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Belotti E, Lacoste N, Iftikhar A, Simonet T, Papin C, Osseni A, Streichenberger N, Mari PO, Girard E, Graies M, Giglia-Mari G, Dimitrov S, Hamiche A, Schaeffer L. H2A.Z is involved in premature aging and DSB repair initiation in muscle fibers. Nucleic Acids Res 2024; 52:3031-3049. [PMID: 38281187 PMCID: PMC11014257 DOI: 10.1093/nar/gkae020] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 01/19/2024] [Indexed: 01/30/2024] Open
Abstract
Histone variants are key epigenetic players, but their functional and physiological roles remain poorly understood. Here, we show that depletion of the histone variant H2A.Z in mouse skeletal muscle causes oxidative stress, oxidation of proteins, accumulation of DNA damages, and both neuromuscular junction and mitochondria lesions that consequently lead to premature muscle aging and reduced life span. Investigation of the molecular mechanisms involved shows that H2A.Z is required to initiate DNA double strand break repair by recruiting Ku80 at DNA lesions. This is achieved via specific interactions of Ku80 vWA domain with H2A.Z. Taken as a whole, our data reveal that H2A.Z containing nucleosomes act as a molecular platform to bring together the proteins required to initiate and process DNA double strand break repair.
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Affiliation(s)
- Edwige Belotti
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Nicolas Lacoste
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Arslan Iftikhar
- For Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, Parc d’innovation, 1 rue Laurent Fries, 67404 Ilkirch Cedex, France
| | - Thomas Simonet
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Christophe Papin
- For Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, Parc d’innovation, 1 rue Laurent Fries, 67404 Ilkirch Cedex, France
| | - Alexis Osseni
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Nathalie Streichenberger
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Pierre-Olivier Mari
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Emmanuelle Girard
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Mohamed Graies
- Institute for Advanced Biosciences (IAB), Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Giuseppina Giglia-Mari
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Stefan Dimitrov
- Institute for Advanced Biosciences (IAB), Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Ali Hamiche
- For Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, Parc d’innovation, 1 rue Laurent Fries, 67404 Ilkirch Cedex, France
| | - Laurent Schaeffer
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
- Centre de Biotechnologie Cellulaire, Hospices Civils de Lyon, Lyon, France
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Sutcu HH, Rassinoux P, Donnio LM, Neuillet D, Vianna F, Gabillot O, Mari PO, Baldeyron C, Giglia-Mari G. Decline of DNA damage response along with myogenic differentiation. Life Sci Alliance 2024; 7:e202302279. [PMID: 37993260 PMCID: PMC10665522 DOI: 10.26508/lsa.202302279] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023] Open
Abstract
DNA integrity is incessantly confronted to agents inducing DNA lesions. All organisms are equipped with a network of DNA damage response mechanisms that will repair DNA lesions and restore proper cellular activities. Despite DNA repair mechanisms have been revealed in replicating cells, still little is known about how DNA lesions are repaired in postmitotic cells. Muscle fibers are highly specialized postmitotic cells organized in syncytia and they are vulnerable to age-related degeneration and atrophy after radiotherapy treatment. We have studied the DNA repair capacity of muscle fiber nuclei and compared it with the one measured in proliferative myoblasts here. We focused on the DNA repair mechanisms that correct ionizing radiation (IR)-induced lesions, namely the base excision repair, the nonhomologous end joining, and the homologous recombination (HR). We found that in the most differentiated myogenic cells, myotubes, these DNA repair mechanisms present weakened kinetics of recruitment of DNA repair proteins to IR-damaged DNA. For base excision repair and HR, this decline can be linked to reduced steady-state levels of key proteins involved in these processes.
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Affiliation(s)
- Haser H Sutcu
- https://ror.org/01ha22c77 Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Phoebe Rassinoux
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Lise-Marie Donnio
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Neuillet
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - François Vianna
- https://ror.org/01ha22c77 Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LMDN, Saint-Paul-Lez-Durance, France
| | - Olivier Gabillot
- https://ror.org/01ha22c77 Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Pierre-Olivier Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Céline Baldeyron
- https://ror.org/01ha22c77 Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Giuseppina Giglia-Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
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Musawi S, Donnio LM, Zhao Z, Magnani C, Rassinoux P, Binda O, Huang J, Jacquier A, Coudert L, Lomonte P, Martinat C, Schaeffer L, Mottet D, Côté J, Mari PO, Giglia-Mari G. Nucleolar reorganization after cellular stress is orchestrated by SMN shuttling between nuclear compartments. Nat Commun 2023; 14:7384. [PMID: 37968267 PMCID: PMC10652021 DOI: 10.1038/s41467-023-42390-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/10/2023] [Indexed: 11/17/2023] Open
Abstract
Spinal muscular atrophy is an autosomal recessive neuromuscular disease caused by mutations in the multifunctional protein Survival of Motor Neuron, or SMN. Within the nucleus, SMN localizes to Cajal bodies, which are associated with nucleoli, nuclear organelles dedicated to the first steps of ribosome biogenesis. The highly organized structure of the nucleolus can be dynamically altered by genotoxic agents. RNAP1, Fibrillarin, and nucleolar DNA are exported to the periphery of the nucleolus after genotoxic stress and, once DNA repair is fully completed, the organization of the nucleolus is restored. We find that SMN is required for the restoration of the nucleolar structure after genotoxic stress. During DNA repair, SMN shuttles from the Cajal bodies to the nucleolus. This shuttling is important for nucleolar homeostasis and relies on the presence of Coilin and the activity of PRMT1.
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Affiliation(s)
- Shaqraa Musawi
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Lise-Marie Donnio
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France.
| | - Zehui Zhao
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Charlène Magnani
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Phoebe Rassinoux
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Olivier Binda
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
- Faculty of Medicine, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Ontario, Canada
| | - Jianbo Huang
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Arnaud Jacquier
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Laurent Coudert
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Patrick Lomonte
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Cécile Martinat
- INSERM/UEPS UMR 861, Paris Saclay Université, I-STEM, 91100, Corbeil-Essonnes, France
| | - Laurent Schaeffer
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Denis Mottet
- GIGA-Molecular Biology of Diseases, Gene Expression and Cancer Laboratory, B34 + 1, University of Liege, Avenue de l'Hôpital 1, B-4000, Liège, Belgium
| | - Jocelyn Côté
- Faculty of Medicine, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Ontario, Canada
| | - Pierre-Olivier Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Giuseppina Giglia-Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France.
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Donnio LM, Cerutti E, Magnani C, Neuillet D, Mari PO, Giglia-Mari G. XAB2 dynamics during DNA damage-dependent transcription inhibition. eLife 2022; 11:77094. [PMID: 35880862 PMCID: PMC9436415 DOI: 10.7554/elife.77094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022] Open
Abstract
Xeroderma Pigmentosum group A-binding protein 2 (XAB2) is a multifunctional protein playing a critical role in distinct cellular processes including transcription, splicing, DNA repair, and messenger RNA export. In this study, we demonstrate that XAB2 is involved specifically and exclusively in Transcription-Coupled Nucleotide Excision Repair (TC-NER) reactions and solely for RNA polymerase 2 (RNAP2)-transcribed genes. Surprisingly, contrary to all the other NER proteins studied so far, XAB2 does not accumulate on the local UV-C damage; on the contrary, it becomes more mobile after damage induction. XAB2 mobility is restored when DNA repair reactions are completed. By scrutinizing from which cellular complex/partner/structure XAB2 is released, we have identified that XAB2 is detached after DNA damage induction from DNA:RNA hybrids, commonly known as R-loops, and from the CSA and XPG proteins. This release contributes to the DNA damage recognition step during TC-NER, as in the absence of XAB2, RNAP2 is blocked longer on UV lesions. Moreover, we also demonstrate that XAB2 has a role in retaining RNAP2 on its substrate without any DNA damage.
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Affiliation(s)
- Lise-Marie Donnio
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Elena Cerutti
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Charlene Magnani
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Neuillet
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Pierre-Olivier Mari
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Giuseppina Giglia-Mari
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
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Donnio LM, Miquel C, Vermeulen W, Giglia-Mari G, Mari PO. Cell-type specific concentration regulation of the basal transcription factor TFIIH in XPB y/y mice model. Cancer Cell Int 2019; 19:237. [PMID: 31516394 PMCID: PMC6734240 DOI: 10.1186/s12935-019-0945-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/18/2019] [Indexed: 11/15/2022] Open
Abstract
Background The basal transcription/repair factor TFIIH is a ten sub-unit complex essential for RNA polymerase II (RNAP2) transcription initiation and DNA repair. In both these processes TFIIH acts as a DNA helix opener, required for promoter escape of RNAP2 in transcription initiation, and to set the stage for strand incision within the nucleotide excision repair (NER) pathway. Methods We used a knock-in mouse model that we generated and that endogenously expresses a fluorescent version of XPB (XPB-YFP). Using different microscopy, cellular biology and biochemistry approaches we quantified the steady state levels of this protein in different cells, and cells imbedded in tissues. Results Here we demonstrate, via confocal imaging of ex vivo tissues and cells derived from this mouse model, that TFIIH steady state levels are tightly regulated at the single cell level, thus keeping nuclear TFIIH concentrations remarkably constant in a cell type dependent manner. Moreover, we show that individual cellular TFIIH levels are proportional to the speed of mRNA production, hence to a cell’s transcriptional activity, which we can correlate to proliferation status. Importantly, cancer tissue presents a higher TFIIH than normal healthy tissues. Conclusion This study shows that TFIIH cellular concentration can be used as a bona-fide quantitative marker of transcriptional activity and cellular proliferation.
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Affiliation(s)
- Lise-Marie Donnio
- 1Institut NeuroMyoGène (INMG), CNRS, UMR 5310, INSERM U1217, Faculté de Médecine, Université Claude Bernard Lyon 1, 8 Avenue Rockefeller, 69008 LYON, France
| | - Catherine Miquel
- 2Pathology Department, Saint-Louis Hospital, Université de Paris, 1 Avenue Claude Vellefaux, 75010 Paris, France
| | - Wim Vermeulen
- 3Department of Genetics, Erasmus MC, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Giuseppina Giglia-Mari
- 1Institut NeuroMyoGène (INMG), CNRS, UMR 5310, INSERM U1217, Faculté de Médecine, Université Claude Bernard Lyon 1, 8 Avenue Rockefeller, 69008 LYON, France
| | - Pierre-Olivier Mari
- 1Institut NeuroMyoGène (INMG), CNRS, UMR 5310, INSERM U1217, Faculté de Médecine, Université Claude Bernard Lyon 1, 8 Avenue Rockefeller, 69008 LYON, France
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Gervais V, Muller I, Mari PO, Mourcet A, Movellan KT, Ramos P, Marcoux J, Guillet V, Javaid S, Burlet-Schiltz O, Czaplicki G, Milon A, Giglia-Mari G. Small molecule-based targeting of TTD-A dimerization to control TFIIH transcriptional activity represents a potential strategy for anticancer therapy. J Biol Chem 2018; 293:14974-14988. [PMID: 30068551 DOI: 10.1074/jbc.ra118.003444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/25/2018] [Indexed: 11/06/2022] Open
Abstract
The human transcription factor TFIIH is a large complex composed of 10 subunits that form an intricate network of protein-protein interactions critical for regulating its transcriptional and DNA repair activities. The trichothiodystrophy group A protein (TTD-A or p8) is the smallest TFIIH subunit, shuttling between a free and a TFIIH-bound state. Its dimerization properties allow it to shift from a homodimeric state, in the absence of a functional partner, to a heterodimeric structure, enabling dynamic binding to TFIIH. Recruitment of p8 at TFIIH stabilizes the overall architecture of the complex, whereas p8's absence reduces its cellular steady-state concentration and consequently decreases basal transcription, highlighting that p8 dimerization may be an attractive target for down-regulating transcription in cancer cells. Here, using a combination of molecular dynamics simulations to study p8 conformational stability and a >3000-member library of chemical fragments, we identified small-molecule compounds that bind to the dimerization interface of p8 and provoke its destabilization, as assessed by biophysical studies. Using quantitative imaging of TFIIH in living mouse cells, we found that these molecules reduce the intracellular concentration of TFIIH and its transcriptional activity to levels similar to that observed in individuals with trichothiodystrophy owing to mutated TTD-A Our results provide a proof of concept of fragment-based drug discovery, demonstrating the utility of small molecules for targeting p8 dimerization to modulate the transcriptional machinery, an approach that may help inform further development in anticancer therapies.
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Affiliation(s)
- Virginie Gervais
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France,
| | - Isabelle Muller
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Pierre-Olivier Mari
- the Université Claude Bernard Lyon 1, INSERM U1217, Institut NeuroMyoGène, CNRS UMR 5310, F-69008 Lyon, France, and
| | - Amandine Mourcet
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Kumar Tekwani Movellan
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Pascal Ramos
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Julien Marcoux
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Valérie Guillet
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Sumaira Javaid
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France.,the Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Odile Burlet-Schiltz
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Georges Czaplicki
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Alain Milon
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Giuseppina Giglia-Mari
- the Université Claude Bernard Lyon 1, INSERM U1217, Institut NeuroMyoGène, CNRS UMR 5310, F-69008 Lyon, France, and
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Ranes M, Boeing S, Wang Y, Wienholz F, Menoni H, Walker J, Encheva V, Chakravarty P, Mari PO, Stewart A, Giglia-Mari G, Snijders AP, Vermeulen W, Svejstrup JQ. A ubiquitylation site in Cockayne syndrome B required for repair of oxidative DNA damage, but not for transcription-coupled nucleotide excision repair. Nucleic Acids Res 2016; 44:5246-55. [PMID: 27060134 PMCID: PMC4914099 DOI: 10.1093/nar/gkw216] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/11/2016] [Accepted: 03/18/2016] [Indexed: 12/23/2022] Open
Abstract
Cockayne syndrome B (CSB), best known for its role in transcription-coupled nucleotide excision repair (TC-NER), contains a ubiquitin-binding domain (UBD), but the functional connection between protein ubiquitylation and this UBD remains unclear. Here, we show that CSB is regulated via site-specific ubiquitylation. Mass spectrometry analysis of CSB identified lysine (K) 991 as a ubiquitylation site. Intriguingly, mutation of this residue (K991R) does not affect CSB's catalytic activity or protein stability, but greatly affects genome stability, even in the absence of induced DNA damage. Moreover, cells expressing CSB K991R are sensitive to oxidative DNA damage, but proficient for TC-NER. K991 becomes ubiquitylated upon oxidative DNA damage, and while CSB K991R is recruited normally to such damage, it fails to dissociate in a timely manner, suggesting a requirement for K991 ubiquitylation in CSB activation. Interestingly, deletion of CSB's UBD gives rise to oxidative damage sensitivity as well, while CSB ΔUBD and CSB K991R affects expression of overlapping groups of genes, further indicating a functional connection. Together, these results shed new light on the regulation of CSB, with K991R representing an important separation-of-function-mutation in this multi-functional protein.
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Affiliation(s)
- Michael Ranes
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Stefan Boeing
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Yuming Wang
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Franziska Wienholz
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Hervé Menoni
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Jane Walker
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Vesela Encheva
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Probir Chakravarty
- Bioinformatics & Biostatistics Laboratory, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Pierre-Olivier Mari
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F-31077 Toulouse, France
| | - Aengus Stewart
- Bioinformatics & Biostatistics Laboratory, The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Giuseppina Giglia-Mari
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F-31077 Toulouse, France
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
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Oksenych V, Zhovmer A, Ziani S, Mari PO, Eberova J, Nardo T, Stefanini M, Giglia-Mari G, Egly JM, Coin F. Histone methyltransferase DOT1L drives recovery of gene expression after a genotoxic attack. PLoS Genet 2013; 9:e1003611. [PMID: 23861670 PMCID: PMC3701700 DOI: 10.1371/journal.pgen.1003611] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [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: 02/05/2013] [Accepted: 05/18/2013] [Indexed: 12/12/2022] Open
Abstract
UV-induced DNA damage causes repression of RNA synthesis. Following the removal of DNA lesions, transcription recovery operates through a process that is not understood yet. Here we show that knocking-out of the histone methyltransferase DOT1L in mouse embryonic fibroblasts (MEFDOT1L) leads to a UV hypersensitivity coupled to a deficient recovery of transcription initiation after UV irradiation. However, DOT1L is not implicated in the removal of the UV-induced DNA damage by the nucleotide excision repair pathway. Using FRAP and ChIP experiments we established that DOT1L promotes the formation of the pre-initiation complex on the promoters of UV-repressed genes and the appearance of transcriptionally active chromatin marks. Treatment with Trichostatin A, relaxing chromatin, recovers both transcription initiation and UV-survival. Our data suggest that DOT1L secures an open chromatin structure in order to reactivate RNA Pol II transcription initiation after a genotoxic attack. Through the deformation of the genomic DNA structure, UV-induced DNA lesions have repressive effect on various nuclear processes including replication and transcription. As a matter of fact, the removal of these lesions is a priority for the cell and takes place at the expense of fundamental cellular processes that are paused to circumvent the risks of mutations that may lead to cancer. The molecular mechanism underlying transcription inhibition and recovery is not clearly understood and appears more complicated than anticipated. Here we analyzed the process of transcription recovery after UV-irradiation and found that it depends on DOT1L, a histone methyltransferase that promotes the reformation of the transcription machinery at the promoters of UV-repressed genes. Our discovery shows that transcription recovery after a genotoxic attack is an active process under the control of chromatin remodelling enzymes.
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Affiliation(s)
- Valentyn Oksenych
- IGBMC, Department of Functional Genomics and Cancer, CNRS/INSERM/Université de Strasbourg, C. U. Strasbourg, France
| | - Alexander Zhovmer
- IGBMC, Department of Functional Genomics and Cancer, CNRS/INSERM/Université de Strasbourg, C. U. Strasbourg, France
| | - Salim Ziani
- IGBMC, Department of Functional Genomics and Cancer, CNRS/INSERM/Université de Strasbourg, C. U. Strasbourg, France
| | | | - Jitka Eberova
- IGBMC, Department of Functional Genomics and Cancer, CNRS/INSERM/Université de Strasbourg, C. U. Strasbourg, France
| | - Tiziana Nardo
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Miria Stefanini
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | | | - Jean-Marc Egly
- IGBMC, Department of Functional Genomics and Cancer, CNRS/INSERM/Université de Strasbourg, C. U. Strasbourg, France
| | - Frédéric Coin
- IGBMC, Department of Functional Genomics and Cancer, CNRS/INSERM/Université de Strasbourg, C. U. Strasbourg, France
- * E-mail:
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9
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Abstract
Trichothiodystrophy group A (TTD-A) patients carry a mutation in the transcription factor II H (TFIIH) subunit TTDA. Using a novel in vivo tripartite split-GFP system, we show that TTDA interacts with the TFIIH subunit p52 and the p52-TTDA-GFP product is incorporated into TFIIH. p52-TTDA-GFP is able to bind DNA and is recruited to UV-damaged DNA. Furthermore, we show that two patient-mutated TTDA proteins can interact with p52, are able to bind to the DNA and can localize to damaged DNA. Our findings give new insights into the behavior of TTDA within the context of a living cell and thereby shed light on the complex phenotype of TTD-A patients.
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10
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Theil AF, Nonnekens J, Steurer B, Mari PO, de Wit J, Lemaitre C, Marteijn JA, Raams A, Maas A, Vermeij M, Essers J, Hoeijmakers JHJ, Giglia-Mari G, Vermeulen W. Disruption of TTDA results in complete nucleotide excision repair deficiency and embryonic lethality. PLoS Genet 2013; 9:e1003431. [PMID: 23637614 PMCID: PMC3630102 DOI: 10.1371/journal.pgen.1003431] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/19/2013] [Indexed: 12/01/2022] Open
Abstract
The ten-subunit transcription factor IIH (TFIIH) plays a crucial role in transcription and nucleotide excision repair (NER). Inactivating mutations in the smallest 8-kDa TFB5/TTDA subunit cause the neurodevelopmental progeroid repair syndrome trichothiodystrophy A (TTD-A). Previous studies have shown that TTDA is the only TFIIH subunit that appears not to be essential for NER, transcription, or viability. We studied the consequences of TTDA inactivation by generating a Ttda knock-out (Ttda−/−) mouse-model resembling TTD-A patients. Unexpectedly, Ttda−/− mice were embryonic lethal. However, in contrast to full disruption of all other TFIIH subunits, viability of Ttda−/− cells was not affected. Surprisingly, Ttda−/− cells were completely NER deficient, contrary to the incomplete NER deficiency of TTD-A patient-derived cells. We further showed that TTD-A patient mutations only partially inactivate TTDA function, explaining the relatively mild repair phenotype of TTD-A cells. Moreover, Ttda−/− cells were also highly sensitive to oxidizing agents. These findings reveal an essential role of TTDA for life, nucleotide excision repair, and oxidative DNA damage repair and identify Ttda−/− cells as a unique class of TFIIH mutants. DNA is under constant attack of various environmental and cellular produced DNA damaging agents. DNA damage hampers normal cell function; however, different DNA repair mechanisms protect our genetic information. Nucleotide Excision Repair is one of the most versatile repair processes, as it removes a large variety of DNA helix-distorting lesions induced by UV light and various chemicals. To remove these lesions, the DNA helix needs to be opened by the transcription/repair factor II H (TFIIH). TFIIH is a multifunctional complex that consists of 10 subunits and plays a fundamental role in opening the DNA helix in both NER and transcription. TTDA, the smallest subunit of TFIIH, was thought to be dispensable for both NER and transcription. However, in this paper, we show for the first time that TTDA is in fact a crucial component of TFIIH for NER. We demonstrate that Ttda−/− mice are embryonic lethal. We also show that Ttda−/− mouse cells are the first known viable TFIIH subunit knock-out cells, which are completely NER deficient and sensitive to oxidative agents (showing a new role for TFIIH outside NER and transcription).
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Affiliation(s)
- Arjan F. Theil
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Julie Nonnekens
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
| | - Barbara Steurer
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Pierre-Olivier Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
| | - Jan de Wit
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Anja Raams
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Alex Maas
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Marcel Vermeij
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Giuseppina Giglia-Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
- * E-mail: (WV); (GG-M)
| | - Wim Vermeulen
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- * E-mail: (WV); (GG-M)
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11
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Baradaran-Heravi A, Raams A, Lubieniecka J, Cho KS, DeHaai KA, Basiratnia M, Mari PO, Xue Y, Rauth M, Olney AH, Shago M, Choi K, Weksberg RA, Nowaczyk MJM, Wang W, Jaspers NGJ, Boerkoel CF. SMARCAL1 deficiency predisposes to non-Hodgkin lymphoma and hypersensitivity to genotoxic agents in vivo. Am J Med Genet A 2012; 158A:2204-13. [PMID: 22888040 DOI: 10.1002/ajmg.a.35532] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/16/2012] [Indexed: 12/19/2022]
Abstract
Schimke immuno-osseous dysplasia (SIOD) is a multisystemic disorder with prominent skeletal, renal, immunological, and ectodermal abnormalities. It is caused by mutations of SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1), which encodes a DNA stress response protein. To determine the relationship of this function to the SIOD phenotype, we profiled the cancer prevalence in SIOD and assessed if defects of nucleotide excision repair (NER) and nonhomologous end joining (NHEJ), respectively, explained the ectodermal and immunological features of SIOD. Finally, we determined if Smarcal1(del/del) mice had hypersensitivity to irinotecan (CPT-11), etoposide, and hydroxyurea (HU) and whether exposure to these agents induced features of SIOD. Among 71 SIOD patients, three had non-Hodgkin lymphoma (NHL) and one had osteosarcoma. We did not find evidence of defective NER or NHEJ; however, Smarcal1-deficient mice were hypersensitive to several genotoxic agents. Also, CPT-11, etoposide, and HU caused decreased growth and loss of growth plate chondrocytes. These data, which identify an increased prevalence of NHL in SIOD and confirm hypersensitivity to DNA damaging agents in vivo, provide guidance for the management of SIOD patients.
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Affiliation(s)
- Alireza Baradaran-Heravi
- Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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12
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Godon C, Mourgues S, Nonnekens J, Mourcet A, Coin F, Vermeulen W, Mari PO, Giglia-Mari G. Generation of DNA single-strand displacement by compromised nucleotide excision repair. EMBO J 2012; 31:3550-63. [PMID: 22863773 DOI: 10.1038/emboj.2012.193] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 06/27/2012] [Indexed: 11/09/2022] Open
Abstract
Nucleotide excision repair (NER) is a precisely coordinated process essential to avoid DNA damage-induced cellular malfunction and mutagenesis. Here, we investigate the mechanistic details and effects of the NER machinery when it is compromised by a pathologically significant mutation in a subunit of the repair/transcription factor TFIIH, namely XPD. In contrast to previous studies, we find that no single- or double-strand DNA breaks are produced at early time points after UV irradiation of cells bearing a specific XPD mutation, despite the presence of a clear histone H2AX phosphorylation (γH2AX) signal in the UV-exposed areas. We show that the observed γH2AX signal can be explained by the presence of longer single-strand gaps possibly generated by strand displacement. Our in vivo measurements also indicate a strongly reduced TFIIH-XPG binding that could promote single-strand displacement at the site of UV lesions. This finding not only highlights the crucial role of XPG's interactions with TFIIH for proper NER, but also sheds new light on how a faulty DNA repair process can induce extreme genomic instability in human patients.
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Affiliation(s)
- Camille Godon
- Department of Cancer Biology, CNRS, IPBS, Toulouse, France
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13
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Kleppa L, Mari PO, Larsen E, Lien GF, Godon C, Theil AF, Nesse GJ, Wiksen H, Vermeulen W, Giglia-Mari G, Klungland A. Kinetics of endogenous mouse FEN1 in base excision repair. Nucleic Acids Res 2012; 40:9044-59. [PMID: 22810208 PMCID: PMC3467068 DOI: 10.1093/nar/gks673] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [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] [Indexed: 11/13/2022] Open
Abstract
The structure specific flap endonuclease 1 (FEN1) plays an essential role in long-patch base excision repair (BER) and in DNA replication. We have generated a fluorescently tagged FEN1 expressing mouse which allows monitoring the localization and kinetics of FEN1 in response to DNA damage in living cells and tissues. The expression of FEN1, which is tagged at its C-terminal end with enhanced yellow fluorescent protein (FEN1-YFP), is under control of the endogenous Fen1 transcriptional regulatory elements. In line with its role in processing of Okazaki fragments during DNA replication, we found that FEN1-YFP expression is mainly observed in highly proliferating tissue. Moreover, the FEN1-YFP fusion protein allowed us to investigate repair kinetics in cells challenged with local and global DNA damage. In vivo multi-photon fluorescence microscopy demonstrates rapid localization of FEN1 to local laser-induced DNA damage sites in nuclei, providing evidence of a highly mobile protein that accumulates fast at DNA lesion sites with high turnover rate. Inhibition of poly (ADP-ribose) polymerase 1 (PARP1) disrupts FEN1 accumulation at sites of DNA damage, indicating that PARP1 is required for FEN1 recruitment to DNA repair intermediates in BER.
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Affiliation(s)
- Liv Kleppa
- Centre for Molecular Biology and Neuroscience and Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, Norway
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14
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Bochet L, Dauvillier S, Dirat B, Dabek M, Gonidec SL, Mari PO, Escourrou G, Valet P, Muller C. Abstract 511: Adipocyte-derived fibroblasts contribute to the desmoplastic reaction in breast cancer: A new link between breast cancer and obesity. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Now, it is widely established that malignant tumors, not merely grow into a preexisting interstitial tissue, but they actively form a new stroma and modify their composition. Accordingly, one of the features of many carcinomas, particularly breast, is the presence of a dense collagenous stroma, the so-called desmoplastic response, comprising fibroblast-like cells which play a crucial role in tumor progression. Peritumoral fibroblasts are composed of several subpopulations that are morphologically undistinguishable and their origins remain debated. Our results suggest that a part of this fibroblast could arise from the “reorientation” of mature adipocytes, highly represented in breast tumour microenvironment. Using an original 2D coculture system, we show that mature adipocytes cocultivated with breast tumour cells for 3 to 8 days lose their lipid content as well as their adipocyte differentiation markers (HSL, Adipsin, Adiponectin, C/EBPα, PPARγ, Resistin). This process is associated with intense morphological and functional changes leading to an activated fibroblast phenotype (exhibition of actin stress fibers, increase of focal adhesion sites). In this way, we have identified for the first time a new fibroblastic population called Adipocyte Derived Fibroblast (ADF). Interestingly, the reorientation occur in vivo since the injection of far red fluorescent tumour cells into a mice fatpad containing GFP-expressing adipocytes induce the apparition of GFP-fibroblast-like cells that interdigitate with tumour cells. Moreover, our results show that the ADF phenotype depends on the reactivation of the Wnt/β-catenin pathway. Finally, ADFs exhibit an increase of migratory and invasive abilities, with enhanced profibrotic secretions (fibronectin and collagen 1) suggesting that these cells could be key players in desmoplastic reaction. Ongoing experiments are performed to assess the presence of ADFs in breast human tumors. Our results might provide an explanation for the poor prognosis observed in localized breast cancer in obese women, since the nature of the desmoplastic reaction and the secretion pattern of ADF might be profoundly altered in this physiopathogical condition.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 511. doi:10.1158/1538-7445.AM2011-511
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Affiliation(s)
- Ludivine Bochet
- 1Team Microenvironment, Cancer and Adipocytes (MICA) Institute of Pharmacology and Structural Biology, IPBS, CNRS UMR 5089, Toulouse, France
| | - Stéphanie Dauvillier
- 1Team Microenvironment, Cancer and Adipocytes (MICA) Institute of Pharmacology and Structural Biology, IPBS, CNRS UMR 5089, Toulouse, France
| | - Béatrice Dirat
- 1Team Microenvironment, Cancer and Adipocytes (MICA) Institute of Pharmacology and Structural Biology, IPBS, CNRS UMR 5089, Toulouse, France
| | - Marta Dabek
- 1Team Microenvironment, Cancer and Adipocytes (MICA) Institute of Pharmacology and Structural Biology, IPBS, CNRS UMR 5089, Toulouse, France
| | | | | | | | | | - Catherine Muller
- 1Team Microenvironment, Cancer and Adipocytes (MICA) Institute of Pharmacology and Structural Biology, IPBS, CNRS UMR 5089, Toulouse, France
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15
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Anindya R, Mari PO, Kristensen U, Kool H, Giglia-Mari G, Mullenders LH, Fousteri M, Vermeulen W, Egly JM, Svejstrup JQ. A ubiquitin-binding domain in Cockayne syndrome B required for transcription-coupled nucleotide excision repair. Mol Cell 2010; 38:637-48. [PMID: 20541997 PMCID: PMC2885502 DOI: 10.1016/j.molcel.2010.04.017] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 03/24/2010] [Accepted: 04/16/2010] [Indexed: 12/31/2022]
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) allows RNA polymerase II (RNAPII)-blocking lesions to be rapidly removed from the transcribed strand of active genes. Defective TCR in humans is associated with Cockayne syndrome (CS), typically caused by defects in either CSA or CSB. Here, we show that CSB contains a ubiquitin-binding domain (UBD). Cells expressing UBD-less CSB (CSB(del)) have phenotypes similar to those of cells lacking CSB, but these can be suppressed by appending a heterologous UBD, so ubiquitin binding is essential for CSB function. Surprisingly, CSB(del) remains capable of assembling nucleotide excision repair factors and repair synthesis proteins around damage-stalled RNAPII, but such repair complexes fail to excise the lesion. Together, our results indicate an essential role for protein ubiquitylation and CSB's UBD in triggering damage incision during TC-NER and allow us to integrate the function of CSA and CSB in a model for the process.
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Affiliation(s)
- Roy Anindya
- Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms EN6 3LD, UK
| | - Pierre-Olivier Mari
- Department of Cell Biology and Genetics, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Ulrik Kristensen
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 16367404 Illkirch Cedex, CU Strasbourg, France
| | - Hanneke Kool
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Giuseppina Giglia-Mari
- Department of Cell Biology and Genetics, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Leon H. Mullenders
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Maria Fousteri
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Wim Vermeulen
- Department of Cell Biology and Genetics, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Jean-Marc Egly
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 16367404 Illkirch Cedex, CU Strasbourg, France
| | - Jesper Q. Svejstrup
- Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms EN6 3LD, UK
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16
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Mari PO, Verbiest V, Sabbioneda S, Gourdin AM, Wijgers N, Dinant C, Lehmann AR, Vermeulen W, Giglia-Mari G. Influence of the live cell DNA marker DRAQ5 on chromatin-associated processes. DNA Repair (Amst) 2010; 9:848-55. [PMID: 20439168 DOI: 10.1016/j.dnarep.2010.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 04/06/2010] [Indexed: 11/29/2022]
Abstract
In the last decade, live cell fluorescence microscopy experiments have revolutionized cellular and molecular biology, enabling the localization of proteins within cellular compartments to be analysed and to determine kinetic parameters of enzymatic reactions in living nuclei to be measured. Recently, in vivo DNA labelling by DNA-stains such as DRAQ5, has provided the opportunity to measure kinetic reactions of GFP-fused proteins in targeted areas of the nucleus with different chromatin compaction levels. To verify the suitability of combining DRAQ5-staining with protein dynamic measurements, we have tested the cellular consequences of DRAQ5 DNA intercalation. We show that DRAQ5 intercalation rapidly modifies both the localization and the mobility properties of several DNA-binding proteins such as histones, DNA repair, replication and transcription factors, by stimulating a release of these proteins from their substrate. Most importantly, the effect of DRAQ5 on the mobility of essential cellular enzymes results in a potent inhibition of the corresponding cellular functions. From these observations, we suggest that great caution must be used when interpreting live cell data obtained using DRAQ5.
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17
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Giglia-Mari G, Theil AF, Mari PO, Mourgues S, Nonnekens J, Andrieux LO, de Wit J, Miquel C, Wijgers N, Maas A, Fousteri M, Hoeijmakers JHJ, Vermeulen W. Differentiation driven changes in the dynamic organization of Basal transcription initiation. PLoS Biol 2009; 7:e1000220. [PMID: 19841728 PMCID: PMC2754661 DOI: 10.1371/journal.pbio.1000220] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 09/07/2009] [Indexed: 01/01/2023] Open
Abstract
A novel mouse model reveals that the dynamic behavior of transcription factors can vary considerably between different cells of an organism. Studies based on cell-free systems and on in vitro–cultured living cells support the concept that many cellular processes, such as transcription initiation, are highly dynamic: individual proteins stochastically bind to their substrates and disassemble after reaction completion. This dynamic nature allows quick adaptation of transcription to changing conditions. However, it is unknown to what extent this dynamic transcription organization holds for postmitotic cells embedded in mammalian tissue. To allow analysis of transcription initiation dynamics directly into living mammalian tissues, we created a knock-in mouse model expressing fluorescently tagged TFIIH. Surprisingly and in contrast to what has been observed in cultured and proliferating cells, postmitotic murine cells embedded in their tissue exhibit a strong and long-lasting transcription-dependent immobilization of TFIIH. This immobilization is both differentiation driven and development dependent. Furthermore, although very statically bound, TFIIH can be remobilized to respond to new transcriptional needs. This divergent spatiotemporal transcriptional organization in different cells of the soma revisits the generally accepted highly dynamic concept of the kinetic framework of transcription and shows how basic processes, such as transcription, can be organized in a fundamentally different fashion in intact organisms as previously deduced from in vitro studies. The accepted model of eukaryotic mRNA production is that transcription factors spend most of their time diffusing throughout the cell nucleus, encountering gene promoters (their substrate) in a random fashion and binding to them for a very short time. A similar modus operandi has been accepted as a paradigm for interactions within most of the chromatin-associated enzymatic processes (transcription, replication, DNA damage response). However, it is not known whether such behavior is indeed a common characteristic for all cells in the organism. To answer this question, we generated a knock-in mouse that expresses in all cells a fluorescently tagged transcription factor (TFIIH) that functions in both transcription initiation and DNA repair. This new tool, when combined with quantitative imaging techniques, allowed us to monitor the mobility of this transcription factor in virtually all living tissues. In this study, we show that, in contrast to the aforementioned paradigm, in highly differentiated postmitotic cells such as neurons, hepatocytes, and cardiac myocytes, TFIIH is effectively immobilized on the chromatin during transcription, whereas in proliferative cells, TFIIH has the same dynamic behavior as in cultured cells. Our study also points out that results obtained from in vitro or cultured cell systems cannot always be directly extrapolated to the whole organism. More importantly, this raises a question for researchers in the transcription field: why do some cells opt for a dynamic framework for transcription, whereas others exhibit a static one?
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Affiliation(s)
- Giuseppina Giglia-Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
- * E-mail: (GG-M); (WV)
| | - Arjan F. Theil
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Pierre-Olivier Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Sophie Mourgues
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Julie Nonnekens
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Jan de Wit
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Nils Wijgers
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Alex Maas
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Maria Fousteri
- Department of Toxicogenetics, LUMC, Leiden, The Netherlands
| | | | - Wim Vermeulen
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- * E-mail: (GG-M); (WV)
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18
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van der Burg M, Ijspeert H, Verkaik NS, Turul T, Wiegant WW, Morotomi-Yano K, Mari PO, Tezcan I, Chen DJ, Zdzienicka MZ, van Dongen JJM, van Gent DC. A DNA-PKcs mutation in a radiosensitive T-B- SCID patient inhibits Artemis activation and nonhomologous end-joining. J Clin Invest 2008; 119:91-8. [PMID: 19075392 DOI: 10.1172/jci37141] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 10/29/2008] [Indexed: 01/12/2023] Open
Abstract
Radiosensitive T-B- severe combined immunodeficiency (RS-SCID) is caused by defects in the nonhomologous end-joining (NHEJ) DNA repair pathway, which results in failure of functional V(D)J recombination. Here we have identified the first human RS-SCID patient to our knowledge with a DNA-PKcs missense mutation (L3062R). The causative mutation did not affect the kinase activity or DNA end-binding capacity of DNA-PKcs itself; rather, the presence of long P-nucleotide stretches in the immunoglobulin coding joints indicated that it caused insufficient Artemis activation, something that is dependent on Artemis interaction with autophosphorylated DNA-PKcs. Moreover, overall end-joining activity was hampered, suggesting that Artemis-independent DNA-PKcs functions were also inhibited. This study demonstrates that the presence of DNA-PKcs kinase activity is not sufficient to rule out a defect in this gene during diagnosis and treatment of RS-SCID patients. Further, the data suggest that residual DNA-PKcs activity is indispensable in humans.
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Affiliation(s)
- Mirjam van der Burg
- Department of Immunology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Uematsu N, Weterings E, Yano KI, Morotomi-Yano K, Jakob B, Taucher-Scholz G, Mari PO, van Gent DC, Chen BPC, Chen DJ. Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks. ACTA ACUST UNITED AC 2007; 177:219-29. [PMID: 17438073 PMCID: PMC2064131 DOI: 10.1083/jcb.200608077] [Citation(s) in RCA: 307] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PK(CS)) plays an important role during the repair of DNA double-strand breaks (DSBs). It is recruited to DNA ends in the early stages of the nonhomologous end-joining (NHEJ) process, which mediates DSB repair. To study DNA-PK(CS) recruitment in vivo, we used a laser system to introduce DSBs in a specified region of the cell nucleus. We show that DNA-PK(CS) accumulates at DSB sites in a Ku80-dependent manner, and that neither the kinase activity nor the phosphorylation status of DNA-PK(CS) influences its initial accumulation. However, impairment of both of these functions results in deficient DSB repair and the maintained presence of DNA-PK(CS) at unrepaired DSBs. The use of photobleaching techniques allowed us to determine that the kinase activity and phosphorylation status of DNA-PK(CS) influence the stability of its binding to DNA ends. We suggest a model in which DNA-PK(CS) phosphorylation/autophosphorylation facilitates NHEJ by destabilizing the interaction of DNA-PK(CS) with the DNA ends.
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Affiliation(s)
- Naoya Uematsu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Mari PO, Florea BI, Persengiev SP, Verkaik NS, Brüggenwirth HT, Modesti M, Giglia-Mari G, Bezstarosti K, Demmers JAA, Luider TM, Houtsmuller AB, van Gent DC. Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4. Proc Natl Acad Sci U S A 2006; 103:18597-602. [PMID: 17124166 PMCID: PMC1693708 DOI: 10.1073/pnas.0609061103] [Citation(s) in RCA: 297] [Impact Index Per Article: 16.5] [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: 12/19/2022] Open
Abstract
DNA double-strand break (DSB) repair by nonhomologous end joining (NHEJ) requires the assembly of several proteins on DNA ends. Although biochemical studies have elucidated several aspects of the NHEJ reaction mechanism, much less is known about NHEJ in living cells, mainly because of the inability to visualize NHEJ repair proteins at DNA damage. Here we provide evidence that a pulsed near IR laser can produce DSBs without any visible alterations in the nucleus, and we show that NHEJ proteins accumulate in the irradiated areas. The levels of DSBs and Ku accumulation diminished in time, showing that this approach allows us to study DNA repair kinetics in vivo. Remarkably, the Ku heterodimers on DNA ends were in dynamic equilibrium with Ku70/80 in solution, showing that NHEJ complex assembly is reversible. Accumulation of XRCC4/ligase IV on DSBs depended on the presence of Ku70/80, but not DNA-PK(CS). We detected a direct interaction between Ku70 and XRCC4 that could explain these requirements. Our results suggest that this assembly constitutes the core of the NHEJ reaction and that XRCC4 may serve as a flexible tether between Ku70/80 and ligase IV.
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Affiliation(s)
- Pierre-Olivier Mari
- Departments of *Cell Biology and Genetics
- Pathology, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, The Netherlands
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- Departments of *Cell Biology and Genetics
- To whom correspondence should be addressed at:
Department of Cell Biology and Genetics, Erasmus MC, University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands. E-mail:
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Giglia-Mari G, Miquel C, Theil AF, Mari PO, Hoogstraten D, Ng JMY, Dinant C, Hoeijmakers JHJ, Vermeulen W. Dynamic interaction of TTDA with TFIIH is stabilized by nucleotide excision repair in living cells. PLoS Biol 2006; 4:e156. [PMID: 16669699 PMCID: PMC1457016 DOI: 10.1371/journal.pbio.0040156] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [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: 11/16/2005] [Accepted: 03/15/2006] [Indexed: 01/11/2023] Open
Abstract
Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair (NER). This multi-subunit complex consists of ten polypeptides, including the recently identified small 8-kDa trichothiodystrophy group A (TTDA)/ hTFB5 protein. Patients belonging to the rare neurodevelopmental repair syndrome TTD-A carry inactivating mutations in the
TTDA/hTFB5 gene. One of these mutations completely inactivates the protein, whereas other TFIIH genes only tolerate point mutations that do not compromise the essential role in transcription. Nevertheless, the severe NER-deficiency in TTD-A suggests that the TTDA protein is critical for repair. Using a fluorescently tagged and biologically active version of TTDA, we have investigated the involvement of TTDA in repair and transcription in living cells. Under non-challenging conditions, TTDA is present in two distinct kinetic pools: one bound to TFIIH, and a free fraction that shuttles between the cytoplasm and nucleus. After induction of NER-specific DNA lesions, the equilibrium between these two pools dramatically shifts towards a more stable association of TTDA to TFIIH. Modulating transcriptional activity in cells did not induce a similar shift in this equilibrium. Surprisingly, DNA conformations that only provoke an abortive-type of NER reaction do not result into a more stable incorporation of TTDA into TFIIH. These findings identify TTDA as the first TFIIH subunit with a primarily NER-dedicated role in vivo and indicate that its interaction with TFIIH reflects productive NER.
Transcription/repair factor IIH (TFIIH) is a multi-subunit protein complex essential for RNA polymerase II transcription and nucleotide excision repair (NER). The authors show that the TTDA subunit is associated with TFIIH specifically during NER.
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Affiliation(s)
- Giuseppina Giglia-Mari
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Catherine Miquel
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Arjan F Theil
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pierre-Olivier Mari
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Deborah Hoogstraten
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Jessica M. Y Ng
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Christoffel Dinant
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Jan H. J Hoeijmakers
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Wim Vermeulen
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
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Alegría A, Colmenero J, Mari PO, Campbell IA. Dielectric investigation of the temperature dependence of the nonexponentiality of the dynamics of polymer melts. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1999; 59:6888-95. [PMID: 11969676 DOI: 10.1103/physreve.59.6888] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/1998] [Revised: 12/24/1998] [Indexed: 11/07/2022]
Abstract
Using broad band dielectric spectroscopy (10(-5)-10(9) Hz), combining time domain and frequency domain techniques, we study the temperature dependence of the non-Debye character of the alpha relaxation of polymer melts in the glass transition temperature T(g) range. The alpha relaxation process is described in terms of the Kohlrausch-Williams-Watts relaxation function which has a single parameter beta to characterize the nonexponentiality of the relaxation. At high temperatures, beta remains nearly insensitive to temperature changes, whereas in the vicinity of T(g) a nearly linear increasing of beta with temperature is found. The temperature range where the change of the beta(T) behavior occurs is located for all the polymers investigated around 1.2T(g). Moreover, our results indicate a common value of beta approximately equal to 1/3 at the temperature where the relaxation time diverges. The beta(T) behavior near T(g) is discussed in terms of a "rugged landscape" phase space which allows us to rationalize both the beta(T) behavior observed as well as the similarities of our findings near T(g) with the results reported in simulations on Ising spin glasses and other model systems.
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Affiliation(s)
- A Alegría
- Departamento de Física de Materiales y Centro Mixto CSIC-UPV/EHU, Facultad de Química, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain
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