes. We define an essential role of a core TFIID TAF in differentiation events during mammalian embryogenesis. The role of TFIID core module TAFs (TATA-binding protein-associated factors) in embryogenesis is unknown. Here, the authors show that Taf4 is essential at mid-gestation and for complete neuronal differentiation of embryonic stem cells, but that Taf4a and Taf4b are redundant at early embryonic stages.
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Affiliation(s)
- Diana Langer
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Igor Martianov
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Daniel Alpern
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France.,L'École polytechnique fédérale de Lausanne, Route Cantonale, 1015 Lausanne, Switzerland
| | - Muriel Rhinn
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Céline Keime
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Pascal Dollé
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
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10
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Han Y, Wang L, Yao QP, Zhang P, Liu B, Wang GL, Shen BR, Cheng B, Wang Y, Jiang ZL, Qi YX. Nuclear envelope proteins Nesprin2 and LaminA regulate proliferation and apoptosis of vascular endothelial cells in response to shear stress. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1165-73. [PMID: 25721888 DOI: 10.1016/j.bbamcr.2015.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/19/2015] [Accepted: 02/15/2015] [Indexed: 11/27/2022]
Abstract
The dysfunction of vascular endothelial cells (ECs) influenced by flow shear stress is crucial for vascular remodeling. However, the roles of nuclear envelope (NE) proteins in shear stress-induced EC dysfunction are still unknown. Our results indicated that, compared with normal shear stress (NSS), low shear stress (LowSS) suppressed the expression of two types of NE proteins, Nesprin2 and LaminA, and increased the proliferation and apoptosis of ECs. Targeted small interfering RNA (siRNA) and gene overexpression plasmid transfection revealed that Nesprin2 and LaminA participate in the regulation of EC proliferation and apoptosis. A protein/DNA array was further used to detect the activation of transcription factors in ECs following transfection with target siRNAs and overexpression plasmids. The regulation of AP-2 and TFIID mediated by Nesprin2 and the activation of Stat-1, Stat-3, Stat-5 and Stat-6 by LaminA were verified under shear stress. Furthermore, using Ingenuity Pathway Analysis software and real-time RT-PCR, the effects of Nesprin2 or LaminA on the downstream target genes of AP-2, TFIID, and Stat-1, Stat-3, Stat-5 and Stat-6, respectively, were investigated under LowSS. Our study has revealed that NE proteins are novel mechano-sensitive molecules in ECs. LowSS suppresses the expression of Nesprin2 and LaminA, which may subsequently modulate the activation of important transcription factors and eventually lead to EC dysfunction.
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Affiliation(s)
- Yue Han
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Wang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Ping Yao
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Zhang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Liu
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guo-Liang Wang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bao-Rong Shen
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Binbin Cheng
- Department of Bioengineering, University of CA, San Diego, USA
| | - Yingxiao Wang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, University of CA, San Diego, USA
| | - Zong-Lai Jiang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying-Xin Qi
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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11
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Diversity in TAF proteomics: consequences for cellular differentiation and migration. Int J Mol Sci 2014; 15:16680-97. [PMID: 25244017 PMCID: PMC4200853 DOI: 10.3390/ijms150916680] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022] Open
Abstract
Development is a highly controlled process of cell proliferation and differentiation driven by mechanisms of dynamic gene regulation. Specific DNA binding factors for establishing cell- and tissue-specific transcriptional programs have been characterised in different cell and animal models. However, much less is known about the role of “core transcription machinery” during cell differentiation, given that general transcription factors and their spatiotemporally patterned activity govern different aspects of cell function. In this review, we focus on the role of TATA-box associated factor 4 (TAF4) and its functional isoforms generated by alternative splicing in controlling lineage-specific differentiation of normal mesenchymal stem cells and cancer stem cells. In the light of our recent findings, induction, control and maintenance of cell differentiation status implies diversification of the transcription initiation apparatus orchestrated by alternative splicing.
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12
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Alpern D, Langer D, Ballester B, Le Gras S, Romier C, Mengus G, Davidson I. TAF4, a subunit of transcription factor II D, directs promoter occupancy of nuclear receptor HNF4A during post-natal hepatocyte differentiation. eLife 2014; 3:e03613. [PMID: 25209997 PMCID: PMC4359380 DOI: 10.7554/elife.03613] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/09/2014] [Indexed: 12/25/2022] Open
Abstract
The functions of the TAF subunits of mammalian TFIID in physiological processes remain poorly characterised. In this study, we describe a novel function of TAFs in directing genomic occupancy of a transcriptional activator. Using liver-specific inactivation in mice, we show that the TAF4 subunit of TFIID is required for post-natal hepatocyte maturation. TAF4 promotes pre-initiation complex (PIC) formation at post-natal expressed liver function genes and down-regulates a subset of embryonic expressed genes by increased RNA polymerase II pausing. The TAF4–TAF12 heterodimer interacts directly with HNF4A and in vivo TAF4 is necessary to maintain HNF4A-directed embryonic gene expression at post-natal stages and promotes HNF4A occupancy of functional cis-regulatory elements adjacent to the transcription start sites of post-natal expressed genes. Stable HNF4A occupancy of these regulatory elements requires TAF4-dependent PIC formation highlighting that these are mutually dependent events. Local promoter-proximal HNF4A–TFIID interactions therefore act as instructive signals for post-natal hepatocyte differentiation. DOI:http://dx.doi.org/10.7554/eLife.03613.001 To decode the information contained within a gene, a number of processes need to occur. For example, the DNA sequence that makes up the gene needs to be copied to make a molecule of RNA, which is then translated to build the corresponding protein. The first steps in the manufacture of RNA involve a structure called a ‘pre-initiation complex’ moving an enzyme called RNA polymerase II to the start of the gene that needs to be copied. The pre-initiation complex is made up of many types of protein, including a set of proteins called TAFs. However, the way that these proteins work in mammals is not well understood. There are good reasons for this: proteins are often studied by seeing what happens when the protein is removed, but many TAFs are so important that removing them is lethal. Alpern et al. have now studied the function of TAF4 by removing this protein from mouse liver cells. This causes severe hypoglycemia (that is, a drop in sugar levels in the blood). Moreover, it seems as if these cells start dying before they become fully mature. In liver cells lacking TAF4, some 1408 genes that are normally turned on just after birth are not properly switched on; these genes are necessary for the metabolic functions of the liver. Furthermore, 776 genes that are normally turned off after birth continue to be expressed. It seems that the absence of TAF4 sometimes disrupts the formation of the pre-initiation complex, which would slow down the production of RNA. However, it can also have the opposite effect by increasing the activity of RNA polymerase II, hence making too many copies of RNA from some genes. Alpern et al. also find that TAF4 is needed to allow a protein called HNF4A, which is important in the development of the liver and in controlling metabolism, to interact with over 7000 important DNA sequences. Mutations in HNF4A are responsible for a syndrome known as Maturity Onset of Diabetes in the Young. The next stage in this work will be to explore if these mutations influence the interaction between HNF4A and TAF4, and if they do, whether these changes contribute to this form of diabetes. DOI:http://dx.doi.org/10.7554/eLife.03613.002
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Affiliation(s)
- Daniil Alpern
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Diana Langer
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Benoit Ballester
- Laboratoire TAGC, Aix-Marseille Université, UMR1090, Marseille, France
| | - Stephanie Le Gras
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Christophe Romier
- Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
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13
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Larivière N, Law J, Trinkle-Mulcahy L. Dissection of a novel autocrine signaling pathway via quantitative secretome and interactome mapping. J Proteome Res 2014; 13:3432-43. [PMID: 24956037 DOI: 10.1021/pr500392m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Epidermal homeostasis is a balancing act governed by a multitude of underlying regulatory events, and several growth factors and signaling pathways have been implicated in regulation of the balance between proliferation and differentiation in keratinocytes. We show here that the signal transducer/transcription factor FIZ1 (Flt3 interacting zinc finger protein-1) is a previously unknown player in this regulatory axis, promoting an increase in proliferation of HaCaT human immortalized keratinocytes that is driven by more rapid G1/S progression and mediated by activation of the MAP/ERK kinase pathway. Utilizing quantitative SILAC-based secretome analysis, we identified the insulin growth factor binding protein IGFBP3 as the key mediating factor, demonstrating that elevated FIZ1 levels promote increased IGFBP3 expression and secretion and a concurrent increased sensitivity to IGF1 signaling, while antibody-based neutralization of IGFBP3 abrogates the FIZ1-induced growth advantage. To identify underlying protein-protein interactions likely to govern these events, we mapped the interactome of FIZ1 and found eight novel binding partners that form complexes with the protein in the cytoplasm and nucleus. These include signal transduction and transcription factors and the cell cycle regulatory NDR (Nuclear Dbf2-related) kinases. Our results provide further insight into the complex balance of epidermal homeostasis and identify FIZ1 as a novel therapeutic target.
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Affiliation(s)
- Nathalie Larivière
- Department of Cellular & Molecular Medicine and Ottawa Institute of Systems Biology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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14
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Ribeiro JR, Lovasco LA, Vanderhyden BC, Freiman RN. Targeting TBP-Associated Factors in Ovarian Cancer. Front Oncol 2014; 4:45. [PMID: 24653979 PMCID: PMC3949196 DOI: 10.3389/fonc.2014.00045] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/25/2014] [Indexed: 12/11/2022] Open
Abstract
As ovarian tumors progress, they undergo a process of dedifferentiation, allowing adaptive changes in growth and morphology that promote metastasis and chemoresistance. Herein, we outline a hypothesis that TATA-box binding protein associated factors (TAFs), which compose the RNA Polymerase II initiation factor, TFIID, contribute to regulation of dedifferentiation states in ovarian cancer. Numerous studies demonstrate that TAFs regulate differentiation and proliferation states; their expression is typically high in pluripotent cells and reduced upon differentiation. Strikingly, TAF2 exhibits copy number increases or mRNA overexpression in 73% of high-grade serous ovarian cancers (HGSC). At the biochemical level, TAF2 directs TFIID to TATA-less promoters by contact with an Initiator element, which may lead to the deregulation of the transcriptional output of these tumor cells. TAF4, which is altered in 66% of HGSC, is crucial for the stability of the TFIID complex and helps drive dedifferentiation of mouse embryonic fibroblasts to induced pluripotent stem cells. Its ovary-enriched paralog, TAF4B, is altered in 26% of HGSC. Here, we show that TAF4B mRNA correlates with Cyclin D2 mRNA expression in human granulosa cell tumors. TAF4B may also contribute to regulation of tumor microenvironment due to its estrogen-responsiveness and ability to act as a cofactor for NFκB. Conversely, TAF9, a cofactor for p53 in regulating apoptosis, may act as a tumor suppressor in ovarian cancer, since it is downregulated or deleted in 98% of HGSC. We conclude that a greater understanding of mechanisms of transcriptional regulation that execute signals from oncogenic signaling cascades is needed in order to expand our understanding of the etiology and progression of ovarian cancer, and most importantly to identify novel targets for therapeutic intervention.
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Affiliation(s)
| | - Lindsay A Lovasco
- Molecular and Cellular Biology and Biochemistry, Brown University , Providence, RI , USA
| | - Barbara C Vanderhyden
- Cellular and Molecular Medicine, University of Ottawa , Ottawa, ON , Canada ; Centre for Cancer Therapeutics, Ottawa Hospital Research Institute , Ottawa, ON , Canada
| | - Richard N Freiman
- Pathobiology Graduate Program, Brown University , Providence, RI , USA ; Molecular and Cellular Biology and Biochemistry, Brown University , Providence, RI , USA
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15
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TAF4 inactivation reveals the 3 dimensional growth promoting activities of collagen 6A3. PLoS One 2014; 9:e87365. [PMID: 24498316 PMCID: PMC3911972 DOI: 10.1371/journal.pone.0087365] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/23/2013] [Indexed: 12/05/2022] Open
Abstract
Collagen 6A3 (Col6a3), a component of extracellular matrix, is often up-regulated in tumours and is believed to play a pro-oncogenic role. However the mechanisms of its tumorigenic activity are poorly understood. We show here that Col6a3 is highly expressed in densely growing mouse embryonic fibroblasts (MEFs). In MEFs where the TAF4 subunit of general transcription factor IID (TFIID) has been inactivated, elevated Col6a3 expression prevents contact inhibition promoting their 3 dimensional growth as foci and fibrospheres. Analyses of gene expression in densely growing Taf4−/− MEFs revealed repression of the Hippo pathway and activation of Wnt signalling. The Hippo activator Kibra/Wwc1 is repressed under dense conditions in Taf4−/− MEFs, leading to nuclear accumulation of the proliferation factor YAP1 in the cells forming 3D foci. At the same time, Wnt9a is activated and the Sfrp2 antagonist of Wnt signalling is repressed. Surprisingly, treatment of Taf4−/− MEFs with all-trans retinoic acid (ATRA) restores contact inhibition suppressing 3D growth. ATRA represses Col6a3 expression independently of TAF4 expression and Col6a3 silencing is sufficient to restore contact inhibition in Taf4−/− MEFs and to suppress 3D growth by reactivating Kibra expression to induce Hippo signalling and by inducing Sfrp2 expression to antagonize Wnt signalling. All together, these results reveal a critical role for Col6a3 in regulating both Hippo and Wnt signalling to promote 3D growth, and show that the TFIID subunit TAF4 is essential to restrain the growth promoting properties of Col6a3. Our data provide new insight into the role of extra cellular matrix components in regulating cell growth.
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16
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Winther M, Walmod PS. Neural cell adhesion molecules belonging to the family of leucine-rich repeat proteins. ADVANCES IN NEUROBIOLOGY 2014; 8:315-95. [PMID: 25300143 DOI: 10.1007/978-1-4614-8090-7_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Leucine-rich repeats (LRRs) are motifs that form protein-ligand interaction domains. There are approximately 140 human genes encoding proteins with extracellular LRRs. These encode cell adhesion molecules (CAMs), proteoglycans, G-protein-coupled receptors, and other types of receptors. Here we give a brief description of 36 proteins with extracellular LRRs that all can be characterized as CAMs or putative CAMs expressed in the nervous system. The proteins are involved in multiple biological processes in the nervous system including the proliferation and survival of cells, neuritogenesis, axon guidance, fasciculation, myelination, and the formation and maintenance of synapses. Moreover, the proteins are functionally implicated in multiple diseases including cancer, hearing impairment, glaucoma, Alzheimer's disease, multiple sclerosis, Parkinson's disease, autism spectrum disorders, schizophrenia, and obsessive-compulsive disorders. Thus, LRR-containing CAMs constitute a large group of proteins of pivotal importance for the development, maintenance, and regeneration of the nervous system.
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17
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Durand A, Papai G, Schultz P. Structure, assembly and dynamics of macromolecular complexes by single particle cryo-electron microscopy. J Nanobiotechnology 2013; 11 Suppl 1:S4. [PMID: 24565374 PMCID: PMC4028798 DOI: 10.1186/1477-3155-11-s1-s4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins in their majority act rarely as single entities. Multisubunit macromolecular complexes are the actors in most of the cellular processes. These nanomachines are hold together by weak protein-protein interactions and undergo functionally important conformational changes. TFIID is such a multiprotein complex acting in eukaryotic transcription initiation. This complex is first to be recruited to the promoter of the genes and triggers the formation of the transcription preinitiation complex involving RNA polymerase II which leads to gene transcription. The exact role of TFIID in this process is not yet understood. METHODS Last generation electron microscopes, improved data collection and new image analysis tools made it possible to obtain structural information of biological molecules at atomic resolution. Cryo-electron microscopy of vitrified samples visualizes proteins in a fully hydrated, close to native state. Molecular images are recorded at liquid nitrogen temperature in low electron dose conditions to reduce radiation damage. Digital image analysis of these noisy images aims at improving the signal-to-noise ratio, at separating distinct molecular views and at reconstructing a three-dimensional model of the biological particle. RESULTS Using these methods we showed the early events of an activated transcription initiation process. We explored the interaction of the TFIID coactivator with the yeast Rap1 activator, the transcription factor TFIIA and the promoter DNA. We demonstrated that TFIID serves as an assembly platform for transient protein-protein interactions, which are essential for transcription initiation. CONCLUSIONS Recent developments in electron microscopy have provided new insights into the structural organization and the dynamic reorganization of large macromolecular complexes. Examples of near-atomic resolutions exist but the molecular flexibility of macromolecular complexes remains the limiting factor in most case. Electron microscopy has the potential to provide both structural and dynamic information of biological assemblies in order to understand the molecular mechanisms of their functions.
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19
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Metzger D, Chambon P. Generation of Spatio-Temporally Controlled Targeted Somatic Mutations in the Mouse. CURRENT PROTOCOLS IN MOUSE BIOLOGY 2011; 1:55-70. [PMID: 26068987 DOI: 10.1002/9780470942390.mo100128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The generation of ligand-activated site-specific Cre recombinases has led to the development of cell type-specific temporally controlled targeted somatic mutagenesis in the mouse. We illustrate this technique using K14-Cre-ER(T2) transgenic mice that express the tamoxifen (tam)-activatable Cre-ER(T2) recombinase in epidermal basal keratinocytes to induce mutations in epidermal keratinocytes of adult mice. Our highly reproducible technique, based on induction of Cre-ER(T2) recombinase activity by tamoxifen administration at low doses (once daily 100-µg intraperitoneal injection for 5 days), has allowed the generation of site-directed somatic mutations of numerous genes in mouse epidermal keratinocytes, and several mouse models of human diseases. The present step-by-step protocol describes how to introduce temporally controlled targeted mutations in epidermal keratinocytes of adult mice. Curr. Protoc. Mouse Biol. 1:55-70. © 2011 by John Wiley & Sons, Inc.
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Affiliation(s)
- Daniel Metzger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, and Collège de France, Illkirch, France
| | - Pierre Chambon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, and Collège de France, Illkirch, France
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20
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Boutet SC, Biressi S, Iori K, Natu V, Rando TA. Taf1 regulates Pax3 protein by monoubiquitination in skeletal muscle progenitors. Mol Cell 2011; 40:749-61. [PMID: 21145483 DOI: 10.1016/j.molcel.2010.09.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 06/22/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022]
Abstract
Pax3 plays critical roles during developmental and postnatal myogenesis. We have previously shown that levels of Pax3 protein are regulated by monoubiquitination and proteasomal degradation during postnatal myogenesis, but none of the key regulators of the monoubiquitination process were known. Here we show that Pax3 monoubiquitination is mediated by the ubiquitin-activating/conjugating activity of Taf1, a component of the core transcriptional machinery that was recently reported to be downregulated during myogenic differentiation. We show that Taf1 binds directly to Pax3 and overexpression of Taf1 increases the level of monoubiquitinated Pax3 and its degradation by the proteasome. A decrease of Taf1 results in a decrease in Pax3 monoubiquitination, an increase in the levels of Pax3 protein, and a concomitant increase in Pax3-mediated inhibition of myogenic differentiation and myoblast migration. These results suggest that Taf1 regulates Pax3 protein levels through its ability to mediate monoubiquitination, revealing a critical interaction between two proteins that are involved in distinct aspects of myogenic differentiation. Finally, these results suggest that the components of the core transcriptional are integrally involved in the process of myogenic differentiation, acting as nodal regulators of the differentiation program.
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Affiliation(s)
- Stéphane C Boutet
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
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21
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Hyter S, Bajaj G, Liang X, Barbacid M, Ganguli-Indra G, Indra AK. Loss of nuclear receptor RXRα in epidermal keratinocytes promotes the formation of Cdk4-activated invasive melanomas. Pigment Cell Melanoma Res 2010; 23:635-48. [PMID: 20629968 DOI: 10.1111/j.1755-148x.2010.00732.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Keratinocytes contribute to melanocyte transformation by affecting their microenvironment, in part through the secretion of paracrine factors. Here we report a loss of expression of nuclear receptor RXRα in epidermal keratinocytes during human melanoma progression. In the absence of keratinocytic RXRα, in combination with mutant Cdk4, cutaneous melanoma was generated that metastasized to lymph nodes in a bigenic mouse model. Expression of several keratinocyte-derived mitogenic growth factors (Et-1, Hgf, Scf, α-MSH and Fgf 2 ) was elevated in skin of bigenic mice, whereas Fas, E-cadherin and Pten, implicated in apoptosis, cellular invasion and melanomagenesis, respectively, were downregulated within the microdissected melanocytic tumors. We demonstrated that RXRα is recruited on the proximal promoter of both Et-1 and Hgf, possibly directly regulating their transcription in keratinocytes. These studies demonstrate the contribution of keratinocytic paracrine signaling during the cellular transformation and malignant conversion of melanocytes.
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Affiliation(s)
- Stephen Hyter
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
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22
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Kalogeropoulou M, Voulgari A, Kostourou V, Sandaltzopoulos R, Dikstein R, Davidson I, Tora L, Pintzas A. TAF4b and Jun/activating protein-1 collaborate to regulate the expression of integrin alpha6 and cancer cell migration properties. Mol Cancer Res 2010; 8:554-68. [PMID: 20353996 DOI: 10.1158/1541-7786.mcr-09-0159] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The TAF4b subunit of the transcription factor IID, which has a central role in transcription by polymerase II, is involved in promoter recognition by selective recruitment of activators. The activating protein-1 (AP-1) family members participate in oncogenic transformation via gene regulation. Utilizing immunoprecipitation of endogenous protein complexes, we documented specific interactions between Jun family members and TATA box binding protein-associated factors (TAF) in colon HT29 adenocarcinoma cells. Particularly, TAF4b and c-Jun were found to colocalize and interact in the nucleus of advanced carcinoma cells and in cells with epithelial-to-mesenchymal transition (EMT) characteristics. TAF4b was found to specifically regulate the AP-1 target gene involved in EMT integrin alpha6, thus altering related cellular properties such as migration potential. Using a chromatin immunoprecipitation approach in colon adenocarcinoma cell lines, we further identified a synergistic role for TAF4b and c-Jun and other AP-1 family members on the promoter of integrin alpha6, underlining the existence of a specific mechanism related to gene expression control. We show evidence for the first time of an interdependence of TAF4b and AP-1 family members in cell type-specific promoter recognition and initiation of transcription in the context of cancer progression and EMT.
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Affiliation(s)
- Margarita Kalogeropoulou
- Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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23
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Halperin Y, Linhart C, Ulitsky I, Shamir R. Allegro: analyzing expression and sequence in concert to discover regulatory programs. Nucleic Acids Res 2009; 37:1566-79. [PMID: 19151090 PMCID: PMC2655690 DOI: 10.1093/nar/gkn1064] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' UTR sequences. The algorithm uses a novel log-likelihood-based, non-parametric model to describe the expression pattern shared by a group of co-regulated genes. We show that Allegro is more accurate and sensitive than existing techniques, and can simultaneously analyze multiple expression datasets with more than 100 conditions. We apply Allegro on datasets from several species and report on the transcriptional modules it uncovers. Our analysis reveals a novel motif over-represented in the promoters of genes highly expressed in murine oocytes, and several new motifs related to fly development. Finally, using stem-cell expression profiles, we identify three miRNA families with pivotal roles in human embryogenesis.
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Affiliation(s)
- Yonit Halperin
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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24
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