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Costallat M, Batsché E, Rachez C, Muchardt C. The 'Alu-ome' shapes the epigenetic environment of regulatory elements controlling cellular defense. Nucleic Acids Res 2022; 50:5095-5110. [PMID: 35544277 PMCID: PMC9122584 DOI: 10.1093/nar/gkac346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/06/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/13/2022] Open
Abstract
Promoters and enhancers are sites of transcription initiation (TSSs) and carry specific histone modifications, including H3K4me1, H3K4me3, and H3K27ac. Yet, the principles governing the boundaries of such regulatory elements are still poorly characterized. Alu elements are good candidates for a boundary function, being highly abundant in gene-rich regions, while essentially excluded from regulatory elements. Here, we show that the interval ranging from TSS to first upstream Alu, accommodates all H3K4me3 and most H3K27ac marks, while excluding DNA methylation. Remarkably, the average length of these intervals greatly varies in-between tissues, being longer in stem- and shorter in immune-cells. The very shortest TSS-to-first-Alu intervals were observed at promoters active in T-cells, particularly at immune genes, where first-Alus were traversed by RNA polymerase II transcription, while accumulating H3K4me1 signal. Finally, DNA methylation at first-Alus was found to evolve with age, regressing from young to middle-aged, then recovering later in life. Thus, the first-Alus upstream of TSSs appear as dynamic boundaries marking the transition from DNA methylation to active histone modifications at regulatory elements, while also participating in the recording of immune gene transcriptional events by positioning H3K4me1-modified nucleosomes.
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Affiliation(s)
- Mickael Costallat
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005, Paris, France
| | - Eric Batsché
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005, Paris, France
| | - Christophe Rachez
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005, Paris, France
| | - Christian Muchardt
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005, Paris, France
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2
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Rachez C, Legendre R, Costallat M, Varet H, Yi J, Kornobis E, Muchardt C. HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions. EMBO Rep 2021; 22:e52320. [PMID: 34312949 DOI: 10.15252/embr.202052320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022] Open
Abstract
HP1 proteins are best known as markers of heterochromatin and gene silencing. Yet, they are also RNA-binding proteins and the HP1γ/CBX3 family member is present on transcribed genes together with RNA polymerase II, where it regulates co-transcriptional processes such as alternative splicing. To gain insight in the role of the RNA-binding activity of HP1γ in transcriptionally active chromatin, we have captured and analysed RNAs associated with this protein. We find that HP1γ is specifically targeted to hexameric RNA motifs and coincidentally transposable elements of the SINE family. As these elements are abundant in introns, while essentially absent from exons, the HP1γ RNA association tethers unspliced pre-mRNA to chromatin via the intronic regions and limits the usage of intronic cryptic splice sites. Thus, our data unveil novel determinants in the relationship between chromatin and co-transcriptional splicing.
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Affiliation(s)
- Christophe Rachez
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Rachel Legendre
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France.,Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Mickaël Costallat
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Hugo Varet
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France.,Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Jia Yi
- Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France.,Sorbonne Université, Ecole Doctorale Complexité du Vivant (ED515), Paris, France
| | - Etienne Kornobis
- Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Christian Muchardt
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
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3
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Mullani N, Porozhan Y, Mangelinck A, Rachez C, Costallat M, Batsché E, Goodhardt M, Cenci G, Mann C, Muchardt C. Reduced RNA turnover as a driver of cellular senescence. Life Sci Alliance 2021; 4:4/3/e202000809. [PMID: 33446491 PMCID: PMC7812316 DOI: 10.26508/lsa.202000809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 06/08/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022] Open
Abstract
RNAs originating from transcription upstream and downstream of genes accumulate in the cytoplasm of a subset of senescent cells, suggesting an RNA alternative to cytoplasmic DNA in the triggering of senescence. Accumulation of senescent cells is an important contributor to chronic inflammation upon aging. The inflammatory phenotype of senescent cells was previously shown to be driven by cytoplasmic DNA. Here, we propose that cytoplasmic double-stranded RNA has a similar effect. We find that several cell types driven into senescence by different routes share an accumulation of long promoter RNAs and 3′ gene extensions rich in retrotransposon sequences. Accordingly, these cells display increased expression of genes involved in response to double stranded RNA of viral origin downstream of the interferon pathway. The RNA accumulation is associated with evidence of reduced RNA turnover, including in some cases, reduced expression of RNA exosome subunits. Reciprocally, depletion of RNA exosome subunit EXOSC3 accelerated expression of multiple senescence markers. A senescence-like RNA accumulation was also observed in cells exposed to oxidative stress, an important trigger of cellular senescence. Altogether, we propose that in a subset of senescent cells, repeat-containing transcripts stabilized by oxidative stress or reduced RNA exosome activity participate in driving and maintaining the permanent inflammatory state characterizing cellular senescence.
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Affiliation(s)
- Nowsheen Mullani
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France.,Sorbonne Université, Ecole Doctorale "Complexité du Vivant" (ED515), Paris, France
| | - Yevheniia Porozhan
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Adèle Mangelinck
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christophe Rachez
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Mickael Costallat
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Eric Batsché
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Michele Goodhardt
- Institut National de la Santé et de la Recherche Médicale (INSERM) U976, Institut de Recherche Saint Louis, Université de Paris, Paris, France
| | - Giovanni Cenci
- Dipartimento Biologia e Biotecnologie "C. Darwin," SAPIENZA Università di Roma, Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Carl Mann
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christian Muchardt
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
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4
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Touati SA, Buffin E, Cladière D, Hached K, Rachez C, van Deursen JM, Wassmann K. Mouse oocytes depend on BubR1 for proper chromosome segregation but not for prophase I arrest. Nat Commun 2015; 6:6946. [PMID: 25897860 DOI: 10.1038/ncomms7946] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/16/2015] [Indexed: 12/19/2022] Open
Abstract
Mammalian female meiosis is error prone, with rates of meiotic chromosome missegregations strongly increasing towards the end of the reproductive lifespan. A strong reduction of BubR1 has been observed in oocytes of women approaching menopause and in ovaries of aged mice, which led to the hypothesis that a gradual decline of BubR1 contributes to age-related aneuploidization. Here we employ a conditional knockout approach in mouse oocytes to dissect the meiotic roles of BubR1. We show that BubR1 is required for diverse meiotic functions, including persistent spindle assembly checkpoint activity, timing of meiosis I and the establishment of robust kinetochore-microtubule attachments in a meiosis-specific manner, but not prophase I arrest. These data reveal that BubR1 plays a multifaceted role in chromosome segregation during the first meiotic division and suggest that age-related decline of BubR1 is a key determinant of the formation of aneuploid oocytes as women approach menopause.
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Affiliation(s)
- Sandra A Touati
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris Seine (IBPS), UMR7622, 75005 Paris, France.,CNRS, IBPS, UMR7622 Developmental Biology Lab, 75005 Paris, France
| | - Eulalie Buffin
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris Seine (IBPS), UMR7622, 75005 Paris, France.,CNRS, IBPS, UMR7622 Developmental Biology Lab, 75005 Paris, France
| | - Damien Cladière
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris Seine (IBPS), UMR7622, 75005 Paris, France.,CNRS, IBPS, UMR7622 Developmental Biology Lab, 75005 Paris, France
| | - Khaled Hached
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris Seine (IBPS), UMR7622, 75005 Paris, France.,CNRS, IBPS, UMR7622 Developmental Biology Lab, 75005 Paris, France
| | - Christophe Rachez
- Departement de Biologie du Développement et Cellules Souches, CNRS URA2578, Unité de Régulation Epigénétique, Institut Pasteur, 75015 Paris, France
| | - Jan M van Deursen
- Department of Pediatric and Adolescent Medicine and Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
| | - Katja Wassmann
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris Seine (IBPS), UMR7622, 75005 Paris, France.,CNRS, IBPS, UMR7622 Developmental Biology Lab, 75005 Paris, France
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5
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Harouz H, Rachez C, Meijer B, Muchardt C, Arbibe L. Targeting of chromatin readers: a novel strategy used by the Shigella flexneri virulence effector OspF to reprogram transcription. Microb Cell 2014; 2:26-28. [PMID: 28357260 PMCID: PMC5361648 DOI: 10.15698/mic2015.01.183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Shigella flexneri, a gram-negative bacterium responsible of bacillary dysentery, uses multiple strategies to overcome host immune defense. We have decrypted how this bacterium manipulates host-cell chromatin binders to take control of immune gene expression. We found that OspF, an injected virulence factor previously identified as a repressor of immune gene expression, targets the chromatin reader HP1γ. Heterochromatin Protein 1 family members specifically recognize and bind histone H3 methylated at Lys 9. Although initially identified as chromatin-associated transcriptional silencers in heterochromatin, their location in euchromatin indicates an active role in gene expression. Notably, HP1γ phosphorylation at Serine 83 defines a subpopulation exclusively located to euchromatin, targeted to the site of transcriptional elongation. We showed that OspF directly interacts with HP1γ, and causes HP1 dephosphorylation, suggesting a model in which this virulence effector “uses” HP1 proteins as beacons to target and repress immune gene expression (Harouz, et al. EMBO J (2014)). OspF alters HP1γ phosphorylation mainly by inactivating the Erk-activated kinase MSK1, spotlighting it as a new HP1 kinase. In vivo, infectious stresses trigger HP1γ phosphorylation in the colon, principally in the lamina propria and the intestinal crypts. Several lines of evidence suggest that HP1 proteins are modified as extensively as histones, and decrypting the impact of these HP1 post-translational modifications on their transcriptional activities in vivo will be the next challenges to be taken up.
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Affiliation(s)
- Habiba Harouz
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Christophe Rachez
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Benoit Meijer
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Christian Muchardt
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Laurence Arbibe
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
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6
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Harouz H, Rachez C, Meijer BM, Marteyn B, Donnadieu F, Cammas F, Muchardt C, Sansonetti P, Arbibe L. Shigella flexneri targets the HP1γ subcode through the phosphothreonine lyase OspF. EMBO J 2014; 33:2606-22. [PMID: 25216677 DOI: 10.15252/embj.201489244] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 01/08/2023] Open
Abstract
HP1 proteins are transcriptional regulators that, like histones, are targets for post-translational modifications defining an HP1-mediated subcode. HP1γ has multiple phosphorylation sites, including serine 83 (S83) that marks it to sites of active transcription. In a guinea pig model for Shigella enterocolitis, we observed that the defective type III secretion mxiD Shigella flexneri strain caused more HP1γ phosphorylation in the colon than the wild-type strain. Shigella interferes with HP1 phosphorylation by injecting the phospholyase OspF. This effector interacts with HP1γ and alters its phosphorylation at S83 by inactivating ERK and consequently MSK1, a downstream kinase. MSK1 that here arises as a novel HP1γ kinase, phosphorylates HP1γ at S83 in the context of an MSK1-HP1γ complex, and thereby favors its accumulation on its target genes. Genome-wide transcriptome analysis reveals that this mechanism is linked to up-regulation of proliferative gene and fine-tuning of immune gene expression. Thus, in addition to histones, bacteria control host transcription by modulating the activity of HP1 proteins, with potential implications in transcriptional reprogramming at the mucosal barrier.
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Affiliation(s)
- Habiba Harouz
- Unité de Pathogénie Microbienne Moléculaire, Unité INSERM 786 Institut Pasteur, Paris, France
| | - Christophe Rachez
- Department of Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Institut Pasteur, Paris, France URA2578 CNRS, Paris, France
| | - Benoit M Meijer
- Unité de Pathogénie Microbienne Moléculaire, Unité INSERM 786 Institut Pasteur, Paris, France
| | - Benoit Marteyn
- Unité de Pathogénie Microbienne Moléculaire, Unité INSERM 786 Institut Pasteur, Paris, France
| | - Françoise Donnadieu
- Unité de Pathogénie Microbienne Moléculaire, Unité INSERM 786 Institut Pasteur, Paris, France
| | - Florence Cammas
- Equipe Epigénétique, différenciation cellulaire et cancer IRCM, Montpellier, France
| | - Christian Muchardt
- Department of Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Institut Pasteur, Paris, France URA2578 CNRS, Paris, France
| | - Philippe Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Unité INSERM 786 Institut Pasteur, Paris, France
| | - Laurence Arbibe
- Unité de Pathogénie Microbienne Moléculaire, Unité INSERM 786 Institut Pasteur, Paris, France
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Lien F, Berthier A, Bouchaert E, Gheeraert C, Alexandre J, Porez G, Prawitt J, Dehondt H, Ploton M, Colin S, Lucas A, Patrice A, Pattou F, Diemer H, Van Dorsselaer A, Rachez C, Kamilic J, Groen AK, Staels B, Lefebvre P. Metformin interferes with bile acid homeostasis through AMPK-FXR crosstalk. J Clin Invest 2014; 124:1037-51. [PMID: 24531544 DOI: 10.1172/jci68815] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/05/2013] [Indexed: 12/24/2022] Open
Abstract
The nuclear bile acid receptor farnesoid X receptor (FXR) is an important transcriptional regulator of bile acid, lipid, and glucose metabolism. FXR is highly expressed in the liver and intestine and controls the synthesis and enterohepatic circulation of bile acids. However, little is known about FXR-associated proteins that contribute to metabolic regulation. Here, we performed a mass spectrometry-based search for FXR-interacting proteins in human hepatoma cells and identified AMPK as a coregulator of FXR. FXR interacted with the nutrient-sensitive kinase AMPK in the cytoplasm of target cells and was phosphorylated in its hinge domain. In cultured human and murine hepatocytes and enterocytes, pharmacological activation of AMPK inhibited FXR transcriptional activity and prevented FXR coactivator recruitment to promoters of FXR-regulated genes. Furthermore, treatment with AMPK activators, including the antidiabetic biguanide metformin, inhibited FXR agonist induction of FXR target genes in mouse liver and intestine. In a mouse model of intrahepatic cholestasis, metformin treatment induced FXR phosphorylation, perturbed bile acid homeostasis, and worsened liver injury. Together, our data indicate that AMPK directly phosphorylates and regulates FXR transcriptional activity to precipitate liver injury under conditions favoring cholestasis.
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8
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Flajollet S, Rachez C, Ploton M, Schulz C, Gallais R, Métivier R, Pawlak M, Leray A, Issulahi AA, Héliot L, Staels B, Salbert G, Lefebvre P. The elongation complex components BRD4 and MLLT3/AF9 are transcriptional coactivators of nuclear retinoid receptors. PLoS One 2013; 8:e64880. [PMID: 23762261 PMCID: PMC3677938 DOI: 10.1371/journal.pone.0064880] [Citation(s) in RCA: 13] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/18/2013] [Indexed: 12/20/2022] Open
Abstract
Nuclear all-trans retinoic acid receptors (RARs) initiate early transcriptional events which engage pluripotent cells to differentiate into specific lineages. RAR-controlled transactivation depends mostly on agonist-induced structural transitions in RAR C-terminus (AF-2), thus bridging coactivators or corepressors to chromatin, hence controlling preinitiation complex assembly. However, the contribution of other domains of RAR to its overall transcriptional activity remains poorly defined. A proteomic characterization of nuclear proteins interacting with RAR regions distinct from the AF-2 revealed unsuspected functional properties of the RAR N-terminus. Indeed, mass spectrometry fingerprinting identified the Bromodomain-containing protein 4 (BRD4) and ALL1-fused gene from chromosome 9 (AF9/MLLT3), known to associate with and regulates the activity of Positive Transcription Elongation Factor b (P-TEFb), as novel RAR coactivators. In addition to promoter sequences, RAR binds to genomic, transcribed regions of retinoid-regulated genes, in association with RNA polymerase II and as a function of P-TEFb activity. Knockdown of either AF9 or BRD4 expression affected differentially the neural differentiation of stem cell-like P19 cells. Clusters of retinoid-regulated genes were selectively dependent on BRD4 and/or AF9 expression, which correlated with RAR association to transcribed regions. Thus RAR establishes physical and functional links with components of the elongation complex, enabling the rapid retinoid-induced induction of genes required for neuronal differentiation. Our data thereby extends the previously known RAR interactome from classical transcriptional modulators to components of the elongation machinery, and unravel a functional role of RAR in transcriptional elongation.
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Affiliation(s)
- Sébastien Flajollet
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Christophe Rachez
- Unité de Régulation Epigénétique, URA 2578 du CNRS, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | - Maheul Ploton
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Céline Schulz
- Interdisciplinary Research Institute, Univ Lille 1, USR 3078 CNRS, Biophotonique Cellulaire Fonctionnelle, Villeneuve d’Ascq, France
| | - Rozenn Gallais
- Equipe SPARTE, UMR CNRS 6026-Université Rennes 1, Rennes, France
| | - Raphaël Métivier
- Equipe SPARTE, UMR CNRS 6026-Université Rennes 1, Rennes, France
| | - Michal Pawlak
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Aymeric Leray
- Interdisciplinary Research Institute, Univ Lille 1, USR 3078 CNRS, Biophotonique Cellulaire Fonctionnelle, Villeneuve d’Ascq, France
| | - Al Amine Issulahi
- Interdisciplinary Research Institute, Univ Lille 1, USR 3078 CNRS, Biophotonique Cellulaire Fonctionnelle, Villeneuve d’Ascq, France
| | - Laurent Héliot
- Interdisciplinary Research Institute, Univ Lille 1, USR 3078 CNRS, Biophotonique Cellulaire Fonctionnelle, Villeneuve d’Ascq, France
| | - Bart Staels
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Gilles Salbert
- Equipe SPARTE, UMR CNRS 6026-Université Rennes 1, Rennes, France
| | - Philippe Lefebvre
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
- * E-mail:
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9
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Attia M, Rachez C, Avner P, Rogner UC. Nucleosome assembly proteins and their interacting proteins in neuronal differentiation. Arch Biochem Biophys 2013; 534:20-6. [DOI: 10.1016/j.abb.2012.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/21/2012] [Accepted: 09/22/2012] [Indexed: 12/21/2022]
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10
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Harel-Bellan A, Zazoua MA, Rachez C, Muchardt C, Batsché E. 10-million-years AGO: argonaute on chromatin in yeast and human, a conserved mode of action? Transcription 2013; 4:89-91. [PMID: 23584094 DOI: 10.4161/trns.24582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 01/22/2023] Open
Abstract
Whereas in yeast the function and mode of action of nuclear RNAi are well documented, mammalian nuclear RNAi is a matter of debates. Several papers support a role for nuclear Argonaute in alternative splicing. However, the molecular mechanism remains elusive. Here, we discuss the human nuclear RNAi mechanism in light of what is known of the yeast process.
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Affiliation(s)
- Annick Harel-Bellan
- Université Paris Sud; Laboratoire Epigenetique et Cancer; Formation de Recherche en Evolution 3377; Gif-Sur-Yvette, France; Centre National de la Recherche Scientifique (CNRS); Gif-Sur-Yvette, France; Commissariat à l'Energie Atomique (CEA); Saclay; Gif-sur-Yvette, France
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11
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Hached K, Xie SZ, Buffin E, Cladière D, Rachez C, Sacras M, Sorger PK, Wassmann K. Mps1 at kinetochores is essential for female mouse meiosis I. J Cell Sci 2011. [DOI: 10.1242/jcs.092858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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12
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Hached K, Xie SZ, Buffin E, Cladière D, Rachez C, Sacras M, Sorger PK, Wassmann K. Mps1 at kinetochores is essential for female mouse meiosis I. Development 2011; 138:2261-71. [DOI: 10.1242/dev.061317] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In female meiosis, chromosome missegregations lead to the generation of aneuploid oocytes and can cause the development of trisomies or infertility. Because mammalian female meiosis I is error prone, the full functionality of control mechanisms, such as the spindle assembly checkpoint (SAC), has been put into question. The SAC monitors the correct orientation, microtubule occupancy and tension on proteinaceous structures named kinetochores. Although it has been shown previously that the SAC exists in meiosis I, where attachments are monopolar, the role of microtubule occupancy for silencing the SAC and the importance of certain essential SAC components, such as the kinase Mps1, are unknown in mammalian oocytes. Using a conditional loss-of-function approach, we address the role of Mps1 in meiotic progression and checkpoint control in meiosis I. Our data demonstrate that kinetochore localization of Mps1 is required for the proper timing of prometaphase and is essential for SAC control, chromosome alignment and aurora C localization in meiosis I. The absence of Mps1 from kinetochores severely impairs chromosome segregation in oocyte meiosis I and, therefore, fertility in mice. In addition, we settle a long-standing question in showing that kinetochore-microtubule attachments are present in prometaphase I at a time when most of the SAC protein Mad2 disappears from kinetochores.
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Affiliation(s)
- Khaled Hached
- UPMC, 9 quai St Bernard, 75005 Paris, France
- CNRS UMR7622 Biologie du Développement, Cell Division and Associated Checkpoints, 9 quai St Bernard, 75005 Paris, France
| | - Stephanie Z. Xie
- Department of Biology, Center for Cancer Research, and Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Eulalie Buffin
- UPMC, 9 quai St Bernard, 75005 Paris, France
- CNRS UMR7622 Biologie du Développement, Cell Division and Associated Checkpoints, 9 quai St Bernard, 75005 Paris, France
| | - Damien Cladière
- UPMC, 9 quai St Bernard, 75005 Paris, France
- CNRS UMR7622 Biologie du Développement, Cell Division and Associated Checkpoints, 9 quai St Bernard, 75005 Paris, France
| | - Christophe Rachez
- Institut Pasteur, CNRS URA2578, 75724 Paris cedex 15, France
- Unité de Régulation Epigénétique, INSERM Avenir, Institut Pasteur, 75724 Paris cedex 15, France
| | - Marina Sacras
- UPMC, 9 quai St Bernard, 75005 Paris, France
- CNRS UMR7622 Biologie du Développement, Cell Division and Associated Checkpoints, 9 quai St Bernard, 75005 Paris, France
| | - Peter K. Sorger
- Department of Biology, Center for Cancer Research, and Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Katja Wassmann
- UPMC, 9 quai St Bernard, 75005 Paris, France
- CNRS UMR7622 Biologie du Développement, Cell Division and Associated Checkpoints, 9 quai St Bernard, 75005 Paris, France
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13
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Attia M, Förster A, Rachez C, Freemont P, Avner P, Rogner UC. Interaction between Nucleosome Assembly Protein 1-like Family Members. J Mol Biol 2011; 407:647-60. [DOI: 10.1016/j.jmb.2011.02.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 01/19/2011] [Accepted: 02/07/2011] [Indexed: 01/08/2023]
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14
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Saint-André V, Batsché E, Rachez C, Muchardt C. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nat Struct Mol Biol 2011; 18:337-44. [PMID: 21358630 DOI: 10.1038/nsmb.1995] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 12/02/2010] [Indexed: 12/14/2022]
Abstract
Pre-messenger RNAs (pre-mRNAs) maturation is initiated cotranscriptionally. It is therefore conceivable that chromatin-borne information participates in alternative splicing. Here we find that elevated levels of trimethylation of histone H3 on Lys9 (H3K9me3) are a characteristic of the alternative exons of several genes including CD44. On this gene the chromodomain protein HP1γ, frequently defined as a transcriptional repressor, facilitates inclusion of the alternative exons via a mechanism involving decreased RNA polymerase II elongation rate. In addition, accumulation of HP1γ on the variant region of the CD44 gene stabilizes association of the pre-mRNA with the chromatin. Altogether, our data provide evidence for localized histone modifications impacting alternative splicing. They further implicate HP1γ as a possible bridging molecule between the chromatin and the maturating mRNA, with a general impact on splicing decisions.
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Affiliation(s)
- Violaine Saint-André
- Institut Pasteur, Département de Biologie du Développement, Unité de Régulation Epigénétique, Paris, France
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15
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Abstract
The deletion of the neuronal Nap1l2 (nucleosome assembly protein 1-like 2) gene in mice causes neural tube defects. We demonstrate here that this phenotype correlates with deficiencies in differentiation and increased maintenance of the neural stem cell stage. Nap1l2 associates with chromatin and interacts with histones H3 and H4. Loss of Nap1l2 results in decreased histone acetylation activity, leading to transcriptional changes in differentiating neurons, which include the marked downregulation of the Cdkn1c (cyclin-dependent kinase inhibitor 1c) gene. Cdkn1c expression normally increases during neuronal differentiation, and this correlates with the specific recruitment of the Nap1l2 protein and an increase in acetylated histone H3K9/14 at the site of Cdkn1c transcription. These results lead us to suggest that the Nap1l2 protein plays an important role in regulating transcription in developing neurons via the control of histone acetylation. Our data support the idea that neuronal nucleosome assembly proteins mediate cell-type-specific mechanisms of establishment/modification of a chromatin-permissive state that can affect neurogenesis and neuronal survival.
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Affiliation(s)
- Mikaël Attia
- Unité Génétique Moléculaire Murine, CNRS URA 2578, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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16
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Attia M, Rachez C, De Pauw A, Avner P, Rogner U. [P43]: The nucleosome assembly protein 1 like 2 modifies the epigenetic control of gene expression to promote neuronal differentiation. Int J Dev Neurosci 2006. [DOI: 10.1016/j.ijdevneu.2006.09.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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17
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Flajollet S, Lefebvre B, Rachez C, Lefebvre P. Distinct Roles of the Steroid Receptor Coactivator 1 and of MED1 in Retinoid-induced Transcription and Cellular Differentiation. J Biol Chem 2006; 281:20338-48. [PMID: 16723356 DOI: 10.1074/jbc.m603023200] [Citation(s) in RCA: 21] [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] [Indexed: 11/06/2022] Open
Abstract
Retinoic acid receptors (RARs) are the molecular relays of retinoid action on transcription, cellular differentiation and apoptosis. Transcriptional activation of retinoid-regulated promoters requires the dismissal of corepressors and the recruitment of coactivators to promoter-bound RAR. RARs recruit in vitro a plethora of coactivators whose actual contribution to retinoid-induced transcription is poorly characterized in vivo. Embryonal carcinoma P19 cells, which are highly sensitive to retinoids, were depleted from archetypical coactivators by RNAi. SRC1-deficient P19 cells showed severely compromised retinoid-induced responses, in agreement with the supposed role of SRC1 as a RAR coactivator. Unexpectedly, Med1/TRAP220/DRIP205-depleted cells exhibited an exacerbated response to retinoids, both in terms transcriptional responses and of cellular differentiation. Med1 depletion affected TFIIH and cdk9 detection at the prototypical retinoid-regulated RARbeta2 promoter, and favored a higher RNA polymerase II detection in transcribed regions of the RARbeta2 gene. Furthermore, the nature of the ligand impacted strongly on the ability of RARs to interact with a given coactivator and to activate transcription in intact cells. Thus RAR accomplishes transcriptional activation as a function of the ligand structure, by recruiting regulatory complexes which control distinct molecular events at retinoid-regulated promoters.
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18
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Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CPB, Burlingame AL, Freedman LP, Bikle DD. Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in VDR transactivation during keratinocyte differentiation. J Steroid Biochem Mol Biol 2004; 89-90:273-6. [PMID: 15225784 DOI: 10.1016/j.jsbmb.2004.03.106] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cell programs such as proliferation and differentiation involve the sequential activation and repression of gene expression. Vitamin D, via its active metabolite 1,25-dihydroxyvitamin D (1,25(OH)(2)D(3)), controls the proliferation and differentiation of a number of cell types, including keratinocytes, by directly regulating transcription. Two classes of coactivators, the Vitamin D receptor (VDR) interacting proteins (DRIP/mediator) and the p160 steroid receptor coactivator family (SRC/p160), control the actions of nuclear hormone receptors, including the Vitamin D receptor. However, the relationship between these two classes of coactivators is not clear. Using GST-VDR affinity beads, we have identified the DRIP/mediator complex as the major VDR binding complex in proliferating keratinocytes. After the cells differentiated, members of the SRC/p160 family were identified in the complex but not major DRIP subunits. Both DRIP205 and SRC-3 potentiated Vitamin D-induced transcription in proliferating cells, but during differentiation, DRIP205 was no longer effective. These results indicate that these two distinct coactivators are differentially involved in Vitamin D regulation of gene transcription during keratinocyte differentiation, suggesting that these coactivators are part of the means by which the temporal sequence of gene expression is regulated during the differentiation process.
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Affiliation(s)
- Yuko Oda
- Department of Medicine, University of California San Francisco, Veterans Affairs Medical Center San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA.
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19
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Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CPB, Burlingame AL, Freedman LP, Bikle DD. Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in vitamin D receptor transactivation during keratinocyte differentiation. Mol Endocrinol 2003; 17:2329-39. [PMID: 12893881 DOI: 10.1210/me.2003-0063] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [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: 11/19/2022] Open
Abstract
Cell programs such as proliferation and differentiation involve the sequential activation and repression of gene expression. Vitamin D, via its active metabolite 1,25-dihydroxyvitamin D [1,25-(OH)2D3)], controls the proliferation and differentiation of a number of cell types, including keratinocytes, by directly regulating transcription. Two classes of coactivators, the vitamin D receptor (VDR)-interacting proteins (DRIP/mediator) and the p160 steroid receptor coactivator family (SRC/p160), control the actions of nuclear hormone receptors, including the VDR. However, the relationship between these two classes of coactivators is not clear. Using glutathione-S-transferase-VDR affinity beads, we have identified the DRIP/mediator complex as the major VDR binding complex in proliferating keratinocytes. After the cells differentiated, members of the SRC/p160 family were identified in the complex but not major DRIP subunits. Both DRIP and SRC proteins were expressed in keratinocytes. DRIP205 expression decreased during differentiation, although SRC-3 levels increased. Both DRIP205 and SRC-3 potentiated vitamin D-induced transcription in proliferating cells, but during differentiation, DRIP205 was no longer effective. These results indicate that these two distinct coactivators are sequentially involved in vitamin D regulation of gene transcription during keratinocyte differentiation, suggesting that these coactivators are part of the means by which the temporal sequence of gene expression is regulated during the differentiation process.
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Affiliation(s)
- Yuko Oda
- Departments of Medicine and Endocrinology University of California San Francisco and Veterans Affairs Medical Center, San Francisco, California 94121, USA.
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20
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Sacchetti P, Dwornik H, Formstecher P, Rachez C, Lefebvre P. Requirements for heterodimerization between the orphan nuclear receptor Nurr1 and retinoid X receptors. J Biol Chem 2002; 277:35088-96. [PMID: 12122012 DOI: 10.1074/jbc.m205816200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [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: 11/06/2022] Open
Abstract
The nuclear receptor nurr1 is a transcription factor involved in the development and maintenance of neurons synthesizing the neurotransmitter dopamine. Although the lack of nurr1 expression has dramatic consequences for these cells either in terms of differentiation or survival, the mechanisms by which nurr1 controls gene transcription still remain unclear. In the intent to understand better the modalities of action of this nuclear receptor, we have undertaken a systematic analysis of the transcriptional effects and DNA binding properties of nurr1 as a monomer or when forming dimers with the different isotypes of the retinoic X receptor (RXR). Here, we show that nurr1 acts as a gene activator independently of RXR and through an AF2-independent mechanism. In addition, heterodimerization with RXR is isotype-specific, involves multiple domains in the C-terminal region of nurr1, and requires RXR binding to DNA. RXR(alpha)-nurr1 and RXRgamma-nurr1 heterodimers bind direct repeat response elements and display no specific requirements with respect to half-site spacing. However, the retinoid responsiveness of DNA-bound heterodimers requires the reiteration of at least three nurr1 binding sites, thereby limiting retinoid-induced nurr1 transcriptional activity to specific direct response elements.
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Affiliation(s)
- Paola Sacchetti
- INSERM Unité 459, Faculté de Medecine Henri Warembourg, 1 Place de Verdun, Lille 59045, France
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21
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Maeda Y, Rachez C, Hawel L, Byus CV, Freedman LP, Sladek FM. Polyamines modulate the interaction between nuclear receptors and vitamin D receptor-interacting protein 205. Mol Endocrinol 2002; 16:1502-10. [PMID: 12089346 DOI: 10.1210/mend.16.7.0883] [Citation(s) in RCA: 24] [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: 11/19/2022] Open
Abstract
Nuclear receptors (NR) activate transcription by interacting with several different coactivator complexes, primarily via LXXLL motifs (NR boxes) of the coactivator that bind a common region in the ligand binding domain of nuclear receptors (activation function-2, AF-2) in a ligand-dependent fashion. However, how nuclear receptors distinguish between different sets of coactivators remains a mystery, as does the mechanism by which orphan receptors such as hepatocyte nuclear factor 4alpha (HNF4alpha) activate transcription. In this study, we show that HNF4alpha interacts with a complex containing vitamin D receptor (VDR)-interacting proteins (DRIPs) in the absence of exogenously added ligand. However, whereas a full-length DRIP205 construct enhanced the activation by HNF4alpha in vivo, it did not interact well with the HNF4alpha ligand binding domain in vitro. In investigating this discrepancy, we found that the polyamine spermine significantly enhanced the interaction between HNF4alpha and full-length DRIP205 in an AF-2, NR-box-dependent manner. Spermine also enhanced the interaction of DRIP205 with the VDR even in the presence of its ligand, but decreased the interaction of both HNF4alpha and VDR with the p160 coactivator glucocorticoid receptor interacting protein 1 (GR1P1). We also found that GR1P1 and DRIP205 synergistically activated HNF4alpha-mediated transcription and that a specific inhibitor of polyamine biosynthesis, alpha-difluoromethylornithine (DFMO), decreased the ability of HNF4alpha to activate transcription in vivo. These results lead us to propose a model in which polyamines may facilitate the switch between different coactivator complexes binding to NRs.
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MESH Headings
- Amino Acid Motifs
- Animals
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
- Binding Sites
- Carrier Proteins
- Cells, Cultured
- DNA-Binding Proteins
- Eflornithine/pharmacology
- Hepatocyte Nuclear Factor 4
- Humans
- Mediator Complex Subunit 1
- Nuclear Receptor Coactivator 2
- Phosphoproteins/drug effects
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Polyamines/metabolism
- Polyamines/pharmacology
- Rats
- Receptors, Calcitriol/drug effects
- Receptors, Calcitriol/genetics
- Receptors, Calcitriol/metabolism
- Receptors, Cytoplasmic and Nuclear/drug effects
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, Thyroid Hormone/drug effects
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Spermine/metabolism
- Spermine/pharmacology
- Transcription Factors/drug effects
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Yutaka Maeda
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, USA
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22
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Abstract
Over the past decade, various components of the transcription machinery have been identified as potential targets for activators. Recently, metazoan versions of yeast Mediator have been isolated and found to act as key coactivators to many transcription factors. Recent work has defined the composition, function and biology of metazoan mediator complexes, which has led us to propose a new nomenclature for the variously named versions of the mediator complex.
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Affiliation(s)
- C Rachez
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
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23
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Yang W, Rachez C, Freedman LP. Discrete roles for peroxisome proliferator-activated receptor gamma and retinoid X receptor in recruiting nuclear receptor coactivators. Mol Cell Biol 2000; 20:8008-17. [PMID: 11027271 PMCID: PMC86411 DOI: 10.1128/mcb.20.21.8008-8017.2000] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.2] [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: 11/20/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARgamma) plays a major role in adipogenesis. PPARgamma binds to DNA as a heterodimer with retinoid X receptor (RXR), and PPARgamma-RXR can be activated by ligands specific for either receptor; the presence of both ligands can result in a cooperative effect on the transactivation of target genes. How these ligands mediate transactivation, however, remains unclear. PPARgamma is known to interact with both the p160/SRC-1 family of coactivators and the distinct, multisubunit coactivator complex called DRIP. A single DRIP subunit, DRIP205 (TRAP220, PBP), binds directly to PPARgamma. Here we report that PPARgamma and RXR selectively interacted with DRIP205 and p160 proteins in a ligand-dependent manner. At physiological concentrations, RXR-specific ligands only induced p160 binding to RXR, and PPARgamma-specific ligands exclusively recruited DRIP205 but not p160 coactivators to PPARgamma. This selectivity was not observed in interaction assays off DNA, implying that the specificity of coactivator binding in response to ligand is strongly influenced by the allosteric effects of DNA-bound heterodimers. These coactivator-selective effects were also observed in transient-transfection assays in the presence of overexpressed p160 or DRIP coactivators. The results suggest that the cooperative effects of PPARgamma- and RXR-specific ligands may occur at the level of selective coactivator recruitment.
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Affiliation(s)
- W Yang
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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24
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Shao W, Rosenauer A, Mann K, Chang CP, Rachez C, Freedman LP, Miller WH. Ligand-inducible interaction of the DRIP/TRAP coactivator complex with retinoid receptors in retinoic acid-sensitive and -resistant acute promyelocytic leukemia cells. Blood 2000; 96:2233-9. [PMID: 10979971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Retinoic acid (RA) signaling is mediated by its nuclear receptors RXR and RAR, which bind to their cognate response elements as a heterodimer, RXR/RAR, and act in concert with coregulatory factors to regulate gene transcription on ligand binding. To identify specific cofactors that interact with the RXR/RAR heterodimer in acute promyelocytic leukemia (APL) cells, a double cistronic construct was used that allowed coexpression of the RXR LBD (ligand binding domain) with the RAR LBD as an affinity matrix to pull down interacting proteins from nuclear extracts prepared from a human APL cell line, NB4. A group of proteins was detected whose interaction with RXR/RAR is ligand inducible. The molecular weight pattern of these proteins is similar to that of a complex of proteins previously identified as DRIP or TRAP, which are ligand-dependent transcription activators of VDR and TR, respectively. The RXR/RAR-interacting proteins from NB4 were confirmed to be identical to the DRIP subunits by comparative electrophoresis, Western blot analysis, and in vitro protein interaction assay. In addition to RXR/RAR, the DRIP component can interact directly with the APL-specific PML-RARalpha fusion protein. The same DRIP complex is present in RA-resistant APL cells and in a variety of cancer cell lines, supporting its global role in transcriptional regulation.
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Affiliation(s)
- W Shao
- Department of Medicine, Division of Experimental Medicine, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montreal, Quebec, Canada
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25
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Burakov D, Wong CW, Rachez C, Cheskis BJ, Freedman LP. Functional interactions between the estrogen receptor and DRIP205, a subunit of the heteromeric DRIP coactivator complex. J Biol Chem 2000; 275:20928-34. [PMID: 10770935 DOI: 10.1074/jbc.m002013200] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [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
Nuclear receptors regulate transcription in direct response to their cognate hormonal ligands. Ligand binding leads to the dissociation of corepressors and the recruitment of coactivators. Many of these factors, acting in large complexes, have emerged as potential chromatin remodelers through intrinsic histone modifying activities. In addition, other ligand-recruited complexes appear to act more directly on the transcriptional apparatus. The DRIP complex is a 15-subunit complex required for nuclear receptor transcriptional activation in vitro. It is recruited to the receptor in response to ligand through specific interactions of one subunit, DRIP205. We present evidence that DRIP205 interacts with another member of the steroid receptor subfamily, estrogen receptor (ER). This interaction occurs in an agonist-stimulated fashion which in turn is inhibited by several ER antagonists. In vivo, a fragment of DRIP205 containing only its receptor interacting region acts to selectively inhibit ER's ability to activate transcription in response to estradiol. These observations suggest a key role for the DRIP coactivator complex in estrogen-ER signaling.
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Affiliation(s)
- D Burakov
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, Sloan-Kettering Division, Cornell University, Graduate School of Medical Sciences, New York, New York 10021, USA
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26
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Abstract
The vitamin D(3) receptor regulates transcription in direct response to its cognate hormonal ligand, 1,25(OH)(2)D(3). Ligand binding leads to the recruitment of coactivators. Many of these factors, acting in large complexes, have emerged as chromatin remodelers partly through intrinsic histone modifying activities. In addition, other ligand-recruited complexes appear to act more directly on the transcriptional apparatus, suggesting that transcriptional regulation by VDR and other nuclear receptors may involve a process of both chromatin alterations and direct recruitment of key initiation components at regulated promoters.
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Affiliation(s)
- C Rachez
- Cell Biology Program Memorial Sloan-Kettering Cancer Center 1275 York Avenue, New York, NY 10021, USA
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27
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Rachez C, Gamble M, Chang CP, Atkins GB, Lazar MA, Freedman LP. The DRIP complex and SRC-1/p160 coactivators share similar nuclear receptor binding determinants but constitute functionally distinct complexes. Mol Cell Biol 2000; 20:2718-26. [PMID: 10733574 PMCID: PMC85487 DOI: 10.1128/mcb.20.8.2718-2726.2000] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Accepted: 01/18/2000] [Indexed: 11/20/2022] Open
Abstract
Transcriptional activation requires both access to DNA assembled as chromatin and functional contact with components of the basal transcription machinery. Using the hormone-bound vitamin D(3) receptor (VDR) ligand binding domain (LBD) as an affinity matrix, we previously identified a novel multisubunit coactivator complex, DRIP (VDR-interacting proteins), required for transcriptional activation by nuclear receptors and several other transcription factors. In this report, we characterize the nuclear receptor binding features of DRIP205, a key subunit of the DRIP complex, that interacts directly with VDR and thyroid hormone receptor in response to ligand and anchors the other DRIP subunits to the nuclear receptor LBD. In common with other nuclear receptor coactivators, DRIP205 interaction occurs through one of two LXXLL motifs and requires the receptor's AF-2 subdomain. Although the second motif of DRIP205 is required only for VDR binding in vitro, both motifs are used in the context of an retinoid X receptor-VDR heterodimer on DNA and in transactivation in vivo. We demonstrate that both endogenous p160 coactivators and DRIP complexes bind to the VDR LBD from nuclear extracts through similar sequence requirements, but they do so as distinct complexes. Moreover, in contrast to the p160 family of coactivators, the DRIP complex is devoid of any histone acetyltransferase activity. The results demonstrate that different coactivator complexes with distinct functions bind to the same transactivation region of nuclear receptors, suggesting that they are both required for transcription activation by nuclear receptors.
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Affiliation(s)
- C Rachez
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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28
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Zhong S, Delva L, Rachez C, Cenciarelli C, Gandini D, Zhang H, Kalantry S, Freedman LP, Pandolfi PP. A RA-dependent, tumour-growth suppressive transcription complex is the target of the PML-RARalpha and T18 oncoproteins. Nat Genet 1999; 23:287-95. [PMID: 10610177 DOI: 10.1038/15463] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.3] [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: 11/09/2022]
Abstract
PML and Tif1a are fused to RARA and Braf, respectively, resulting in the production of PML-RARalpha and Tif1alpha-B-Raf (T18) oncoproteins. Here we show that PML, Tif1alpha and RXRalpha/RARalpha function together in a transcription complex that is dependent on retinoic acid (RA). We found that PML acts as a ligand-dependent coactivator of RXRalpha/RARalpha. PML interacts with Tif1alpha and CBP. In Pml-/- cells, the RA-dependent induction of genes such as RARB2 and the ability of Tif1alpha and CBP to act as transcriptional coactivators on RA are impaired. We show that both PML and Tif1alpha are growth suppressors required for the growth-inhibitory activity of RA. T18, similar to PML-RARalpha, disrupts the RA-dependent activity of this complex in a dominant-negative manner resulting in a growth advantage. Our data define a new pathway for the control of cell growth and tumorigenesis, and provide a new model for the pathogenesis of acute promyelocytic leukaemia (APL).
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MESH Headings
- Animals
- CREB-Binding Protein
- Cell Differentiation/drug effects
- Cell Division/drug effects
- Cell Line
- Cell Nucleus/metabolism
- Cell Transformation, Neoplastic/drug effects
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- DNA/genetics
- DNA/metabolism
- Gene Expression Regulation, Neoplastic/drug effects
- Genes, Tumor Suppressor/genetics
- Genes, Tumor Suppressor/physiology
- Humans
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Mutation
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/chemistry
- Nuclear Proteins/metabolism
- Oncogene Proteins, Fusion/chemistry
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/metabolism
- Retinoid X Receptors
- Trans-Activators/metabolism
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transfection
- Tretinoin/metabolism
- Tretinoin/pharmacology
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Affiliation(s)
- S Zhong
- Department of Human Genetics, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, Sloan-Kettering Division, Graduate School of Medical Sciences, Cornell University, New York, New York, USA
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29
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Abstract
A mutation in the nuclear orphan receptor RORalpha results in a severe impairment of cerebellar development by unknown mechanisms. We have shown previously that RORalpha contains a strong constitutive activation domain in its C terminus. We therefore searched for mammalian RORalpha coactivators using the minimal activation domain as bait in a two-hybrid screen. Several known and putative coactivators were isolated, including glucocorticoid receptor-interacting protein-1 (GRIP-1) and peroxisome proliferator-activated receptor (PPAR)-binding protein (PBP/TRAP220/DRIP205). These interactions were confirmed in vitro and require the intact activation domain of RORalpha although different requirements for interaction with GRIP-1 and PBP were detected. Even in the absence of exogenous ligand, RORalpha interacts with a complex or complexes of endogenous proteins, similar to those that bind to ligand-occupied thyroid hormone and vitamin D receptors. Both PBP and GRIP-1 were shown to be present in these complexes. Thus we have identified several potential RORalpha coactivators that, in contrast to the interactions with hormone receptors, interact with RORalpha in yeast, in bacterial extracts, and in mammalian cells in vivo and in vitro in the absence of exogenous ligand. GRIP-1 functioned as a coactivator for the RORalpha both in yeast and in mammalian cells. Thus, GRIP-1 is the first proven coactivator for RORalpha.
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Affiliation(s)
- G B Atkins
- Department of Medicine, The Penn Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia 19104-6149, USA
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30
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Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Näär AM, Erdjument-Bromage H, Tempst P, Freedman LP. Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex. Nature 1999; 398:824-8. [PMID: 10235266 DOI: 10.1038/19783] [Citation(s) in RCA: 599] [Impact Index Per Article: 24.0] [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: 01/17/2023]
Abstract
Nuclear receptors modulate the transcription of genes in direct response to small lipophilic ligands. Binding to ligands induces conformational changes in the nuclear receptors that enable the receptors to interact with several types of cofactor that are critical for transcription activation (transactivation). We previously described a distinct set of ligand-dependent proteins called DRIPs, which interact with the vitamin D receptor (VDR); together, these proteins constitute a new cofactor complex. DRIPs bind to several nuclear receptors and mediate ligand-dependent enhancement of transcription by VDR and the thyroid-hormone receptor in cell-free transcription assays. Here we report the identities of thirteen DRIPs that constitute this complex, and show that the complex has a central function in hormone-dependent transactivation by VDR on chromatin templates. The DRIPs are almost indistinguishable from components of another new cofactor complex called ARC, which is recruited by other types of transcription activators to mediate transactivation on chromatin-assembled templates. Several DRIP/ARC subunits are also components of other potentially related cofactors, such as CRSP, NAT, SMCC and the mouse Mediator, indicating that unique classes of activators may share common sets or subsets of cofactors. The role of nuclear-receptor ligands may, in part, be to recruit such a cofactor complex to the receptor and, in doing so, to enhance transcription of target genes.
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Affiliation(s)
- C Rachez
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, Graduate School of Medical Sciences, Cornell University, New York, New York 10021, USA
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31
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Rachez C, Suldan Z, Ward J, Chang CP, Burakov D, Erdjument-Bromage H, Tempst P, Freedman LP. A novel protein complex that interacts with the vitamin D3 receptor in a ligand-dependent manner and enhances VDR transactivation in a cell-free system. Genes Dev 1998; 12:1787-800. [PMID: 9637681 PMCID: PMC316901 DOI: 10.1101/gad.12.12.1787] [Citation(s) in RCA: 314] [Impact Index Per Article: 12.1] [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: 12/18/1997] [Accepted: 04/17/1998] [Indexed: 11/25/2022]
Abstract
Nuclear receptors transduce hormonal signals by binding directly to DNA target sites in promoters and modulating the transcription of linked genes. Receptor-mediated transactivation appears to be potentiated in response to ligand by a number of coactivators that may provide key interactions with components of the transcription preinitiation complex and/or alter chromatin structure. Here, we use the vitamin D3 receptor ligand-binding domain (VDR LBD) as an affinity matrix to identify components of a transcriptionally active nuclear extract that interact with VDR in response to ligand. We describe the purification of a complex of at least 10 VDR interacting proteins (DRIPs) ranging from 65 to 250 kD that associate with the receptor in a strictly 1,25-dihydroxyvitamin D3-dependent manner. These proteins also appear to interact with other, but not all, nuclear receptors, such as the thyroid hormone receptor. The DRIPs are distinct from known nuclear receptor coactivators, although like these coactivators, their interaction also requires the AF-2 transactivation motif of VDR. In addition, the DRIP complex contains histone acetyltransferase activity, indicating that at least one or more of the DRIPs may function at the level of nucleosomal modification. However, we show that the DRIPs selectively enhance the transcriptional activity of VDR on a naked DNA template utilizing a cell-free, ligand-dependent transcription assay. Moreover, this activity can be specifically depleted from the extract by liganded, but not unliganded, VDR-LBD. Overexpression of DRIP100 in vivo resulted in a strong squelching of VDR transactivation, suggesting the sequestration of other limiting factors, including components of the DRIP complex. These results demonstrate the existence of a new complex of novel functional nuclear receptor coactivators.
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Affiliation(s)
- C Rachez
- Cell Biology Program,Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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32
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Tahayato A, Rachez C, Formstecher P, Lefebvre P. Analysis of retinoid receptor phosphorylation. Methods Mol Biol 1998; 89:277-291. [PMID: 9664335 DOI: 10.1385/0-89603-438-0:277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- A Tahayato
- CJF INSERM, Laboratoire de Biochimie Structurale, Faculté de Médecine de Lille, France
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33
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Rachez C, Sautière P, Formstecher P, Lefebvre P. Identification of amino acids critical for the DNA binding and dimerization properties of the human retinoic acid receptor alpha. Importance of lysine 360, lysine 365, and valine 361. J Biol Chem 1996; 271:17996-8006. [PMID: 8663386 DOI: 10.1074/jbc.271.30.17996] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [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: 02/01/2023] Open
Abstract
Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) activate target genes by binding to retinoic acid response elements (RAREs) as heterodimeric, asymmetrical complexes, and display a high degree of cooperativity in binding to RAREs. We have examined here the effect of lysine, cysteine, arginine, histidine, and tyrosine side chain chemical modification on the DNA binding, homo- and heterodimerization properties of the full-length human retinoic acid receptor alpha (hRARalpha). Lysines are the only residues to be engaged in the dimerization with human retinoid X receptor alpha (hRXRalpha) in the absence of DNA, whereas histidines are selectively involved in the homodimerization of hRARalpha in the presence of a RARE. Arginine modification affected the DNA binding activity of each type of dimer, whereas cysteines and tyrosines were primarily involved in the homo- or heterodimerization process in the presence of the same RARE. Modified lysines, interfering with the dimerization with hRXRalpha, were identified by receptor labeling and peptide mapping. They are located in the hormone binding domain eighth heptad repeat, at positions 360 and 365. In keeping with these results, mutation of Lys360, Val361, and Lys365 diminished strongly the DNA binding activity of hRARalpha as a homodimer or a heterodimer. Our results thus provide direct evidence for the differential involvement of basic, polar, or aromatic amino acids in the DNA binding, homodimerization, and heterodimerization properties of hRARalpha. Furthermore, they demonstrate the use of distinct dimerization interfaces and identify the type of amino acids involved in these protein-protein interactions.
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Affiliation(s)
- C Rachez
- CJF INSERM 92-03, Laboratoire de Biochimie Structurale, Faculté de Médecine de Lille 1, France
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34
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Lefebvre B, Rachez C, Formstecher P, Lefebvre P. Structural determinants of the ligand-binding site of the human retinoic acid receptor alpha. Biochemistry 1995; 34:5477-85. [PMID: 7727406 DOI: 10.1021/bi00016a019] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [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: 01/26/2023]
Abstract
The ligand-dependent transactivating properties of retinoic acid receptors are controlled through a complex structure at the C-terminus of these proteins, commonly referred to as the hormone binding domain. This domain is involved not only in ligand recognition but also in protein-protein interactions such as homo- and heterodimerization processes. To identify more precisely regions of the human all-trans-retinoic acid receptor alpha (hRAR alpha) that are involved in ligand binding, we constructed a series of deletion mutants of this molecule and overexpressed them in bacteria. We found that the C-terminal part of the D domain (amino acids 186-198) was necessary for ligand binding. The F domain and the 10 C-terminal amino acids of the E domain were dispensable for high-affinity binding of various natural and synthetic retinoids. A further deletion to position 403 resulted in a moderate decrease in affinity for all-trans-(ATRA) and 9-cis-retinoic acids, whereas the binding of two RAR alpha-specific ligands (Am80 and Am580) was abolished. In addition, hRAR alpha and the minimal hormone binding domain (amino acids 186-410) bound ATRA with a positive, cooperative mechanism. This behavior was not observed with CD367, a conformationally restricted synthetic retinoid. The positive cooperativity could be correlated with stable ATRA binding to RAR homodimers, whose formation was triggered by ligand. In the same conditions, only monomeric CD367-RAR alpha complexes were detected. These data indicate that ligand binding to hRAR alpha requires the presence of part of the D domain, whereas the C-terminal end of the E domain is involved in more subtle ligand recognition processes.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- B Lefebvre
- CJF-INSERM 92-03, Laboratoire de Biochimie Structurale, Faculté de Médecine de Lille, France
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35
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Thon VJ, Vigneron-Lesens C, Marianne-Pepin T, Montreuil J, Decq A, Rachez C, Ball SG, Cannon JF. Coordinate regulation of glycogen metabolism in the yeast Saccharomyces cerevisiae. Induction of glycogen branching enzyme. J Biol Chem 1992; 267:15224-8. [PMID: 1634552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The yeast glycogen branching enzyme (EC 2.4.1.18) is shown to be induced in batch culture simultaneously with the onset of intracellular glycogen accumulation. The branching enzyme structural gene (GLC3) has been cloned. Its predicted amino acid sequence is very similar to procaryotic branching enzymes. Northern analysis indicates that GLC3 mRNA abundance increases in late exponential growth phase coincident with glycogen accumulation. Disruption of the branching enzyme structural gene establishes that branching enzyme activity is an absolute requirement for maximal glycogen synthesis.
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Affiliation(s)
- V J Thon
- School of Medicine, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia 65212
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