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Ricciardiello R, Forleo G, Cipolla L, van Winckel G, Marconi C, Nouspikel T, Halazonetis TD, Zgheib O, Sabbioneda S. Homozygous substitution of threonine 191 by proline in polymerase η causes Xeroderma pigmentosum variant. Sci Rep 2024; 14:1117. [PMID: 38212351 PMCID: PMC10784498 DOI: 10.1038/s41598-023-51120-1] [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: 11/19/2023] [Accepted: 12/31/2023] [Indexed: 01/13/2024] Open
Abstract
DNA polymerase eta (Polη) is the only translesion synthesis polymerase capable of error-free bypass of UV-induced cyclobutane pyrimidine dimers. A deficiency in Polη function is associated with the human disease Xeroderma pigmentosum variant (XPV). We hereby report the case of a 60-year-old woman known for XPV and carrying a Polη Thr191Pro variant in homozygosity. We further characterize the variant in vitro and in vivo, providing molecular evidence that the substitution abrogates polymerase activity and results in UV sensitivity through deficient damage bypass. This is the first functional molecular characterization of a missense variant of Polη, whose reported pathogenic variants have thus far been loss of function truncation or frameshift mutations. Our work allows the upgrading of Polη Thr191Pro from 'variant of uncertain significance' to 'likely pathogenic mutant', bearing direct impact on molecular diagnosis and genetic counseling. Furthermore, we have established a robust experimental approach that will allow a precise molecular analysis of further missense mutations possibly linked to XPV. Finally, it provides insight into critical Polη residues that may be targeted to develop small molecule inhibitors for cancer therapeutics.
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Affiliation(s)
- Roberto Ricciardiello
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
- Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università degli Studi di Pavia, Pavia, Italy
| | - Giulia Forleo
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Geraldine van Winckel
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Caterina Marconi
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Thierry Nouspikel
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Omar Zgheib
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland.
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy.
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2
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Cardano M, Magni M, Alfieri R, Chan SY, Sabbioneda S, Buscemi G, Zannini L. Sex specific regulation of TSPY-Like 2 in the DNA damage response of cancer cells. Cell Death Dis 2023; 14:197. [PMID: 36918555 PMCID: PMC10015022 DOI: 10.1038/s41419-023-05722-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
Females have a lower probability to develop somatic cancers and a better response to chemotherapy than males. However, the reasons for these differences are still not well understood. The X-linked gene TSPY-Like 2 (TSPYL2) encodes for a putative tumor suppressor protein involved in cell cycle regulation and DNA damage response (DDR) pathways. Here, we demonstrate that in unstressed conditions TSPYL2 is maintained at low levels by MDM2-dependent ubiquitination and proteasome degradation. Upon genotoxic stress, E2F1 promotes TSPYL2 expression and protein accumulation in non-transformed cell lines. Conversely, in cancer cells, TSPYL2 accumulates only in females or in those male cancer cells that lost the Y-chromosome during the oncogenic process. Hence, we demonstrate that while TSPYL2 mRNA is induced in all the tested tumor cell lines after DNA damage, TSPYL2 protein stability is increased only in female cancer cells. Indeed, we found that TSPYL2 accumulation, in male cancer cells, is prevented by the Y-encoded protein SRY, which modulates MDM2 protein levels. In addition, we demonstrated that TSPYL2 accumulation is required to sustain cell growth arrest after DNA damage, possibly contributing to protect normal and female cancer cells from tumor progression. Accordingly, TSPYL2 has been found more frequently mutated in female-specific cancers. These findings demonstrate for the first time a sex-specific regulation of TSPYL2 in the DDR of cancer cells and confirm the existence of sexual dimorphism in DNA surveillance pathways.
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Affiliation(s)
- Miriana Cardano
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100, Pavia, Italy
| | - Martina Magni
- Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Roberta Alfieri
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100, Pavia, Italy
| | - Siu Yuen Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong-Kong, Hong-Kong SAR, China
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100, Pavia, Italy
| | - Giacomo Buscemi
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100, Pavia, Italy
| | - Laura Zannini
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100, Pavia, Italy.
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3
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Zardoni L, Nardini E, Brambati A, Lucca C, Choudhary R, Loperfido F, Sabbioneda S, Liberi G. Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions. Nucleic Acids Res 2021; 49:12769-12784. [PMID: 34878142 PMCID: PMC8682787 DOI: 10.1093/nar/gkab1146] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 06/29/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Uncoordinated clashes between replication forks and transcription cause replication stress and genome instability, which are hallmarks of cancer and neurodegeneration. Here, we investigate the outcomes of head-on replication-transcription collisions, using as a model system budding yeast mutants for the helicase Sen1, the ortholog of human Senataxin. We found that RNA Polymerase II accumulates together with RNA:DNA hybrids at sites of head-on collisions. The replication fork and RNA Polymerase II are both arrested during the clash, leading to DNA damage and, in the long run, the inhibition of gene expression. The inactivation of RNA Polymerase II elongation factors, such as the HMG-like protein Spt2 and the DISF and PAF complexes, but not alterations in chromatin structure, allows replication fork progression through transcribed regions. Attenuation of RNA Polymerase II elongation rescues RNA:DNA hybrid accumulation and DNA damage sensitivity caused by the absence of Sen1, but not of RNase H proteins, suggesting that such enzymes counteract toxic RNA:DNA hybrids at different stages of the cell cycle with Sen1 mainly acting in replication. We suggest that the main obstacle to replication fork progression is the elongating RNA Polymerase II engaged in an R-loop, rather than RNA:DNA hybrids per se or hybrid-associated chromatin modifications.
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Affiliation(s)
- Luca Zardoni
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy.,Scuola Universitaria Superiore IUSS, 27100 Pavia, Italy
| | - Eleonora Nardini
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Alessandra Brambati
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | | | | | - Federica Loperfido
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy.,IFOM Foundation, 20139 Milan, Italy
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Cabrini M, Roncador M, Galbiati A, Cipolla L, Maffia A, Iannelli F, Sabbioneda S, d'Adda di Fagagna F, Francia S. DROSHA is recruited to DNA damage sites by the MRN complex to promote non-homologous end joining. J Cell Sci 2021; 134:jcs.249706. [PMID: 33558311 PMCID: PMC8015226 DOI: 10.1242/jcs.249706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/23/2021] [Indexed: 11/20/2022] Open
Abstract
The DNA damage response (DDR) is the signaling cascade that recognizes DNA double-strand breaks (DSBs) and promotes their resolution via the DNA repair pathways of non-homologous end joining (NHEJ) or homologous recombination (HR). We and others have shown that DDR activation requires DROSHA; however, whether DROSHA exerts its functions by associating with damage sites, what controls its recruitment, and how DROSHA influences DNA repair remains poorly understood. Here, we show that DROSHA associates with DSBs independently of transcription. Neither H2AX, nor ATM or DNA-PK kinase activities are required for recruitment of DROSHA to break sites. Rather, DROSHA interacts with RAD50, and inhibition of the MRN complex by mirin treatment abolishes this interaction. MRN complex inactivation by RAD50 knockdown or mirin treatment prevents DROSHA recruitment to DSBs and, as a consequence, also prevents 53BP1 (also known as TP53BP1) recruitment. During DNA repair, DROSHA inactivation reduces NHEJ and boosts HR frequency. Indeed, DROSHA knockdown also increases the association of downstream HR factors such as RAD51 to DNA ends. Overall, our results demonstrate that DROSHA is recruited at DSBs by the MRN complex and directs DNA repair towards NHEJ.
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Affiliation(s)
- Matteo Cabrini
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy.,IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Marco Roncador
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Alessandro Galbiati
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Antonio Maffia
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Fabio Iannelli
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Fabrizio d'Adda di Fagagna
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy .,IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy .,IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
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5
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Mentegari E, Bertoletti F, Kissova M, Zucca E, Galli S, Tagliavini G, Garbelli A, Maffia A, Bione S, Ferrari E, d’Adda di Fagagna F, Francia S, Sabbioneda S, Chen LY, Lingner J, Bergoglio V, Hoffmann JS, Hübscher U, Crespan E, Maga G. A Role for Human DNA Polymerase λ in Alternative Lengthening of Telomeres. Int J Mol Sci 2021; 22:ijms22052365. [PMID: 33673424 PMCID: PMC7956399 DOI: 10.3390/ijms22052365] [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] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Telomerase negative cancer cell types use the Alternative Lengthening of Telomeres (ALT) pathway to elongate telomeres ends. Here, we show that silencing human DNA polymerase (Pol λ) in ALT cells represses ALT activity and induces telomeric stress. In addition, replication stress in the absence of Pol λ, strongly affects the survival of ALT cells. In vitro, Pol λ can promote annealing of even a single G-rich telomeric repeat to its complementary strand and use it to prime DNA synthesis. The noncoding telomeric repeat containing RNA TERRA and replication protein A negatively regulate this activity, while the Protection of Telomeres protein 1 (POT1)/TPP1 heterodimer stimulates Pol λ. Pol λ associates with telomeres and colocalizes with TPP1 in cells. In summary, our data suggest a role of Pol λ in the maintenance of telomeres by the ALT mechanism.
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Affiliation(s)
- Elisa Mentegari
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Federica Bertoletti
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Miroslava Kissova
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Elisa Zucca
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Silvia Galli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Giulia Tagliavini
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Antonio Maffia
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Silvia Bione
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; (E.F.); (U.H.)
| | - Fabrizio d’Adda di Fagagna
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- IFOM-The FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Sofia Francia
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Simone Sabbioneda
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Liuh-Yow Chen
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland; (L.-Y.C.); (J.L.)
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland; (L.-Y.C.); (J.L.)
| | - Valerie Bergoglio
- UMR1037 INSERM, Cancer Research Center of Toulouse, 2 Avenue Curien, 31037 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
| | - Ulrich Hübscher
- Department of Molecular Mechanisms of Disease, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; (E.F.); (U.H.)
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- Correspondence: (E.C.); (G.M.)
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- Correspondence: (E.C.); (G.M.)
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6
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Riva V, Garbelli A, Casiraghi F, Arena F, Trivisani CI, Gagliardi A, Bini L, Schroeder M, Maffia A, Sabbioneda S, Maga G. Novel alternative ribonucleotide excision repair pathways in human cells by DDX3X and specialized DNA polymerases. Nucleic Acids Res 2021; 48:11551-11565. [PMID: 33137198 PMCID: PMC7672437 DOI: 10.1093/nar/gkaa948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 01/02/2023] Open
Abstract
Removal of ribonucleotides (rNMPs) incorporated into the genome by the ribonucleotide excision repair (RER) is essential to avoid genetic instability. In eukaryotes, the RNaseH2 is the only known enzyme able to incise 5' of the rNMP, starting the RER process, which is subsequently carried out by replicative DNA polymerases (Pols) δ or ϵ, together with Flap endonuclease 1 (Fen-1) and DNA ligase 1. Here, we show that the DEAD-box RNA helicase DDX3X has RNaseH2-like activity and can support fully reconstituted in vitro RER reactions, not only with Pol δ but also with the repair Pols β and λ. Silencing of DDX3X causes accumulation of rNMPs in the cellular genome. These results support the existence of alternative RER pathways conferring high flexibility to human cells in responding to the threat posed by rNMPs incorporation.
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Affiliation(s)
- Valentina Riva
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Federica Casiraghi
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Francesca Arena
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Claudia Immacolata Trivisani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Assunta Gagliardi
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy
| | - Luca Bini
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy
| | - Martina Schroeder
- Kathleen Lonsdale Institute for Human Health Research, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Antonio Maffia
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Simone Sabbioneda
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
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7
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Cipolla L, Bertoletti F, Maffia A, Liang CC, Lehmann AR, Cohn MA, Sabbioneda S. UBR5 interacts with the replication fork and protects DNA replication from DNA polymerase η toxicity. Nucleic Acids Res 2020; 47:11268-11283. [PMID: 31586398 PMCID: PMC6868395 DOI: 10.1093/nar/gkz824] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 02/13/2019] [Revised: 09/06/2019] [Accepted: 09/25/2019] [Indexed: 11/26/2022] Open
Abstract
Accurate DNA replication is critical for the maintenance of genome integrity and cellular survival. Cancer-associated alterations often involve key players of DNA replication and of the DNA damage-signalling cascade. Post-translational modifications play a fundamental role in coordinating replication and repair and central among them is ubiquitylation. We show that the E3 ligase UBR5 interacts with components of the replication fork, including the translesion synthesis (TLS) polymerase polη. Depletion of UBR5 leads to replication problems, such as slower S-phase progression, resulting in the accumulation of single stranded DNA. The effect of UBR5 knockdown is related to a mis-regulation in the pathway that controls the ubiquitylation of histone H2A (UbiH2A) and blocking this modification is sufficient to rescue the cells from replication problems. We show that the presence of polη is the main cause of replication defects and cell death when UBR5 is silenced. Finally, we unveil a novel interaction between polη and H2A suggesting that UbiH2A could be involved in polη recruitment to the chromatin and the regulation of TLS.
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Affiliation(s)
- Lina Cipolla
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Federica Bertoletti
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Antonio Maffia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Martin A Cohn
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
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8
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Belloni E, Di Matteo A, Pradella D, Vacca M, Wyatt CDR, Alfieri R, Maffia A, Sabbioneda S, Ghigna C. Gene Expression Profiles Controlled by the Alternative Splicing Factor Nova2 in Endothelial Cells. Cells 2019; 8:cells8121498. [PMID: 31771184 PMCID: PMC6953062 DOI: 10.3390/cells8121498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/11/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) plays an important role in expanding the complexity of the human genome through the production of specialized proteins regulating organ development and physiological functions, as well as contributing to several pathological conditions. How AS programs impact on the signaling pathways controlling endothelial cell (EC) functions and vascular development is largely unknown. Here we identified, through RNA-seq, changes in mRNA steady-state levels in ECs caused by the neuro-oncological ventral antigen 2 (Nova2), a key AS regulator of the vascular morphogenesis. Bioinformatics analyses identified significant enrichment for genes regulated by peroxisome proliferator-activated receptor-gamma (Ppar-γ) and E2F1 transcription factors. We also showed that Nova2 in ECs controlled the AS profiles of Ppar-γ and E2F dimerization partner 2 (Tfdp2), thus generating different protein isoforms with distinct function (Ppar-γ) or subcellular localization (Tfdp2). Collectively, our results supported a mechanism whereby Nova2 integrated splicing decisions in order to regulate Ppar-γ and E2F1 activities. Our data added a layer to the sequential series of events controlled by Nova2 in ECs to orchestrate vascular biology.
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Affiliation(s)
- Elisa Belloni
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Anna Di Matteo
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Davide Pradella
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Margherita Vacca
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Christopher D. R. Wyatt
- Centre for Biodiversity and Environment Research, University College London, Gower Street, London WC1E 6BT, UK
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10-12, 08002 Barcelona, Spain
| | - Roberta Alfieri
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Antonio Maffia
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Claudia Ghigna
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
- Correspondence:
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9
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González Besteiro MA, Calzetta NL, Loureiro SM, Habif M, Bétous R, Pillaire MJ, Maffia A, Sabbioneda S, Hoffmann JS, Gottifredi V. Chk1 loss creates replication barriers that compromise cell survival independently of excess origin firing. EMBO J 2019; 38:e101284. [PMID: 31294866 DOI: 10.15252/embj.2018101284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 01/18/2023] Open
Abstract
The effectiveness of checkpoint kinase 1 (Chk1) inhibitors at killing cancer cells is considered to be fully dependent on their effect on DNA replication initiation. Chk1 inhibition boosts origin firing, presumably limiting the availability of nucleotides and in turn provoking the slowdown and subsequent collapse of forks, thus decreasing cell viability. Here we show that slow fork progression in Chk1-inhibited cells is not an indirect effect of excess new origin firing. Instead, fork slowdown results from the accumulation of replication barriers, whose bypass is impeded by CDK-dependent phosphorylation of the specialized DNA polymerase eta (Polη). Also in contrast to the linear model, the accumulation of DNA damage in Chk1-deficient cells depends on origin density but is largely independent of fork speed. Notwithstanding this, origin dysregulation contributes only mildly to the poor proliferation rates of Chk1-depleted cells. Moreover, elimination of replication barriers by downregulation of helicase components, but not their bypass by Polη, improves cell survival. Our results thus shed light on the molecular basis of the sensitivity of tumors to Chk1 inhibition.
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Affiliation(s)
- Marina A González Besteiro
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Nicolás L Calzetta
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Sofía M Loureiro
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Martín Habif
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Rémy Bétous
- Equipe «Labellisée LA LIGUE CONTRE LE CANCER», Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, University Paul Sabatier, Toulouse, France
| | - Marie-Jeanne Pillaire
- Equipe «Labellisée LA LIGUE CONTRE LE CANCER», Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, University Paul Sabatier, Toulouse, France
| | - Antonio Maffia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - CNR, Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - CNR, Pavia, Italy
| | - Jean-Sébastien Hoffmann
- Equipe «Labellisée LA LIGUE CONTRE LE CANCER», Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, University Paul Sabatier, Toulouse, France
| | - Vanesa Gottifredi
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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10
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Besio R, Garibaldi N, Leoni L, Cipolla L, Sabbioneda S, Biggiogera M, Mottes M, Aglan M, Otaify GA, Temtamy SA, Rossi A, Forlino A. Cellular stress due to impairment of collagen prolyl hydroxylation complex is rescued by the chaperone 4-phenylbutyrate. Dis Model Mech 2019; 12:dmm.038521. [PMID: 31171565 PMCID: PMC6602311 DOI: 10.1242/dmm.038521] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/20/2019] [Indexed: 12/30/2022] Open
Abstract
Osteogenesis imperfecta (OI) types VII, VIII and IX, caused by recessive mutations in cartilage-associated protein (CRTAP), prolyl-3-hydroxylase 1 (P3H1) and cyclophilin B (PPIB), respectively, are characterized by the synthesis of overmodified collagen. The genes encode for the components of the endoplasmic reticulum (ER) complex responsible for the 3-hydroxylation of specific proline residues in type I collagen. Our study dissects the effects of mutations in the proteins of the complex on cellular homeostasis, using primary fibroblasts from seven recessive OI patients. In all cell lines, the intracellular retention of overmodified type I collagen molecules causes ER enlargement associated with the presence of protein aggregates, activation of the PERK branch of the unfolded protein response and apoptotic death. The administration of 4-phenylbutyrate (4-PBA) alleviates cellular stress by restoring ER cisternae size, and normalizing the phosphorylated PERK (p-PERK):PERK ratio and the expression of apoptotic marker. The drug also has a stimulatory effect on autophagy. We proved that the rescue of cellular homeostasis following 4-PBA treatment is associated with its chaperone activity, since it increases protein secretion, restoring ER proteostasis and reducing PERK activation and cell survival also in the presence of pharmacological inhibition of autophagy. Our results provide a novel insight into the mechanism of 4-PBA action and demonstrate that intracellular stress in recessive OI can be alleviated by 4-PBA therapy, similarly to what we recently reported for dominant OI, thus allowing a common target for OI forms characterized by overmodified collagen. This article has an associated First Person interview with the first author of the paper. Editor's choice: Mutations in the collagen 3-prolyl hydroxylation complex cause a cellular stress that is rescued by the chaperone ability of 4-phenylbutyrate.
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Affiliation(s)
- Roberta Besio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
| | - Nadia Garibaldi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy.,Istituto Universitario di Studi Superiori - IUSS, 27100 Pavia, Italy
| | - Laura Leoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Marco Biggiogera
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Monica Mottes
- Department of Neuroscience, Biomedicine and Movement, University of Verona, 37134 Verona, Italy
| | - Mona Aglan
- Department of Clinical Genetics, Human Genetics & Genome Research Division, Center of Excellence for Human Genetics, National Research Centre, Cairo 12622, Egypt
| | - Ghada A Otaify
- Department of Clinical Genetics, Human Genetics & Genome Research Division, Center of Excellence for Human Genetics, National Research Centre, Cairo 12622, Egypt
| | - Samia A Temtamy
- Department of Clinical Genetics, Human Genetics & Genome Research Division, Center of Excellence for Human Genetics, National Research Centre, Cairo 12622, Egypt
| | - Antonio Rossi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
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11
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Besio R, Iula G, Garibaldi N, Cipolla L, Sabbioneda S, Biggiogera M, Marini JC, Rossi A, Forlino A. 4-PBA ameliorates cellular homeostasis in fibroblasts from osteogenesis imperfecta patients by enhancing autophagy and stimulating protein secretion. Biochim Biophys Acta Mol Basis Dis 2018; 1864:1642-1652. [PMID: 29432813 PMCID: PMC5908783 DOI: 10.1016/j.bbadis.2018.02.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/11/2022]
Abstract
The clinical phenotype in osteogenesis imperfecta (OI) is attributed to the dominant negative function of mutant type I collagen molecules in the extracellular matrix, by altering its structure and function. Intracellular retention of mutant collagen has also been reported, but its effect on cellular homeostasis is less characterized. Using OI patient fibroblasts carrying mutations in the α1(I) and α2(I) chains we demonstrate that retained collagen molecules are responsible for endoplasmic reticulum (ER) enlargement and activation of the unfolded protein response (UPR) mainly through the eukaryotic translation initiation factor 2 alpha kinase 3 (PERK) branch. Cells carrying α1(I) mutations upregulate autophagy, while cells with α2(I) mutations only occasionally activate the autodegradative response. Despite the autophagy activation to face stress conditions, apoptosis occurs in all mutant fibroblasts. To reduce cellular stress, mutant fibroblasts were treated with the FDA-approved chemical chaperone 4-phenylbutyric acid. The drug rescues cell death by modulating UPR activation thanks to both its chaperone and histone deacetylase inhibitor abilities. As chaperone it increases general cellular protein secretion in all patients' cells as well as collagen secretion in cells with the most C-terminal mutation. As histone deacetylase inhibitor it enhances the expression of the autophagic gene Atg5 with a consequent stimulation of autophagy. These results demonstrate that the cellular response to ER stress can be a relevant target to ameliorate OI cell homeostasis.
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Affiliation(s)
- Roberta Besio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia 27100, Italy.
| | - Giusy Iula
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia 27100, Italy.
| | - Nadia Garibaldi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia 27100, Italy.
| | - Lina Cipolla
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia 27100, Italy.
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia 27100, Italy.
| | - Marco Biggiogera
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
| | - Joan C Marini
- Bone and Extracellular Matrix Branch, NICHD, National Institute of Health, Bethesda, MD 20892, USA.
| | - Antonio Rossi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia 27100, Italy.
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia 27100, Italy.
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12
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Bertoletti F, Cea V, Liang CC, Lanati T, Maffia A, Avarello MDM, Cipolla L, Lehmann AR, Cohn MA, Sabbioneda S. Phosphorylation regulates human polη stability and damage bypass throughout the cell cycle. Nucleic Acids Res 2017; 45:9441-9454. [PMID: 28934491 PMCID: PMC5766190 DOI: 10.1093/nar/gkx619] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/06/2017] [Indexed: 01/22/2023] Open
Abstract
DNA translesion synthesis (TLS) is a crucial damage tolerance pathway that oversees the completion of DNA replication in the presence of DNA damage. TLS polymerases are capable of bypassing a distorted template but they are generally considered inaccurate and they need to be tightly regulated. We have previously shown that polη is phosphorylated on Serine 601 after DNA damage and we have demonstrated that this modification is important for efficient damage bypass. Here we report that polη is also phosphorylated by CDK2, in the absence of damage, in a cell cycle-dependent manner and we identify serine 687 as an important residue targeted by the kinase. We discover that phosphorylation on serine 687 regulates the stability of the polymerase during the cell cycle, allowing it to accumulate in late S and G2 when productive TLS is critical for cell survival. Furthermore, we show that alongside the phosphorylation of S601, the phosphorylation of S687 and S510, S512 and/or S514 are important for damage bypass and cell survival after UV irradiation. Taken together our results provide new insights into how cells can, at different times, modulate DNA TLS for improved cell survival.
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Affiliation(s)
| | - Valentina Cea
- Istituto di Genetica Molecolare-CNR, 27100, Pavia, Italy
| | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Taiba Lanati
- Istituto di Genetica Molecolare-CNR, 27100, Pavia, Italy
| | - Antonio Maffia
- Istituto di Genetica Molecolare-CNR, 27100, Pavia, Italy.,Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Universita' degli Studi di Pavia, 27100, Pavia, Italy
| | | | - Lina Cipolla
- Istituto di Genetica Molecolare-CNR, 27100, Pavia, Italy
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ, Brighton, UK
| | - Martin A Cohn
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
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13
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Mentegari E, Crespan E, Bavagnoli L, Kissova M, Bertoletti F, Sabbioneda S, Imhof R, Sturla SJ, Nilforoushan A, Hübscher U, van Loon B, Maga G. Ribonucleotide incorporation by human DNA polymerase η impacts translesion synthesis and RNase H2 activity. Nucleic Acids Res 2017; 45:2600-2614. [PMID: 27994034 PMCID: PMC5389505 DOI: 10.1093/nar/gkw1275] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/07/2016] [Indexed: 12/25/2022] Open
Abstract
Ribonucleotides (rNs) incorporated in the genome by DNA polymerases (Pols) are removed by RNase H2. Cytidine and guanosine preferentially accumulate over the other rNs. Here we show that human Pol η can incorporate cytidine monophosphate (rCMP) opposite guanine, 8-oxo-7,8-dihydroguanine, 8-methyl-2΄-deoxyguanosine and a cisplatin intrastrand guanine crosslink (cis-PtGG), while it cannot bypass a 3-methylcytidine or an abasic site with rNs as substrates. Pol η is also capable of synthesizing polyribonucleotide chains, and its activity is enhanced by its auxiliary factor DNA Pol δ interacting protein 2 (PolDIP2). Human RNase H2 removes cytidine and guanosine less efficiently than the other rNs and incorporation of rCMP opposite DNA lesions further reduces the efficiency of RNase H2. Experiments with XP-V cell extracts indicate Pol η as the major basis of rCMP incorporation opposite cis-PtGG. These results suggest that translesion synthesis by Pol η can contribute to the accumulation of rCMP in the genome, particularly opposite modified guanines.
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Affiliation(s)
- Elisa Mentegari
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Emmanuele Crespan
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Laura Bavagnoli
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Miroslava Kissova
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Federica Bertoletti
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Simone Sabbioneda
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Ralph Imhof
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zürich, Switzerland
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zürich, Switzerland
| | - Ulrich Hübscher
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Barbara van Loon
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Giovanni Maga
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
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14
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Kanu N, Zhang T, Burrell RA, Chakraborty A, Cronshaw J, Da Costa C, Grönroos E, Pemberton HN, Anderton E, Gonzalez L, Sabbioneda S, Ulrich HD, Swanton C, Behrens A. RAD18, WRNIP1 and ATMIN promote ATM signalling in response to replication stress. Oncogene 2016; 35:4009-19. [PMID: 26549024 PMCID: PMC4842010 DOI: 10.1038/onc.2015.427] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 01/22/2023]
Abstract
The DNA replication machinery invariably encounters obstacles that slow replication fork progression, and threaten to prevent complete replication and faithful segregation of sister chromatids. The resulting replication stress activates ATR, the major kinase involved in resolving impaired DNA replication. In addition, replication stress also activates the related kinase ATM, which is required to prevent mitotic segregation errors. However, the molecular mechanism of ATM activation by replication stress is not defined. Here, we show that monoubiquitinated Proliferating Cell Nuclear Antigen (PCNA), a marker of stalled replication forks, interacts with the ATM cofactor ATMIN via WRN-interacting protein 1 (WRNIP1). ATMIN, WRNIP1 and RAD18, the E3 ligase responsible for PCNA monoubiquitination, are specifically required for ATM signalling and 53BP1 focus formation induced by replication stress, not ionising radiation. Thus, WRNIP1 connects PCNA monoubiquitination with ATMIN/ATM to activate ATM signalling in response to replication stress and contribute to the maintenance of genomic stability.
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Affiliation(s)
- Nnennaya Kanu
- Mammalian Genetics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Tianyi Zhang
- Mammalian Genetics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Rebecca A. Burrell
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK and UCL Cancer Institute, 72 Huntley Street, London WC1E 6BT, UK
| | - Atanu Chakraborty
- Mammalian Genetics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Janet Cronshaw
- Mammalian Genetics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Clive Da Costa
- Mammalian Genetics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK and UCL Cancer Institute, 72 Huntley Street, London WC1E 6BT, UK
| | - Helen N. Pemberton
- Molecular Oncology Laboratory, Cancer Research UK, London Research Institute, 44, Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Emma Anderton
- Molecular Oncology Laboratory, Cancer Research UK, London Research Institute, 44, Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Laure Gonzalez
- DNA Damage Tolerance Laboratory, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Herts EN6 3LD, UK
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare-CNR, Via Abbiategrasso, 207 - 27100 Pavia, Italy
| | - Helle D. Ulrich
- DNA Damage Tolerance Laboratory, Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Herts EN6 3LD, UK
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK and UCL Cancer Institute, 72 Huntley Street, London WC1E 6BT, UK
| | - Axel Behrens
- Mammalian Genetics Laboratory, The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
- School of Medicine, King’s College London, Guy’s Campus, London, SE1 1UL, UK
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15
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Kanu N, Zhang T, Burrell RA, Chakraborty A, Cronshaw J, DaCosta C, Grönroos E, Pemberton HN, Anderton E, Gonzalez L, Sabbioneda S, Ulrich HD, Swanton C, Behrens A. Erratum: RAD18, WRNIP1 and ATMIN promote ATM signalling in response to replication stress. Oncogene 2016; 35:4020. [DOI: 10.1038/onc.2015.500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Cipolla L, Maffia A, Bertoletti F, Sabbioneda S. The Regulation of DNA Damage Tolerance by Ubiquitin and Ubiquitin-Like Modifiers. Front Genet 2016; 7:105. [PMID: 27379156 PMCID: PMC4904029 DOI: 10.3389/fgene.2016.00105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 03/01/2016] [Accepted: 05/25/2016] [Indexed: 11/13/2022] Open
Abstract
DNA replication is an extremely complex process that needs to be executed in a highly accurate manner in order to propagate the genome. This task requires the coordination of a number of enzymatic activities and it is fragile and prone to arrest after DNA damage. DNA damage tolerance provides a last line of defense that allows completion of DNA replication in the presence of an unrepaired template. One of such mechanisms is called post-replication repair (PRR) and it is used by the cells to bypass highly distorted templates caused by damaged bases. PRR is extremely important for the cellular life and performs the bypass of the damage both in an error-free and in an error-prone manner. In light of these two possible outcomes, PRR needs to be tightly controlled in order to prevent the accumulation of mutations leading ultimately to genome instability. Post-translational modifications of PRR proteins provide the framework for this regulation with ubiquitylation and SUMOylation playing a pivotal role in choosing which pathway to activate, thus controlling the different outcomes of damage bypass. The proliferating cell nuclear antigen (PCNA), the DNA clamp for replicative polymerases, plays a central role in the regulation of damage tolerance and its modification by ubiquitin, and SUMO controls both the error-free and error-prone branches of PRR. Furthermore, a significant number of polymerases are involved in the bypass of DNA damage possess domains that can bind post-translational modifications and they are themselves target for ubiquitylation. In this review, we will focus on how ubiquitin and ubiquitin-like modifications can regulate the DNA damage tolerance systems and how they control the recruitment of different proteins to the replication fork.
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Affiliation(s)
- Lina Cipolla
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Antonio Maffia
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Federica Bertoletti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
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17
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Harley ME, Murina O, Leitch A, Higgs MR, Bicknell LS, Yigit G, Blackford AN, Zlatanou A, Mackenzie KJ, Reddy K, Halachev M, McGlasson S, Reijns MAM, Fluteau A, Martin CA, Sabbioneda S, Elcioglu NH, Altmüller J, Thiele H, Greenhalgh L, Chessa L, Maghnie M, Salim M, Bober MB, Nürnberg P, Jackson SP, Hurles ME, Wollnik B, Stewart GS, Jackson AP. TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism. Nat Genet 2016; 48:36-43. [PMID: 26595769 PMCID: PMC4697364 DOI: 10.1038/ng.3451] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [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: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022]
Abstract
DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.
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Affiliation(s)
- Margaret E Harley
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Olga Murina
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrea Leitch
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Louise S Bicknell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Gökhan Yigit
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | | | - Anastasia Zlatanou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Karen J Mackenzie
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Kaalak Reddy
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Mihail Halachev
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah McGlasson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Martin A M Reijns
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Carol-Anne Martin
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | | | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Janine Altmüller
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Lynn Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Liverpool Women's Hospital, Liverpool, L12 2AP, UK
| | - Luciana Chessa
- Department of Clinical and Molecular Medicine, University Sapienza, A.O.S. Andrea, I-00189 Roma, Italy
| | - Mohamad Maghnie
- Department of Pediatrics, IRCCS, Giannina Gaslini, University of Genova, 16147 Genova, Italy
| | - Mahmoud Salim
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Michael B Bober
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Stephen P Jackson
- The Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | | | - Bernd Wollnik
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Institute of Human Genetics, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
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18
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Abstract
DNA replication is an extremely risky process that cells have to endure in order to correctly duplicate and segregate their genome. This task is particularly sensitive to DNA damage and multiple mechanisms have evolved to protect DNA replication as a block to the replication fork could lead to genomic instability and possibly cell death. The DNA in the genome folds, for the most part, into the canonical B-form but in some instances can form complex secondary structures such as G-quadruplexes (G4). These G rich regions are thermodynamically stable and can constitute an obstacle to DNA and RNA metabolism. The human genome contains more than 350,000 sequences potentially capable to form G-quadruplexes and these structures are involved in a variety of cellular processes such as initiation of DNA replication, telomere maintenance and control of gene expression. Only recently, we started to understand how G4 DNA poses a problem to DNA replication and how its successful bypass requires the coordinated activity of ssDNA binding proteins, helicases and specialized DNA polymerases. Their role in the resolution and replication of structured DNA crucially prevents both genetic and epigenetic instability across the genome.
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Affiliation(s)
- Valentina Cea
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche , Pavia, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche , Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche , Pavia, Italy
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19
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Göhler T, Sabbioneda S, Green CM, Lehmann AR. ATR-mediated phosphorylation of DNA polymerase η is needed for efficient recovery from UV damage. ACTA ACUST UNITED AC 2011; 192:219-27. [PMID: 21242293 PMCID: PMC3172178 DOI: 10.1083/jcb.201008076] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Phosphorylation of Polη links DNA damage–induced checkpoint activation and translesion synthesis in mammalian cells. DNA polymerase η (polη) belongs to the Y-family of DNA polymerases and facilitates translesion synthesis past UV damage. We show that, after UV irradiation, polη becomes phosphorylated at Ser601 by the ataxia-telangiectasia mutated and Rad3-related (ATR) kinase. DNA damage–induced phosphorylation of polη depends on its physical interaction with Rad18 but is independent of PCNA monoubiquitination. It requires the ubiquitin-binding domain of polη but not its PCNA-interacting motif. ATR-dependent phosphorylation of polη is necessary to restore normal survival and postreplication repair after ultraviolet irradiation in xeroderma pigmentosum variant fibroblasts, and is involved in the checkpoint response to UV damage. Taken together, our results provide evidence for a link between DNA damage–induced checkpoint activation and translesion synthesis in mammalian cells.
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Affiliation(s)
- Thomas Göhler
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, England, UK
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20
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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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21
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Bienko M, Green CM, Sabbioneda S, Crosetto N, Matic I, Hibbert RG, Begovic T, Niimi A, Mann M, Lehmann AR, Dikic I. Regulation of translesion synthesis DNA polymerase eta by monoubiquitination. Mol Cell 2010; 37:396-407. [PMID: 20159558 DOI: 10.1016/j.molcel.2009.12.039] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 09/03/2009] [Accepted: 12/08/2009] [Indexed: 01/12/2023]
Abstract
DNA polymerase eta is a Y family polymerase involved in translesion synthesis (TLS). Its action is initiated by simultaneous interaction between the PIP box in pol eta and PCNA and between the UBZ in pol eta and monoubiquitin attached to PCNA. Whereas monoubiquitination of PCNA is required for its interaction with pol eta during TLS, we now show that monoubiquitination of pol eta inhibits this interaction, preventing its functions in undamaged cells. Identification of monoubiquitination sites within pol eta nuclear localization signal (NLS) led to the discovery that pol eta NLS directly contacts PCNA, forming an extended pol eta-PCNA interaction surface. We name this the PCNA-interacting region (PIR) and show that its monoubiquitination is downregulated by various DNA-damaging agents. We propose that this mechanism ensures optimal availability of nonubiquitinated, TLS-competent pol eta after DNA damage. Our work shows how monoubiquitination can either positively or negatively regulate the assembly of a protein complex, depending on which substrates are targeted by ubiquitin.
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Affiliation(s)
- Marzena Bienko
- Institute of Biochemistry II, Goethe University Medical School, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
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22
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Sabbioneda S, Gourdin AM, Green CM, Zotter A, Giglia-Mari G, Houtsmuller A, Vermeulen W, Lehmann AR. Effect of proliferating cell nuclear antigen ubiquitination and chromatin structure on the dynamic properties of the Y-family DNA polymerases. Mol Biol Cell 2008; 19:5193-202. [PMID: 18799611 DOI: 10.1091/mbc.e08-07-0724] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Y-family DNA polymerases carry out translesion synthesis past damaged DNA. DNA polymerases (pol) eta and iota are usually uniformly distributed through the nucleus but accumulate in replication foci during S phase. DNA-damaging treatments result in an increase in S phase cells containing polymerase foci. Using photobleaching techniques, we show that poleta is highly mobile in human fibroblasts. Even when localized in replication foci, it is only transiently immobilized. Although ubiquitination of proliferating cell nuclear antigen (PCNA) is not required for the localization of poleta in foci, it results in an increased residence time in foci. poliota is even more mobile than poleta, both when uniformly distributed and when localized in foci. Kinetic modeling suggests that both poleta and poliota diffuse through the cell but that they are transiently immobilized for approximately 150 ms, with a larger proportion of poleta than poliota immobilized at any time. Treatment of cells with DRAQ5, which results in temporary opening of the chromatin structure, causes a dramatic immobilization of poleta but not poliota. Our data are consistent with a model in which the polymerases are transiently probing the DNA/chromatin. When DNA is exposed at replication forks, the polymerase residence times increase, and this is further facilitated by the ubiquitination of PCNA.
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Affiliation(s)
- Simone Sabbioneda
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
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23
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Lehmann AR, Niimi A, Ogi T, Brown S, Sabbioneda S, Wing JF, Kannouche PL, Green CM. Translesion synthesis: Y-family polymerases and the polymerase switch. DNA Repair (Amst) 2007; 6:891-9. [PMID: 17363342 DOI: 10.1016/j.dnarep.2007.02.003] [Citation(s) in RCA: 300] [Impact Index Per Article: 17.6] [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: 11/29/2022]
Abstract
Replicative DNA polymerases are blocked at DNA lesions. Synthesis past DNA damage requires the replacement of the replicative polymerase by one of a group of specialised translesion synthesis (TLS) polymerases, most of which belong to the Y-family. Each of these has different substrate specificities for different types of damage. In eukaryotes mono-ubiquitination of PCNA plays a crucial role in the switch from replicative to TLS polymerases at stalled forks. All the Y-family polymerases have ubiquitin binding sites that increase their binding affinity for ubiquitinated PCNA at the sites of stalled forks.
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Affiliation(s)
- Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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24
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Bilancia G, Facchini A, Ferrando M, Giola M, Maluta F, Mariani M, Mazzuccato M, Madic C, Sabbioneda S. Selective Actinide Extraction with a Tri‐Synergistic Mixture Using a Centrifugal Contactor Battery. Solvent Extraction and Ion Exchange 2007. [DOI: 10.1080/07366290500294905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- G. Bilancia
- a ENEA CR SALUGGIA, Strada per Crescentino , Saluggia , VC , Italy
| | - A. Facchini
- b Politecnico di Milano, Dipartimento di Ingegneria Nucleare, CeSNEF , Milano , MI , Italy
| | - M. Ferrando
- a ENEA CR SALUGGIA, Strada per Crescentino , Saluggia , VC , Italy
| | - M. Giola
- b Politecnico di Milano, Dipartimento di Ingegneria Nucleare, CeSNEF , Milano , MI , Italy
| | - F. Maluta
- b Politecnico di Milano, Dipartimento di Ingegneria Nucleare, CeSNEF , Milano , MI , Italy
| | - M. Mariani
- b Politecnico di Milano, Dipartimento di Ingegneria Nucleare, CeSNEF , Milano , MI , Italy
| | - M. Mazzuccato
- b Politecnico di Milano, Dipartimento di Ingegneria Nucleare, CeSNEF , Milano , MI , Italy
| | - C. Madic
- c CEA, DEN‐SAC , CEA/Saclay , Gif‐s‐Yvette , France
| | - S. Sabbioneda
- a ENEA CR SALUGGIA, Strada per Crescentino , Saluggia , VC , Italy
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25
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Sabbioneda S, Bortolomai I, Giannattasio M, Plevani P, Muzi-Falconi M. Yeast Rev1 is cell cycle regulated, phosphorylated in response to DNA damage and its binding to chromosomes is dependent upon MEC1. DNA Repair (Amst) 2006; 6:121-7. [PMID: 17035102 DOI: 10.1016/j.dnarep.2006.09.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 08/30/2006] [Accepted: 09/01/2006] [Indexed: 11/26/2022]
Abstract
Translesion DNA synthesis (TLS) is one of the mechanisms involved in lesion bypass during DNA replication. Three TLS polymerases (Pol) are present in the yeast Saccharomyces cerevisiae: Pol zeta, Pol eta and the product of the REV1 gene. Rev1 is considered a deoxycytidyl transferase because it almost exclusively inserts a C residue in front of the lesion. Even though REV1 is required for most of the UV-induced and spontaneous mutagenesis events, the role of Rev1 is poorly understood since its polymerase activity is often dispensable. Rev1 interacts with several TLS polymerases in mammalian cells and may act as a platform in the switching mechanism required to substitute a replicative polymerase with a TLS polymerase at the sites of DNA lesions. Here we show that yeast Rev1 is a phosphoprotein, and the level of this modification is cell cycle regulated under normal growing conditions. Rev1 is unphosphorylated in G1, starts to be modified while cells are passing S phase and it becomes hyper-phosphorylated in mitosis. Rev1 is also hyper-phosphorylated in response to a variety of DNA damaging agents, including treatment with a radiomimetic drug mostly causing double-strand breaks (DSB). By using the chromosome spreading technique we found the Rev1 is bound to chromosomes throughout the cell cycle, and its binding does not significantly increase in response to genotoxic stress. Therefore, Rev1 phosphorylation does not appear to modulate its binding to chromosomes, suggesting that such modification may influence other aspects of the TLS process. Rev1 binding under damaged and undamaged conditions, is at least partially dependent on MEC1, a gene playing a pivotal role in the DNA damage checkpoint cascade. This genetic dependency may suggest a role for MEC1 in spontaneous mutagenesis events, which require a functional REV1 gene.
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Affiliation(s)
- Simone Sabbioneda
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano., Via Celoria 26, 20133 Milano, Italy
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26
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Sabbioneda S, Minesinger BK, Giannattasio M, Plevani P, Muzi-Falconi M, Jinks-Robertson S. The 9-1-1 checkpoint clamp physically interacts with polzeta and is partially required for spontaneous polzeta-dependent mutagenesis in Saccharomyces cerevisiae. J Biol Chem 2005; 280:38657-65. [PMID: 16169844 DOI: 10.1074/jbc.m507638200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The use of translesion synthesis (TLS) polymerases to bypass DNA lesions during replication constitutes an important mechanism to restart blocked/stalled DNA replication forks. Because TLS polymerases generally have low fidelity on undamaged DNA, the cell must regulate the interaction of TLS polymerases with damaged versus undamaged DNA to maintain genome integrity. The Saccharomyces cerevisiae checkpoint proteins Ddc1, Rad17, and Mec3 form a clamp-like structure (the 9-1-1 clamp) that has physical similarity to the homotrimeric sliding clamp proliferating cell nuclear antigen, which interacts with and promotes the processivity of the replicative DNA polymerases. In this work, we demonstrate both an in vivo and in vitro physical interaction between the Mec3 and Ddc1 subunits of the 9-1-1 clamp and the Rev7 subunit of the Polzeta TLS polymerase. In addition, we demonstrate that loss of Mec3, Ddc1, or Rad17 results in a decrease in Polzeta-dependent spontaneous mutagenesis. These results suggest that, in addition to its checkpoint signaling role, the 9-1-1 clamp may physically regulate Polzeta-dependent mutagenesis by controlling the access of Polzeta to damaged DNA.
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Affiliation(s)
- Simone Sabbioneda
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milano, Italy 20133
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27
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Muzi-Falconi M, Sabbioneda S, Plevani P, Foiani M. Sometimes size does matter. Eur J Cancer 2003; 39:1337-8. [PMID: 12826033 DOI: 10.1016/s0959-8049(03)00127-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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28
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Giannattasio M, Sabbioneda S, Minuzzo M, Plevani P, Muzi-Falconi M. Correlation between checkpoint activation and in vivo assembly of the yeast checkpoint complex Rad17-Mec3-Ddc1. J Biol Chem 2003; 278:22303-8. [PMID: 12672803 DOI: 10.1074/jbc.m301260200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [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
Rad17-Mec3-Ddc1 forms a proliferating cell nuclear antigen-like complex that is required for the DNA damage response in Saccharomyces cerevisiae and acts at an early step of the signal transduction cascade activated by DNA lesions. We used the mec3-dn allele, which causes a dominant negative checkpoint defect in G1 but not in G2, to test the stability of the complex in vivo and to correlate its assembly and disassembly with the mechanisms controlling checkpoint activation. Under physiological conditions, the mutant complex is formed both in G1 and G2, although the mutant phenotype is detectable only in G1, suggesting that is not the presence of the mutant complex per se to cause a checkpoint defect. Our data indicate that the Rad17-Mec3-Ddc1 complex is very stable, and it takes several hours to replace Mec3 with Mec3-dn within a wild type complex. On the other hand, the mutant complex is rapidly assembled when starting from a condition where the complex is not pre-assembled, indicating that the critical factor for the substitution is the disassembly step rather than complex formation. Moreover, the kinetics of mutant complex assembly, starting from conditions in which the wild type form is present, parallels the kinetics of checkpoint inactivation, suggesting that the complex acts in a stoichiometric way, rather than catalytically.
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Affiliation(s)
- Michele Giannattasio
- Dipartimento di Genetica e di Biologia dei Microrganismi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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