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Di Nardo M, Musio A. Cohesin - bridging the gap among gene transcription, genome stability, and human diseases. FEBS Lett 2024. [PMID: 38852996 DOI: 10.1002/1873-3468.14949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024]
Abstract
The intricate landscape of cellular processes governing gene transcription, chromatin organization, and genome stability is a fascinating field of study. A key player in maintaining this delicate equilibrium is the cohesin complex, a molecular machine with multifaceted roles. This review presents an in-depth exploration of these intricate connections and their significant impact on various human diseases.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
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Di Nardo M, Astigiano S, Baldari S, Pallotta MM, Porta G, Pigozzi S, Antonini A, Emionite L, Frattini A, Valli R, Toietta G, Soddu S, Musio A. The synergism of SMC1A cohesin gene silencing and bevacizumab against colorectal cancer. J Exp Clin Cancer Res 2024; 43:49. [PMID: 38365745 PMCID: PMC10870497 DOI: 10.1186/s13046-024-02976-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND SMC1A is a subunit of the cohesin complex that participates in many DNA- and chromosome-related biological processes. Previous studies have established that SMC1A is involved in cancer development and in particular, is overexpressed in chromosomally unstable human colorectal cancer (CRC). This study aimed to investigate whether SMC1A could serve as a therapeutic target for CRC. METHODS At first, we studied the effects of either SMC1A overexpression or knockdown in vitro. Next, the outcome of SMC1A knocking down (alone or in combination with bevacizumab, a monoclonal antibody against vascular endothelial growth factor) was analyzed in vivo. RESULTS We found that SMC1A knockdown affects cell proliferation and reduces the ability to grow in anchorage-independent manner. Next, we demonstrated that the silencing of SMC1A and the combo treatment were effective in increasing overall survival in a xenograft mouse model. Functional analyses indicated that both treatments lead to atypical mitotic figures and gene expression dysregulation. Differentially expressed genes were implicated in several pathways including gene transcription regulation, cellular proliferation, and other transformation-associated processes. CONCLUSIONS These results indicate that SMC1A silencing, in combination with bevacizumab, can represent a promising therapeutic strategy for human CRC.
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Affiliation(s)
- Maddalena Di Nardo
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy
| | | | - Silvia Baldari
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Maria Michela Pallotta
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy
| | - Giovanni Porta
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
| | - Simona Pigozzi
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate, Università degli Studi di Genova, Genoa, Italy
| | - Annalisa Antonini
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | | | - Annalisa Frattini
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Roberto Valli
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
| | - Gabriele Toietta
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Silvia Soddu
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Antonio Musio
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy.
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Li J, Zhou Q, Liu L, He J. Effects of SMC1A on immune microenvironment and cancer stem cells in colon adenocarcinoma. Cancer Med 2023. [PMID: 37096492 DOI: 10.1002/cam4.5891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/12/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Our previous study suggested that SMC1 has significant functions in colorectal cancer (CRC). However, few reports have shown the effects of structural maintenance of chromosomes 1 (SMC1A) on the immune microenvironment and tumor stem cells. METHODS The Cancer Genome Atlas (TCGA) database, CPTAC database, Human Protein Atlas (HPA) database, the Cancer Cell Line Encyclopedia (CCLE) and Tumor Immune Single-cell Hub were used. Flow cytometry and immunohistochemical analysis were checked for immune infiltration on MC38 mice model. Human CRC tissues were tested with RT-qPCR. RESULTS The mRNA and protein levels of SMC1A were increased in colon adenocarcinoma (COAD) samples. SMC1A was associated with DNA activity. Interestingly, SMC1A was highly expressed in many types of immune cells at single-cell levels. Moreover, the high expression of SMC1A was positively correlated with immune infiltration, and immunohistochemical analysis showed that SMC1A was positively associated with CD45 expression in MC38 mice model. Also, the percentage of IL4+ CD4+ T cells (Th2) and FoxP3+ CD4+ T cells (Tregs) was significantly higher in the SMC1A overexpression group than in control by flow cytometry assay in vivo. SMC1A expression could affect the proliferation of T cells in the mice model. The mutation and somatic cell copy number variation (SCNV) of SMC1A were also associated with immune cell infiltration. In addition to SMC1A in the "hot" T-cell inflammatory microenvironment of colon cancer, SMC1A also positively correlates with the immune checkpoint genes CD274, CTLA4, and PDCD1 in colon adenocarcinoma (COAD) samples. Furthermore, we also found that SMC1A plays a positive correlation with the induction of cancer stem cells (CSCs). Our results also showed that miR-23b-3p binds SMC1A. CONCLUSION SMC1A may be a bidirectional target switch that simultaneously regulates the immune microenvironment and tumor stem cells. Moreover, SMC1A may be a biomarker for the prediction of immune checkpoint inhibitor (ICI) therapy.
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Affiliation(s)
- Jin Li
- Department of Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Qian Zhou
- The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Li Liu
- The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Jingdong He
- Department of Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
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Pallotta MM, Di Nardo M, Sarogni P, Krantz ID, Musio A. Disease-associated c-MYC downregulation in human disorders of transcriptional regulation. Hum Mol Genet 2022; 31:1599-1609. [PMID: 34849865 PMCID: PMC9122636 DOI: 10.1093/hmg/ddab348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 11/12/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare multiorgan developmental disorder caused by pathogenic variants in cohesin genes. It is a genetically and clinically heterogeneous dominant (both autosomal and X-linked) rare disease. Increasing experimental evidence indicates that CdLS is caused by a combination of factors, such as gene expression dysregulation, accumulation of cellular damage and cellular aging, which collectively contribute to the CdLS phenotype. The CdLS phenotype overlaps with a number of related diagnoses such as KBG syndrome and Rubinstein-Taybi syndrome both caused by variants in chromatin-associated factors other than cohesin. The molecular basis underlying these overlapping phenotypes is not clearly defined. Here, we found that cells from individuals with CdLS and CdLS-related diagnoses are characterized by global transcription disturbance and share common dysregulated pathways. Intriguingly, c-MYC (subsequently referred to as MYC) is downregulated in all cell lines and represents a convergent hub lying at the center of dysregulated pathways. Subsequent treatment with estradiol restores MYC expression by modulating cohesin occupancy at its promoter region. In addition, MYC activation leads to modification in expression in hundreds of genes, which in turn reduce the oxidative stress level and genome instability. Together, these results show that MYC plays a pivotal role in the etiopathogenesis of CdLS and CdLS-related diagnoses and represents a potential therapeutic target for these conditions.
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Affiliation(s)
- Maria M Pallotta
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), 56124 Pisa, Italy
| | - Maddalena Di Nardo
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), 56124 Pisa, Italy
| | - Patrizia Sarogni
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), 56124 Pisa, Italy
| | - Ian D Krantz
- Roberts Individualized Medical Genetics Center, Division of Human Genetics, The Department of Pediatrics, The Children's Hospital of Philadelphia, and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Antonio Musio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), 56124 Pisa, Italy
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Di Nardo M, Pallotta MM, Musio A. The multifaceted roles of cohesin in cancer. J Exp Clin Cancer Res 2022; 41:96. [PMID: 35287703 PMCID: PMC8919599 DOI: 10.1186/s13046-022-02321-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
The cohesin complex controls faithful chromosome segregation by pairing sister chromatids after DNA replication until mitosis. In addition, it is crucial for hierarchal three-dimensional organization of the genome, transcription regulation and maintaining DNA integrity. The core complex subunits SMC1A, SMC3, STAG1/2, and RAD21 as well as its modulators, have been found to be recurrently mutated in human cancers. The mechanisms by which cohesin mutations trigger cancer development and disease progression are still poorly understood. Since cohesin is involved in a range of chromosome-related processes, the outcome of cohesin mutations in cancer is complex. Herein, we discuss recent discoveries regarding cohesin that provide new insight into its role in tumorigenesis.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Maria M. Pallotta
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
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Abstract
Structural Maintenance of Chromosomes (SMCs) are part of a large family of ring complexes that participates in a number of DNA transactions. Among SMCs, SMC1A gene is unique. It encodes a subunit of the cohesin-core complex that tethers sister chromatids together to ensure correct chromosome segregation in both mitosis and meiosis. As a member of the cohesin ring, SMC1A takes part in gene transcription regulation and genome organization; and it participates in the DNA Damage Repair (DDR) pathway, being phosphorylated by Ataxia Telangiectasia Mutated (ATM) and Ataxia Telangiectasia and Rad3 Related (ATR) threonine/serine kinases. It is also a component of the Recombination protein complex (RC-1) involved in DNA repair by recombination. SMC1A pathogenic variants have been described in Cornelia de Lange syndrome (CdLS), a human rare disease, and recently SMC1A variants have been associated with epilepsy or resembling Rett syndrome phenotype. Finally, SMC1A variants have been identified in several human cancers. In this review, our current knowledge of the SMC1A gene has been summarized.
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Affiliation(s)
- Antonio Musio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Pisa, Italy.
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Sarogni P, Pallotta MM, Musio A. Cornelia de Lange syndrome: from molecular diagnosis to therapeutic approach. J Med Genet 2020; 57:289-295. [PMID: 31704779 PMCID: PMC7231464 DOI: 10.1136/jmedgenet-2019-106277] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/08/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a severe genetic disorder characterised by multisystemic malformations. CdLS is due to pathogenetic variants in NIPBL, SMC1A, SMC3, RAD21 and HDAC8 genes which belong to the cohesin pathway. Cohesin plays a pivotal role in chromatid cohesion, gene expression, and DNA repair. In this review, we will discuss how perturbations in those biological processes contribute to CdLS phenotype and will emphasise the state-of-art of CdLS therapeutic approaches.
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Affiliation(s)
- Patrizia Sarogni
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Maria M Pallotta
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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Brahme A, Hultén M, Bengtsson C, Hultgren A, Zetterberg A. Radiation-Induced Chromosomal Breaks may be DNA Repair Fragile Sites with Larger-scale Correlations to Eight Double-Strand-Break Related Data Sets over the Human Genome. Radiat Res 2019; 192:562-576. [PMID: 31545677 DOI: 10.1667/rr15424.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this work, we compared the genomic distribution of common radiation-induced chromosomal breaks to eight different data sets covering the whole human genome. Sites with a high probability of chromatid breakage after exposure to low and high ionization density radiations were often located inside common and rare fragile sites, indicating that they may be a new and more local type of DNA repair-related fragility. Breaks in specific chromosome bands after acute exposure to oil and benzene also showed strong correlation with these sites and fragile sites. In addition, close correlation was found with cytologically detected chiasma and MLH1 immunofluorescence sites and with the HapMap recombination density distributions. Also, of interest, copy number changes occurred predominantly at radiation-induced breaks and fragile sites, at least for breast cancers with poor prognosis, and they decreased weakly but significantly in regions with increasing recombination and CpG density. An increased CpG density is linked to regions of high gene density to secure high-fidelity reproduction and survival. To minimize cancer induction, cancer-related genes are often located in regions of decreased recombination density and/or higher-than-average CpG density. It is compelling that all these data sets were influenced by the cells' handling of double-strand breaks and, more generally, DNA damage on its genome. In fact, the DNA repair genes systematically avoid regions with a high recombination density, as they need to be intact to accurately handle repairable DNA lesions.
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Affiliation(s)
- Anders Brahme
- Department of Oncology-Pathology, Karolinska Institutet, Box 260, SE-171 76 Stockholm, Sweden
| | - Maj Hultén
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, S-171 76 Stockholm, Sweden
| | - Carin Bengtsson
- Department of Oncology-Pathology, Karolinska Institutet, Box 260, SE-171 76 Stockholm, Sweden
| | - Andreas Hultgren
- Department of Oncology-Pathology, Karolinska Institutet, Box 260, SE-171 76 Stockholm, Sweden
| | - Anders Zetterberg
- Department of Oncology-Pathology, Karolinska Institutet, Box 260, SE-171 76 Stockholm, Sweden
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9
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Sarogni P, Palumbo O, Servadio A, Astigiano S, D'Alessio B, Gatti V, Cukrov D, Baldari S, Pallotta MM, Aretini P, Dell'Orletta F, Soddu S, Carella M, Toietta G, Barbieri O, Fontanini G, Musio A. Overexpression of the cohesin-core subunit SMC1A contributes to colorectal cancer development. J Exp Clin Cancer Res 2019; 38:108. [PMID: 30823889 PMCID: PMC6397456 DOI: 10.1186/s13046-019-1116-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/21/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cancer cells are characterized by chromosomal instability (CIN) and it is thought that errors in pathways involved in faithful chromosome segregation play a pivotal role in the genesis of CIN. Cohesin forms a large protein ring that binds DNA strands by encircling them. In addition to this central role in chromosome segregation, cohesin is also needed for DNA repair, gene transcription regulation and chromatin architecture. Though mutations in both cohesin and cohesin-regulator genes have been identified in many human cancers, the contribution of cohesin to cancer development is still under debate. METHODS Normal mucosa, early adenoma, and carcinoma samples deriving from 16 subjects affected by colorectal cancer (CRC) were analyzed by OncoScan for scoring both chromosome gains and losses (CNVs) and loss of heterozygosity (LOH). Then the expression of SMC1A was analyzed by immunochemistry in 66 subjects affected by CRC. The effects of SMC1A overexpression and mutated SMC1A were analyzed in vivo using immunocompromised mouse models. Finally, we measured global gene expression profiles in induced-tumors by RNA-seq. RESULTS Here we showed that SMC1A cohesin core gene was present as extra-copies, mutated, and overexpressed in human colorectal carcinomas. We then demonstrated that cohesin overexpression led to the development of aggressive cancers in immunocompromised mice through gene expression dysregulation. CONCLUSION Collectively, these results support a role of defective cohesin in the development of human colorectal cancer.
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Affiliation(s)
- Patrizia Sarogni
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Orazio Palumbo
- Division of Medical Genetics, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Adele Servadio
- Division of Pathology, Department of Surgery, University of Pisa, Pisa, Italy
| | - Simonetta Astigiano
- IRCCS Ospedale Policlinico San Martino, Department of Translational Oncology, Genoa, Italy
| | - Barbara D'Alessio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Veronica Gatti
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy.,Present address: Institute of Cell Biology and Neurobiology, National Research Council (CNR), Monterotondo, Italy
| | - Dubravka Cukrov
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Silvia Baldari
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Maria Michela Pallotta
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Paolo Aretini
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, Italy
| | - Felice Dell'Orletta
- Institute for Computational Linguistics (ILC) "A. Zampolli", National Research Council (CNR), Pisa, Italy
| | - Silvia Soddu
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Massimo Carella
- Division of Medical Genetics, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Gabriele Toietta
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Ottavia Barbieri
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Gabriella Fontanini
- Division of Pathology, Department of Surgery, University of Pisa, Pisa, Italy
| | - Antonio Musio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy.
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DNA replication stress and its impact on chromosome segregation and tumorigenesis. Semin Cancer Biol 2018; 55:61-69. [PMID: 29692334 DOI: 10.1016/j.semcancer.2018.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 01/11/2023]
Abstract
Genome instability and cell cycle dysregulation are commonly associated with cancer. DNA replication stress driven by oncogene activation during tumorigenesis is now well established as a source of genome instability. Replication stress generates DNA damage not only during S phase, but also in the subsequent mitosis, where it impacts adversely on chromosome segregation. Some regions of the genome seem particularly sensitive to replication stress-induced instability; most notably, chromosome fragile sites. In this article, we review some of the important issues that have emerged in recent years concerning DNA replication stress and fragile site expression, as well as how chromosome instability is minimized by a family of ring-shaped protein complexes known as SMC proteins. Understanding how replication stress impacts on S phase and mitosis in cancer should provide opportunities for the development of novel and tumour-specific treatments.
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Abstract
A fragile site is a chromosomal locus that is prone to form a gap or constriction visible within a condensed metaphase chromosome, particularly following exposure of cells to DNA replication stress. Based on their frequency, fragile sites are classified as either common (CFSs; present in all individuals) or rare (RFSs; present in only a few individuals). Interest in fragile sites has remained high since their discovery in 1965, because of their association with human disease. CFSs are recognized as drivers of oncogene activation and genome instability in cancer cells, while some RFSs are associated with neurodegenerative diseases. This review summaries our current understanding of the nature and causes of fragile site "expression", including the recently characterized phenomenon of telomere fragility. In particular, we focus on a description of the methodologies and technologies for detection and analysis of chromosome fragile sites.
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Yi F, Wang Z, Liu J, Zhang Y, Wang Z, Xu H, Li X, Bai N, Cao L, Song X. Structural Maintenance of Chromosomes protein 1: Role in Genome Stability and Tumorigenesis. Int J Biol Sci 2017; 13:1092-1099. [PMID: 28924389 PMCID: PMC5599913 DOI: 10.7150/ijbs.21206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 07/05/2017] [Indexed: 01/05/2023] Open
Abstract
SMC1 (Structural Maintenance of Chromosomes protein 1), well known as one of the SMC superfamily members, has been explored to function in many activities including chromosome dynamics, cell cycle checkpoint, DNA damage repair and genome stability. Upon being properly assembled as part of cohesin, SMC1 can be phosphorylated by ATM and mediate downstream DNA damage repair after ionizing irradiation. Abnormal gene expression or mutation of SMC1 can cause defect in the DNA damage repair pathway, which has been strongly associated with tumorigenesis. Here we focus to discuss SMC1's role in genome stability maintenance and tumorigenesis. Deciphering the underlying molecular mechanism can provide insight into novel strategies for cancer treatment.
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Affiliation(s)
- Fei Yi
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Zhuo Wang
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Jingwei Liu
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Ying Zhang
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Zhijun Wang
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Hongde Xu
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Xiaoman Li
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Ning Bai
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Liu Cao
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
| | - Xiaoyu Song
- Key Laboratory of Medical Cell Biology, Ministry of Education; Institute of Translational Medicine, China Medical University; Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, Shenyang, Liaoning Province, China
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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Beresova L, Vesela E, Chamrad I, Voller J, Yamada M, Furst T, Lenobel R, Chroma K, Gursky J, Krizova K, Mistrik M, Bartek J. Role of DNA Repair Factor Xeroderma Pigmentosum Protein Group C in Response to Replication Stress As Revealed by DNA Fragile Site Affinity Chromatography and Quantitative Proteomics. J Proteome Res 2016; 15:4505-4517. [PMID: 27794614 DOI: 10.1021/acs.jproteome.6b00622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Replication stress (RS) fuels genomic instability and cancer development and may contribute to aging, raising the need to identify factors involved in cellular responses to such stress. Here, we present a strategy for identification of factors affecting the maintenance of common fragile sites (CFSs), which are genomic loci that are particularly sensitive to RS and suffer from increased breakage and rearrangements in tumors. A DNA probe designed to match the high flexibility island sequence typical for the commonly expressed CFS (FRA16D) was used as specific DNA affinity bait. Proteins significantly enriched at the FRA16D fragment under normal and replication stress conditions were identified using stable isotope labeling of amino acids in cell culture-based quantitative mass spectrometry. The identified proteins interacting with the FRA16D fragment included some known CFS stabilizers, thereby validating this screening approach. Among the hits from our screen so far not implicated in CFS maintenance, we chose Xeroderma pigmentosum protein group C (XPC) for further characterization. XPC is a key factor in the DNA repair pathway known as global genomic nucleotide excision repair (GG-NER), a mechanism whose several components were enriched at the FRA16D fragment in our screen. Functional experiments revealed defective checkpoint signaling and escape of DNA replication intermediates into mitosis and the next generation of XPC-depleted cells exposed to RS. Overall, our results provide insights into an unexpected biological role of XPC in response to replication stress and document the power of proteomics-based screening strategies to elucidate mechanisms of pathophysiological significance.
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Affiliation(s)
- Lucie Beresova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic.,Department of Protein Biochemistry and Proteomics, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of Science, Palacky University , Olomouc, Czech Republic
| | - Eva Vesela
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Ivo Chamrad
- Department of Protein Biochemistry and Proteomics, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of Science, Palacky University , Olomouc, Czech Republic
| | - Jiri Voller
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Masayuki Yamada
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Tomas Furst
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Rene Lenobel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of Science, Palacky University , Olomouc, Czech Republic
| | - Katarina Chroma
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Jan Gursky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Katerina Krizova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Jiri Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic.,Danish Cancer Society Research Center , Copenhagen, Denmark.,Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Biochemistry and Biophysics, Karolinska Institute , Stockholm, Sweden
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15
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Gelot C, Guirouilh-Barbat J, Lopez BS. The cohesin complex prevents the end-joining of distant DNA double-strand ends in S phase: Consequences on genome stability maintenance. Nucleus 2016; 7:339-45. [PMID: 27326661 DOI: 10.1080/19491034.2016.1194159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
DNA double-strand break (DSB) repair is essential for genome stability maintenance, but the joining of distant DNA double strand ends (DSEs) inevitably leads to genome rearrangements. Therefore, DSB repair should be tightly controlled to secure genome stability while allowing genetic variability. Tethering of the proximal ends of a 2-ended DSB limits their mobility, protecting thus against their joining with a distant DSE. However, replication stress generates DSBs with only one DSE, on which tethering is impossible. Consistently, we demonstrated that the joining of 2 DSBs only 3.2 kb apart is repressed in the S, but not the G1, phase, revealing an additional mechanism limiting DNA ends mobility in S phase. The cohesin complex, by maintaining the 2 sister chromatids linked, limits DSEs mobility and thus represses the joining of distant DSEs, while allowing that of adjacent DSEs. At the genome scale, the cohesin complex protects against deletions, inversions, translocations and chromosome fusion.
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Affiliation(s)
- Camille Gelot
- a CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer , Villejuif , France
| | - Josée Guirouilh-Barbat
- a CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer , Villejuif , France
| | - Bernard S Lopez
- a CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer , Villejuif , France
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16
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Cucco F, Musio A. Genome stability: What we have learned from cohesinopathies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2016; 172:171-8. [PMID: 27091086 DOI: 10.1002/ajmg.c.31492] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cohesin is a multiprotein complex involved in many DNA-related processes such as proper chromosome segregation, replication, transcription, and repair. Mutations in cohesin gene pathways are responsible for human diseases, collectively referred to as cohesinopathies. In addition, both cohesin gene expression dysregulation and mutations have been identified in cancer. Cohesinopathy cells are characterized by genome instability (GIN) visualized by a constellation of markers such as chromosome aneuploidies, chromosome aberrations, precocious sister chromatid separation, premature centromere separation, micronuclei formation, and sensitivity to genotoxic drugs. The emerging picture suggests that GIN observed in cohesinopathies may result from the synergistic effects of the multiple cohesin dysfunctions. © 2016 Wiley Periodicals, Inc.
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17
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Abstract
Replication perturbations activate DNA damage tolerance (DDT) pathways, which are crucial to promote replication completion and to prevent fork breakage, a leading cause of genome instability. One mode of DDT uses translesion synthesis polymerases, which however can also introduce mutations. The other DDT mode involves recombination-mediated mechanisms, which are generally accurate. DDT occurs prevalently postreplicatively, but in certain situations homologous recombination is needed to restart forks. Fork reversal can function to stabilize stalled forks, but may also promote error-prone outcome when used for fork restart. Recent years have witnessed important advances in our understanding of the mechanisms and DNA structures that mediate recombination-mediated damage-bypass and highlighted principles that regulate DDT pathway choice locally and temporally. In this review we summarize the current knowledge and paradoxes on recombination-mediated DDT pathways and their workings, discuss how the intermediate DNA structures may influence genome integrity, and outline key open questions for future research.
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Affiliation(s)
- Dana Branzei
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Barnabas Szakal
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
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18
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Gelot C, Guirouilh-Barbat J, Le Guen T, Dardillac E, Chailleux C, Canitrot Y, Lopez BS. The Cohesin Complex Prevents the End Joining of Distant DNA Double-Strand Ends. Mol Cell 2016; 61:15-26. [PMID: 26687679 DOI: 10.1016/j.molcel.2015.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 09/25/2015] [Accepted: 11/02/2015] [Indexed: 02/07/2023]
Abstract
The end joining of distant DNA double-strand ends (DSEs) can produce potentially deleterious rearrangements. We show that depletion of cohesion complex proteins specifically stimulates the end joining (both C-NHEJ and A-EJ) of distant, but not close, I-SceI-induced DSEs in S/G2 phases. At the genome level, whole-exome sequencing showed that ablation of RAD21 or Sororin produces large chromosomal rearrangements (translocation, duplication, deletion). Moreover, cytogenetic analysis showed that RAD21 silencing leads to the formation of chromosome fusions synergistically with replication stress, which generates distant single-ended DSEs. These data reveal a role for the cohesin complex in protecting against genome rearrangements arising from the ligation of distant DSEs in S/G2 phases (both long-range DSEs and those that are only a few kilobases apart), while keeping end joining fully active for close DSEs. Therefore, this role likely involves limitation of DSE motility specifically in S phase, rather than inhibition of the end-joining machinery itself.
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Affiliation(s)
- Camille Gelot
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Josée Guirouilh-Barbat
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Tangui Le Guen
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Elodie Dardillac
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Catherine Chailleux
- Université de Toulouse UPS, CNRS UMR 5088, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), 31062 Toulouse, France
| | - Yvan Canitrot
- Université de Toulouse UPS, CNRS UMR 5088, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), 31062 Toulouse, France
| | - Bernard S Lopez
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France.
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19
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Mannini L, Cucco F, Quarantotti V, Amato C, Tinti M, Tana L, Frattini A, Delia D, Krantz ID, Jessberger R, Musio A. SMC1B is present in mammalian somatic cells and interacts with mitotic cohesin proteins. Sci Rep 2015; 5:18472. [PMID: 26673124 PMCID: PMC4682075 DOI: 10.1038/srep18472] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/18/2015] [Indexed: 01/02/2023] Open
Abstract
Cohesin is an evolutionarily conserved protein complex that plays a role in many biological processes: it ensures faithful chromosome segregation, regulates gene expression and preserves genome stability. In mammalian cells, the mitotic cohesin complex consists of two structural maintenance of chromosome proteins, SMC1A and SMC3, the kleisin protein RAD21 and a fourth subunit either STAG1 or STAG2. Meiotic paralogs in mammals were reported for SMC1A, RAD21 and STAG1/STAG2 and are called SMC1B, REC8 and STAG3 respectively. It is believed that SMC1B is only a meiotic-specific cohesin member, required for sister chromatid pairing and for preventing telomere shortening. Here we show that SMC1B is also expressed in somatic mammalian cells and is a member of a mitotic cohesin complex. In addition, SMC1B safeguards genome stability following irradiation whereas its ablation has no effect on chromosome segregation. Finally, unexpectedly SMC1B depletion impairs gene transcription, particularly at genes mapping to clusters such as HOX and PCDHB. Genome-wide analyses show that cluster genes changing in expression are enriched for cohesin-SMC1B binding.
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Affiliation(s)
- Linda Mannini
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Francesco Cucco
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Valentina Quarantotti
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Clelia Amato
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Mara Tinti
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Luigi Tana
- Azienda Ospedaliero Universitaria Pisana, U.O. Fisica Sanitaria, Pisa, Italy
| | - Annalisa Frattini
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
- Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi dell’Insubria, Varese, Italy
| | - Domenico Delia
- Fondazione IRCCS Istituto Nazionale Tumori, Department of Experimental Oncology, Milan, Italy
| | - Ian D. Krantz
- Division of Human Genetics, The Children’s Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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20
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Thys RG, Lehman CE, Pierce LCT, Wang YH. DNA secondary structure at chromosomal fragile sites in human disease. Curr Genomics 2015; 16:60-70. [PMID: 25937814 PMCID: PMC4412965 DOI: 10.2174/1389202916666150114223205] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 11/22/2022] Open
Abstract
DNA has the ability to form a variety of secondary structures that can interfere with normal cellular processes, and many of these structures have been associated with neurological diseases and cancer. Secondary structure-forming sequences are often found at chromosomal fragile sites, which are hotspots for sister chromatid exchange, chromosomal translocations, and deletions. Structures formed at fragile sites can lead to instability by disrupting normal cellular processes such as DNA replication and transcription. The instability caused by disruption of replication and transcription can lead to DNA breakage, resulting in gene rearrangements and deletions that cause disease. In this review, we discuss the role of DNA secondary structure at fragile sites in human disease.
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Affiliation(s)
- Ryan G Thys
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Christine E Lehman
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | | | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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21
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Cornelia de Lange Syndrome: A Variable Disorder of Cohesin Pathology. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0065-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Abstract
The primary goal of mitosis is to partition duplicated chromosomes into daughter cells. Eukaryotic chromosomes are equipped with two distinct classes of intrinsic machineries, cohesin and condensins, that ensure their faithful segregation during mitosis. Cohesin holds sister chromatids together immediately after their synthesis during S phase until the establishment of bipolar attachments to the mitotic spindle in metaphase. Condensins, on the other hand, attempt to "resolve" sister chromatids by counteracting cohesin. The products of the balancing acts of cohesin and condensins are metaphase chromosomes, in which two rod-shaped chromatids are connected primarily at the centromere. In anaphase, this connection is released by the action of separase that proteolytically cleaves the remaining population of cohesin. Recent studies uncover how this series of events might be mechanistically coupled with each other and intricately regulated by a number of regulatory factors.
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Affiliation(s)
- Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
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23
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Franchitto A, Pichierri P. Replication fork recovery and regulation of common fragile sites stability. Cell Mol Life Sci 2014; 71:4507-17. [PMID: 25216703 PMCID: PMC11113654 DOI: 10.1007/s00018-014-1718-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
The acquisition of genomic instability is a triggering factor in cancer development, and common fragile sites (CFS) are the preferential target of chromosomal instability under conditions of replicative stress in the human genome. Although the mechanisms leading to CFS expression and the cellular factors required to suppress CFS instability remain largely undefined, it is clear that DNA becomes more susceptible to breakage when replication is impaired. The models proposed so far to explain how CFS instability arises imply that replication fork progression along these regions is perturbed due to intrinsic features of fragile sites and events that directly affect DNA replication. The observation that proteins implicated in the safe recovery of stalled forks or in engaging recombination at collapsed forks increase CFS expression when downregulated or mutated suggests that the stabilization and recovery of perturbed replication forks are crucial to guarantee CFS integrity.
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Affiliation(s)
- Annapaola Franchitto
- Section of Molecular Epidemiology, Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy,
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24
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Ozeri-Galai E, Tur-Sinai M, Bester AC, Kerem B. Interplay between genetic and epigenetic factors governs common fragile site instability in cancer. Cell Mol Life Sci 2014; 71:4495-506. [PMID: 25297918 PMCID: PMC11113459 DOI: 10.1007/s00018-014-1719-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 11/28/2022]
Abstract
Common fragile sites (CFSs) are regions within the normal chromosomal structure that were characterized as hotspots for genomic instability in cancer almost 30 years ago. In recent years, many efforts have been made to understand the basis of CFS fragility and their involvement in the genomic signature of instability found in malignant tumors. CFSs are among the first regions to undergo genomic instability during cancer development because of their intrinsic sensitivity to replication stress conditions, which result from oncogene expression. The preferred sensitivity of CFSs to replication stress stems from various mechanisms including: replication fork arrest at AT-rich repeats, origin paucity along large genomic regions, failure in activation of dormant origins, late replication timing, collision between replication and transcription along large genes, all leading to incomplete replication of the CFS region and resulting in chromosomal instability. Here we review shared and unique characteristics of CFSs, their underlying causes and implications, particularly for the development of cancer.
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Affiliation(s)
- Efrat Ozeri-Galai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Michal Tur-Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Assaf C. Bester
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
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25
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Georgakilas AG, Tsantoulis P, Kotsinas A, Michalopoulos I, Townsend P, Gorgoulis VG. Are common fragile sites merely structural domains or highly organized "functional" units susceptible to oncogenic stress? Cell Mol Life Sci 2014; 71:4519-44. [PMID: 25238782 PMCID: PMC4232749 DOI: 10.1007/s00018-014-1717-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 01/07/2023]
Abstract
Common fragile sites (CFSs) are regions of the genome with a predisposition to DNA double-strand breaks in response to intrinsic (oncogenic) or extrinsic replication stress. CFS breakage is a common feature in carcinogenesis from its earliest stages. Given that a number of oncogenes and tumor suppressors are located within CFSs, a question that emerges is whether fragility in these regions is only a structural “passive” incident or an event with a profound biological effect. Furthermore, there is sparse evidence that other elements, like non-coding RNAs, are positioned with them. By analyzing data from various libraries, like miRbase and ENCODE, we show a prevalence of various cancer-related genes, miRNAs, and regulatory binding sites, such as CTCF within CFSs. We propose that CFSs are not only susceptible structural domains, but highly organized “functional” entities that when targeted, severe repercussion for cell homeostasis occurs.
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Affiliation(s)
- Alexandros G Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780, Athens, Greece
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26
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Cucco F, Servadio A, Gatti V, Bianchi P, Mannini L, Prodosmo A, De Vitis E, Basso G, Friuli A, Laghi L, Soddu S, Fontanini G, Musio A. Mutant cohesin drives chromosomal instability in early colorectal adenomas. Hum Mol Genet 2014; 23:6773-8. [PMID: 25080505 DOI: 10.1093/hmg/ddu394] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chromosome missegregation leads to chromosomal instability (CIN), thought to play a role in cancer development. As cohesin functions in guaranteeing correct chromosome segregation, increasing data suggest its involvement in tumorigenesis. In a screen of a large series of early colorectal adenomas, a precocious step during colorectal tumorigenesis, we identified 11 mutations in SMC1A core cohesin subunit. In addition, we sequenced the SMC1A gene in colorectal carcinomas and we found only one mutation. Finally, the transfection of the SMC1A mutations identified in early adenomas and wild-type SMC1A gene silencing in normal human fibroblasts led to CIN. Our findings that SMC1A mutations decrease from early adenomas to colorectal cancers and that mutations lead to CIN suggest that mutant cohesin could play a pivotal role during colorectal cancer development.
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Affiliation(s)
- Francesco Cucco
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy Dipartimento di Biologia, Università degli Studi di Pisa, Pisa, Italy
| | - Adele Servadio
- Dipartimento di Patologia Chirurgica, Medica, Molecolare e di Area Critica, Università di Pisa, Pisa, Italy
| | - Veronica Gatti
- Oncologia Sperimentale, Istituto Nazionale Tumori Regina Elena, Roma, Italy
| | - Paolo Bianchi
- Humanitas Clinical and Research Center, Rozzano (MI), Italy and
| | - Linda Mannini
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Andrea Prodosmo
- Oncologia Sperimentale, Istituto Nazionale Tumori Regina Elena, Roma, Italy
| | - Elisa De Vitis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Gianluca Basso
- Humanitas Clinical and Research Center, Rozzano (MI), Italy and
| | - Alessandro Friuli
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Luigi Laghi
- Humanitas Clinical and Research Center, Rozzano (MI), Italy and
| | - Silvia Soddu
- Oncologia Sperimentale, Istituto Nazionale Tumori Regina Elena, Roma, Italy
| | - Gabriella Fontanini
- Dipartimento di Patologia Chirurgica, Medica, Molecolare e di Area Critica, Università di Pisa, Pisa, Italy
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy Istituto Toscano Tumori, Firenze, Italy
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27
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Laugsch M, Seebach J, Schnittler H, Jessberger R. Imbalance of SMC1 and SMC3 cohesins causes specific and distinct effects. PLoS One 2013; 8:e65149. [PMID: 23776448 PMCID: PMC3680458 DOI: 10.1371/journal.pone.0065149] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 04/23/2013] [Indexed: 11/24/2022] Open
Abstract
SMC1 and SMC3 form a high-affinity heterodimer, which provides an open backbone of the cohesin ring, to be closed by a kleisin protein. RNAi mediated knock-down of either one heterodimer partner, SMC1 or SMC3, is expected to cause very similar if not identical phenotypes. However, we observed highly distinct, protein-specific phenotypes. Upon knock-down of human SMC1, much of SMC3 remains stable, accumulates in the cytoplasm and does not associate with other cohesin proteins. Most of the excess nuclear SMC3 is highly mobile and not or only weakly chromosome-associated. In contrast, human SMC3 knock-down rendered SMC1 instable without cytoplasmic accumulation. As observed by differential protein extraction and in FRAP experiments the remaining SMC1 or SMC3 proteins in the respective SMC1 or SMC3 knock-down experiments constituted a cohesin pool, which is associated with chromatin with highest affinity, likely the least expendable. Expression of bovine EGFP-SMC1 or mouse EGFP-SMC3 in human cells under conditions of human SMC1 or SMC3 knock-down rescued the respective phenotypes, but in untreated cells over-expressed exogenous SMC proteins mis-localized. Paucity of either one of the SMC proteins causes RAD21 degradation. These results argue for great caution in interpreting SMC1 and SMC3 RNAi or over-expression experiments. Under challenged conditions these two proteins unexpectedly behave differently, which may have biological consequences for regulation of cohesin-associated functions and for human cohesin pathologies.
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Affiliation(s)
- Magdalena Laugsch
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Jochen Seebach
- Dept. of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Hans Schnittler
- Dept. of Anatomy and Vascular Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
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Lee KH, Onitsuka M, Honda K, Ohtake H, Omasa T. Rapid construction of transgene-amplified CHO cell lines by cell cycle checkpoint engineering. Appl Microbiol Biotechnol 2013; 97:5731-41. [DOI: 10.1007/s00253-013-4923-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/07/2013] [Accepted: 04/10/2013] [Indexed: 01/02/2023]
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Lu X, Parvathaneni S, Hara T, Lal A, Sharma S. Replication stress induces specific enrichment of RECQ1 at common fragile sites FRA3B and FRA16D. Mol Cancer 2013; 12:29. [PMID: 23601052 PMCID: PMC3663727 DOI: 10.1186/1476-4598-12-29] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/10/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Stalled replication forks at common fragile sites are a major cause of genomic instability. RecQ helicases, a highly conserved family of DNA-unwinding enzymes, are believed to ease 'roadblocks' that pose challenge to replication fork progression. Among the five known RecQ homologs in humans, functions of RECQ1, the most abundant of all, are poorly understood. We previously determined that RECQ1 helicase preferentially binds and unwinds substrates that mimic DNA replication/repair intermediates, and interacts with proteins involved in DNA replication restart mechanisms. METHOD We have utilized chromatin immunoprecipitation followed by quantitative real-time PCR to investigate chromatin interactions of RECQ1 at defined genetic loci in the presence or absence of replication stress. We have also tested the sensitivity of RECQ1-depleted cells to aphidicolin induced replication stress. RESULTS RECQ1 binds to the origins of replication in unperturbed cells. We now show that conditions of replication stress induce increased accumulation of RECQ1 at the lamin B2 origin in HeLa cells. Consistent with a role in promoting fork recovery or repair, RECQ1 is specifically enriched at two major fragile sites FRA3B and FRA16D where replication forks have stalled following aphidicolin treatment. RECQ1-depletion results in attenuated checkpoint activation in response to replication stress, increased sensitivity to aphidicolin and chromosomal instability. CONCLUSIONS Given a recent biochemical observation that RECQ1 catalyzes strand exchange on stalled replication fork structures in vitro, our results indicate that RECQ1 facilitates repair of stalled or collapsed replication forks and preserves genome integrity. Our findings provide the first evidence of a crucial role for RECQ1 at naturally occurring fork stalling sites and implicate RECQ1 in mechanisms underlying common fragile site instability in cancer.
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Affiliation(s)
- Xing Lu
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, 520 W Street, NW, Washington, DC 20059, USA. 2Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Swetha Parvathaneni
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, 520 W Street, NW, Washington, DC 20059, USA. 2Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Toshifumi Hara
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ashish Lal
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, 520 W Street, NW, Washington, DC 20059, USA. 2Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Zhang YF, Jiang R, Li JD, Zhang XY, Zhao P, He M, Zhang HZ, Sun LP, Shi DL, Zhang GX, Sun M. SMC1A knockdown induces growth suppression of human lung adenocarcinoma cells through G1/S cell cycle phase arrest and apoptosis pathways in vitro. Oncol Lett 2013; 5:749-755. [PMID: 23426528 PMCID: PMC3576224 DOI: 10.3892/ol.2013.1116] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 11/27/2012] [Indexed: 02/05/2023] Open
Abstract
SMC1A (structural maintenance of chromosomes 1A), which encodes a structural subunit of the cohesin protein complex, is necessary for the process of sister chromatid cohesion during the cell cycle. Mutation and deregulation of SMC1A are highly relevant to diverse human diseases, including Cornelia de Lange syndrome and malignant carcinomas. In order to further investigate the role of SMC1A in the oncogenesis of lung cancer, SMC1A-specific short hairpin RNA (shRNA)-expressing lentivirus (Lv-shSMC1A) was constructed and used to infect A549 and H1299 cells. SMC1A mRNA and protein expression levels were downregulated in A549 and H1299 cells as demonstrated by real-time PCR and western blot assays. We found that SMC1A inhibition resulted in significantly impaired proliferation and colony formation as well as reduced invasiveness of tumor cells. Notably, Lv-shSMC1A-infected cancer cells exhibited a greater proportion of cells in the G0/G1 phase, but a lower proportion of S phase cells, compared to the parent or Lv-shCon infected cancer cells. Moreover, a greater proportion of sub-G1 apoptotic cells was observed in Lv-shSMC1A-infected cells. These results suggest that SMC1A is a novel proliferation regulator that promotes the growth of lung cancer cells, and that down-regulation of SMC1A expression induces growth suppression of A549 and H1299 cells via G1/S cell cycle phase arrest and apoptosis pathways. Therefore, SMC1A may serve as a new molecular target for lung cancer therapy.
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Affiliation(s)
- Yi-Fan Zhang
- Department of Thoracic Surgery, The Second Hospital of Jilin University, Changchun 130041
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Gimigliano A, Mannini L, Bianchi L, Puglia M, Deardorff MA, Menga S, Krantz ID, Musio A, Bini L. Proteomic profile identifies dysregulated pathways in Cornelia de Lange syndrome cells with distinct mutations in SMC1A and SMC3 genes. J Proteome Res 2012; 11:6111-23. [PMID: 23106691 DOI: 10.1021/pr300760p] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mutations in cohesin genes have been identified in Cornelia de Lange syndrome (CdLS), but its etiopathogenetic mechanisms are still poorly understood. To define biochemical pathways that are affected in CdLS, we analyzed the proteomic profile of CdLS cell lines carrying mutations in the core cohesin genes, SMC1A and SMC3. Dysregulated protein expression was found in CdLS probands compared to controls. The proteomics analysis was able to discriminate between probands harboring mutations in the different domains of the SMC proteins. In particular, proteins involved in the response to oxidative stress were specifically down-regulated in hinge mutated probands. In addition, the finding that CdLS cell lines show an increase in global oxidative stress argues that it could contribute to some CdLS phenotypic features such as premature physiological aging and genome instability. Finally, the c-MYC gene represents a convergent hub lying at the center of dysregulated pathways, and is down-regulated in CdLS. This study allowed us to highlight, for the first time, specific biochemical pathways that are affected in CdLS, providing plausible causal evidence for some of the phenotypic features seen in CdLS.
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Affiliation(s)
- Anna Gimigliano
- Functional Proteomics Laboratory, Department of Biotechnologies, University of Siena, Siena, Italy
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32
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Common fragile sites: genomic hotspots of DNA damage and carcinogenesis. Int J Mol Sci 2012; 13:11974-11999. [PMID: 23109895 PMCID: PMC3472787 DOI: 10.3390/ijms130911974] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/09/2012] [Accepted: 09/05/2012] [Indexed: 01/08/2023] Open
Abstract
Genomic instability, a hallmark of cancer, occurs preferentially at specific genomic regions known as common fragile sites (CFSs). CFSs are evolutionarily conserved and late replicating regions with AT-rich sequences, and CFS instability is correlated with cancer. In the last decade, much progress has been made toward understanding the mechanisms of chromosomal instability at CFSs. However, despite tremendous efforts, identifying a cancer-associated CFS gene (CACG) remains a challenge and little is known about the function of CACGs at most CFS loci. Recent studies of FATS (for Fragile-site Associated Tumor Suppressor), a new CACG at FRA10F, reveal an active role of this CACG in regulating DNA damage checkpoints and suppressing tumorigenesis. The identification of FATS may inspire more discoveries of other uncharacterized CACGs. Further elucidation of the biological functions and clinical significance of CACGs may be exploited for cancer biomarkers and therapeutic benefits.
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33
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Deardorff M, Wilde J, Albrecht M, Dickinson E, Tennstedt S, Braunholz D, Mönnich M, Yan Y, Xu W, Gil-Rodríguez M, Clark D, Hakonarson H, Halbach S, Michelis L, Rampuria A, Rossier E, Spranger S, Van Maldergem L, Lynch S, Gillessen-Kaesbach G, Lüdecke HJ, Ramsay R, McKay M, Krantz I, Xu H, Horsfield J, Kaiser F. RAD21 mutations cause a human cohesinopathy. Am J Hum Genet 2012; 90:1014-27. [PMID: 22633399 PMCID: PMC3370273 DOI: 10.1016/j.ajhg.2012.04.019] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 04/03/2012] [Accepted: 04/23/2012] [Indexed: 10/28/2022] Open
Abstract
The evolutionarily conserved cohesin complex was originally described for its role in regulating sister-chromatid cohesion during mitosis and meiosis. Cohesin and its regulatory proteins have been implicated in several human developmental disorders, including Cornelia de Lange (CdLS) and Roberts syndromes. Here we show that human mutations in the integral cohesin structural protein RAD21 result in a congenital phenotype consistent with a "cohesinopathy." Children with RAD21 mutations display growth retardation, minor skeletal anomalies, and facial features that overlap findings in individuals with CdLS. Notably, unlike children with mutations in NIPBL, SMC1A, or SMC3, these individuals have much milder cognitive impairment than those with classical CdLS. Mechanistically, these mutations act at the RAD21 interface with the other cohesin proteins STAG2 and SMC1A, impair cellular DNA damage response, and disrupt transcription in a zebrafish model. Our data suggest that, compared to loss-of-function mutations, dominant missense mutations result in more severe functional defects and cause worse structural and cognitive clinical findings. These results underscore the essential role of RAD21 in eukaryotes and emphasize the need for further understanding of the role of cohesin in human development.
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Affiliation(s)
- Matthew A. Deardorff
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104 USA
| | - Jonathan J. Wilde
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Melanie Albrecht
- Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany
| | - Emma Dickinson
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin 9054, New Zealand
| | | | - Diana Braunholz
- Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany
| | - Maren Mönnich
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin 9054, New Zealand
| | - Yuqian Yan
- Research Division, Peter MacCallum Cancer Centre, East Melbourne 3002, Australia
| | - Weizhen Xu
- Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany
- Zhejiang Cancer Research Institute, Hangzhou 310058, China
| | - María Concepcion Gil-Rodríguez
- Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany
- Unit of Clinical Genetics and Functional Genomics. Medical School, University of Zaragoza, Zaragoza 50009, Spain
| | - Dinah Clark
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Hakon Hakonarson
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104 USA
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sara Halbach
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Laura Daniela Michelis
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Abhinav Rampuria
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | | | | | - Lionel Van Maldergem
- Centre de Génétique Humaine, Université de Franche-Comté, Besançon 25030, France
| | - Sally Ann Lynch
- Our Lady's Children's Hospital, National Centre for Medical Genetics, Dublin 12, Ireland
| | | | | | - Robert G. Ramsay
- Research Division, Peter MacCallum Cancer Centre, East Melbourne 3002, Australia
- Sir Peter MacCallum Department of Oncology and Department of Pathology, Faculty of Medicine and Dental Sciences, The University of Melbourne, Elizabeth Street, Parkville, Victoria 3000, Australia
| | - Michael J. McKay
- North Coast Cancer Institute, Lismore, New South Wales 2480, Australia
- The University of Sydney Medical School, Sydney, New South Wales 2006, Australia
| | - Ian D. Krantz
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104 USA
| | - Huiling Xu
- Research Division, Peter MacCallum Cancer Centre, East Melbourne 3002, Australia
- Sir Peter MacCallum Department of Oncology and Department of Pathology, Faculty of Medicine and Dental Sciences, The University of Melbourne, Elizabeth Street, Parkville, Victoria 3000, Australia
| | - Julia A. Horsfield
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin 9054, New Zealand
| | - Frank J. Kaiser
- Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany
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Ozeri-Galai E, Bester AC, Kerem B. The complex basis underlying common fragile site instability in cancer. Trends Genet 2012; 28:295-302. [PMID: 22465609 DOI: 10.1016/j.tig.2012.02.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
Abstract
Common fragile sites (CFSs) were characterized almost 30 years ago as sites undergoing genomic instability in cancer. Recently, in vitro studies have found that oncogene-induced replication stress leads to CFS instability. In vivo, CFSs were found to be preferentially unstable during early stages of cancer development and to leave a unique signature of instability. It is now increasingly clear that, along the spectrum of replication features characterizing CFSs, failure of origin activation is a common feature. This and other features of CFSs, together with the replication stress characterizing early stages of cancer development, lead to incomplete replication that results in genomic instability preferentially at CFSs. Here, we review the shared and unique characteristics of CFSs, their underlying causes and their implications, particularly with respect to the development of cancer.
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Affiliation(s)
- Efrat Ozeri-Galai
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University, Jerusalem 91904, Israel
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35
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Abstract
Genome instability is a hallmark of cancer cells and how it arises is still not completely understood. Correct chromosome segregation is a pre-requisite for preserving genome integrity. Cohesin helps to ensure faithful chromosome segregation during cell cycle, however, much evidence regarding its functions have come to light over the last few years and suggest that cohesin plays multiple roles in the maintenance of genome stability. Here we review our rapidly increasing knowledge on the involvement of cohesin pathway in genome stability and cancer.
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Affiliation(s)
- Linda Mannini
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Richerche, Pisa, Italy
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36
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Isolated NIBPL missense mutations that cause Cornelia de Lange syndrome alter MAU2 interaction. Eur J Hum Genet 2011; 20:271-6. [PMID: 21934712 DOI: 10.1038/ejhg.2011.175] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS; or Brachmann-de Lange syndrome) is a dominantly inherited congenital malformation disorder with features that include characteristic facies, cognitive delays, growth retardation and limb anomalies. Mutations in nearly 60% of CdLS patients have been identified in NIPBL, which encodes a regulator of the sister chromatid cohesion complex. NIPBL, also known as delangin, is a homolog of yeast and amphibian Scc2 and C. elegans PQN-85. Although the exact mechanism of NIPBL function in sister chromatid cohesion is unclear, in vivo yeast and C. elegans experiments and in vitro vertebrate cell experiments have demonstrated that NIPBL/Scc2 functionally interacts with the MAU2/Scc4 protein to initiate loading of cohesin onto chromatin. To test the significance of this model in the clinical setting of CdLS, we fine-mapped the NIBPL-MAU2 interaction domain and tested the functional significance of missense mutations and variants in NIPBL and MAU2 identified in these minimal domains in a cohort of patients with CdLS. We demonstrate that specific novel mutations at the N-terminus of the MAU2-interacting domain of NIBPL result in markedly reduced MAU2 binding, although we appreciate no consistent clinical difference in the small group of patients with these mutations. These data suggest that factors in addition to MAU2 are essential in determining the clinical features and severity of CdLS.
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Dillon LW, Burrow AA, Wang YH. DNA instability at chromosomal fragile sites in cancer. Curr Genomics 2011; 11:326-37. [PMID: 21286310 PMCID: PMC2944998 DOI: 10.2174/138920210791616699] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 05/06/2010] [Accepted: 05/18/2010] [Indexed: 01/02/2023] Open
Abstract
Human chromosomal fragile sites are specific genomic regions which exhibit gaps or breaks on metaphase chromosomes following conditions of partial replication stress. Fragile sites often coincide with genes that are frequently rearranged or deleted in human cancers, with over half of cancer-specific translocations containing breakpoints within fragile sites. But until recently, little direct evidence existed linking fragile site breakage to the formation of cancer-causing chromosomal aberrations. Studies have revealed that DNA breakage at fragile sites can induce formation of RET/PTC rearrangements, and deletions within the FHIT gene, resembling those observed in human tumors. These findings demonstrate the important role of fragile sites in cancer development, suggesting that a better understanding of the molecular basis of fragile site instability is crucial to insights in carcinogenesis. It is hypothesized that under conditions of replication stress, stable secondary structures form at fragile sites and stall replication fork progress, ultimately resulting in DNA breaks. A recent study examining an FRA16B fragment confirmed the formation of secondary structure and DNA polymerase stalling within this sequence in vitro, as well as reduced replication efficiency and increased instability in human cells. Polymerase stalling during synthesis of FRA16D has also been demonstrated. The ATR DNA damage checkpoint pathway plays a critical role in maintaining stability at fragile sites. Recent findings have confirmed binding of the ATR protein to three regions of FRA3B under conditions of mild replication stress. This review will discuss recent advances made in understanding the role and mechanism of fragile sites in cancer development.
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Affiliation(s)
- Laura W Dillon
- Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1016, USA
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Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Li JR, Clark D, Kaur M, Tatsuro K, Kline AD, Chang C, Vega H, Jackson LG, Spinner NB, Shirahige K, Krantz ID. Genome-wide DNA methylation analysis in cohesin mutant human cell lines. Nucleic Acids Res 2010; 38:5657-71. [PMID: 20448023 PMCID: PMC2943628 DOI: 10.1093/nar/gkq346] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Revised: 04/19/2010] [Accepted: 04/21/2010] [Indexed: 12/17/2022] Open
Abstract
The cohesin complex has recently been shown to be a key regulator of eukaryotic gene expression, although the mechanisms by which it exerts its effects are poorly understood. We have undertaken a genome-wide analysis of DNA methylation in cohesin-deficient cell lines from probands with Cornelia de Lange syndrome (CdLS). Heterozygous mutations in NIPBL, SMC1A and SMC3 genes account for ∼65% of individuals with CdLS. SMC1A and SMC3 are subunits of the cohesin complex that controls sister chromatid cohesion, whereas NIPBL facilitates cohesin loading and unloading. We have examined the methylation status of 27 578 CpG dinucleotides in 72 CdLS and control samples. We have documented the DNA methylation pattern in human lymphoblastoid cell lines (LCLs) as well as identified specific differential DNA methylation in CdLS. Subgroups of CdLS probands and controls can be classified using selected CpG loci. The X chromosome was also found to have a unique DNA methylation pattern in CdLS. Cohesin preferentially binds to hypo-methylated DNA in control LCLs, whereas the differential DNA methylation alters cohesin binding in CdLS. Our results suggest that in addition to DNA methylation multiple mechanisms may be involved in transcriptional regulation in human cells and in the resultant gene misexpression in CdLS.
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Affiliation(s)
- Jinglan Liu
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Masashige Bando
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Takehiko Itoh
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew A. Deardorff
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer R. Li
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Dinah Clark
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Maninder Kaur
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Kondo Tatsuro
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Antonie D. Kline
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Celia Chang
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Hugo Vega
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Laird G. Jackson
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Nancy B. Spinner
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Katsuhiko Shirahige
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Ian D. Krantz
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
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Mannini L, Menga S, Musio A. The expanding universe of cohesin functions: a new genome stability caretaker involved in human disease and cancer. Hum Mutat 2010; 31:623-30. [PMID: 20513141 DOI: 10.1002/humu.21252] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cohesin is responsible for sister chromatid cohesion, ensuring the correct chromosome segregation. Beyond this role, cohesin and regulatory cohesin genes seem to play a role in preserving genome stability and gene transcription regulation. DNA damage is thought to be a major culprit for many human diseases, including cancer. Our present knowledge of the molecular basis underlying genome instability is extremely limited. Mutations in cohesin genes cause human diseases such as Cornelia de Lange syndrome and Roberts syndrome/SC phocomelia, and all the cell lines derived from affected patients show genome instability. Cohesin mutations have also been identified in colorectal cancer. Here, we will discuss the human disorders caused by alterations of cohesin function, with emphasis on the emerging role of cohesin as a genome stability caretaker.
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Affiliation(s)
- Linda Mannini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa, Italy
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Wan C, Kulkarni A, Wang YH. ATR preferentially interacts with common fragile site FRA3B and the binding requires its kinase activity in response to aphidicolin treatment. Mutat Res 2010; 686:39-46. [PMID: 20060399 DOI: 10.1016/j.mrfmmm.2009.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 12/17/2009] [Accepted: 12/29/2009] [Indexed: 11/17/2022]
Abstract
The instability of common fragile sites (CFSs) contributes to the development of a variety of cancers. The ATR-dependent DNA damage checkpoint pathway has been implicated in maintaining CFS stability, but the mechanism is incompletely understood. The goal of our study was to elucidate the action of the ATR protein in the CFS-specific ATR-dependent checkpoint response. Using a chromatin immunoprecipitation assay, we demonstrated that ATR protein preferentially binds (directly or through complexes) to fragile site FRA3B as compared to non-fragile site regions, under conditions of mild replication stress. Interestingly, the amount of ATR protein that bound to three regions of FRA3B peaked at 0.4microM aphidicolin (APH) treatment and decreased again at higher concentrations of APH. The total amounts of cellular ATR and several ATR-interacting proteins remained unchanged, suggesting that ATR binding to the fragile site is guided initially by the level of replication stress signals generated at FRA3B due to APH treatment and then sequestered from FRA3B regions by successive signals from other non-fragile site regions, which are produced at the higher concentrations of APH. This decrease in ATR binding to fragile site FRA3B at the higher concentrations of APH may account for the increasing number of chromosome gaps and breaks observed under the same conditions. Furthermore, inhibition of ATR kinase activity by treatment with 2-aminopurine (2-AP) or by over-expression of a kinase-dead ATR mutant showed that the kinase activity is required for the binding of ATR to fragile DNAs in response to APH treatment. Our results provide novel insight into the mechanism for the regulation of fragile site stability by ATR.
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Affiliation(s)
- Cheng Wan
- Department of Biochemistry, Wake Forest University School of Medicine, 1 Medical Center Boulevard, Winston-Salem, NC 27157-1016, USA
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41
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Takahashi A, Mori E, Ohnishi T. The foci of DNA double strand break-recognition proteins localize with gammaH2AX after heat treatment. JOURNAL OF RADIATION RESEARCH 2010; 51:91-95. [PMID: 20173316 DOI: 10.1269/jrr.09111] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recently, there have been many reports concerning proteins which can recognize DNA double strand break (DSBs), and such proteins include histone H2AX phosphorylated at serine 139 (gammaH2AX), ataxia telangiectasia mutated (ATM) phospho-serine 1981, DNA-dependent protein kinase catalytic subunit (DNA-PKcs) phospho-threonine 2609, Nijmegen breakage syndrome 1 (NBS1) phospho-serine 343, checkpoint kinase 2 (CHK2), phospho-threonine 68, and structural maintenance of chromosomes 1 (SMC1) phospho-serine 966. Thus, it should be possible to follow the formation of DSBs and their repair using immunohistochemical methods with multiple antibodies to detect these proteins. When normal human fibroblasts (AG1522 cells) were exposed to 3 Gy of X-rays as a control, clearly discernable foci for these proteins were detected, and these foci localized with gammaH2AX foci. After heat treatment at 45.5 degrees C for 20 min, these proteins are partially localized with gammaH2AX foci. Here we show that there were slight differences in the localization pattern among these proteins, such as a disappearance from the nucleus (phospho-ATM) and translocation to the cytoplasm (phospho-NBS1) at 30 min after heat treatment, and some foci (phospho-DNA-PKcs and phospho-CHK2) appeared at 8 h after heat treatment. These results are discussed from perspectives of heat-induced denaturation of proteins and formation of DSBs.
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Affiliation(s)
- Akihisa Takahashi
- Department of Biology, School of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, Japan
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Mannini L, Liu J, Krantz ID, Musio A. Spectrum and consequences of SMC1A mutations: the unexpected involvement of a core component of cohesin in human disease. Hum Mutat 2010; 31:5-10. [PMID: 19842212 PMCID: PMC2797832 DOI: 10.1002/humu.21129] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
SMC1A encodes a structural component of the cohesin complex, which is necessary for sister chromatid cohesion. In addition to its canonical role, cohesin has been shown to be involved in gene expression regulation and maintenance of genome stability. Recently, it has been demonstrated that mutations in the SMC1A gene are responsible for Cornelia de Lange syndrome (CdLS). CdLS is a genetically heterogeneous multisystem developmental disorder with variable expressivity, typically characterized by consistent facial dysmorphia, upper extremity malformations, hirsutism, cardiac defects, growth and cognitive retardation, gastrointestinal abnormalities, and other systemic involvement. SMC1A mutations have also been identified in colorectal cancers. So far a total of 26 different mutations of the SMC1A gene have been reported. All mutations reported to date are either missense or small in-frame deletions that maintain the open reading frame and presumably result in a protein with residual function. The mutations involve all domains of the protein but appear to cluster in key functional loci. At the functional level, elucidation of the effects that specific SMC1A mutations have on cohesin activity will be necessary to understand the etiopathology of CdLS and its possible involvement in tumorigenesis. In this review, we summarize the current knowledge of SMC1A mutations.
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Affiliation(s)
- Linda Mannini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Jinglan Liu
- Division of Human Genetics, The Children’s Hospital of Philadelphia, PA 19104, USA
| | - Ian D. Krantz
- Division of Human Genetics, The Children’s Hospital of Philadelphia, PA 19104, USA
- The University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Antonio Musio
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa, Italy
- Istituto Toscano Tumori, Florence, Italy
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43
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Focarelli ML, Soza S, Mannini L, Paulis M, Montecucco A, Musio A. Claspin inhibition leads to fragile site expression. Genes Chromosomes Cancer 2009; 48:1083-90. [PMID: 19760606 DOI: 10.1002/gcc.20710] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Fragile sites are hot spots for sister chromatid exchanges, translocations, deletions, complex rearrangements, and gene amplification. It has been hypothesized that rearrangements at fragile sites derive from unreplicated regions resulting from stalled forks that escape the ATR replication checkpoint. In the present study, we investigated the role of the Claspin (CLSPN) gene, which codes for an adaptor protein in the ATR pathway, during DNA replication stress in human cells. We show that the inhibition of the CLSPN gene leads to both genome instability and fragile site expression. Following aphidicolin treatment, we found a transient increase of Claspin synthesis due to its requirement to checkpoint activation. However, Claspin synthesis decreased after a prolonged aphidicolin treatment. We propose that CLSPN modulation, following an extreme replication block, allows rare cells to escape checkpoint mechanisms and enter mitosis with a defect in genome assembly. Our observations provide the basis for a better understanding of cell cycle checkpoints deregulation in cancer.
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Affiliation(s)
- Maria Luisa Focarelli
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (Mi), Italy
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Revenkova E, Focarelli ML, Susani L, Paulis M, Bassi MT, Mannini L, Frattini A, Delia D, Krantz I, Vezzoni P, Jessberger R, Musio A. Cornelia de Lange syndrome mutations in SMC1A or SMC3 affect binding to DNA. Hum Mol Genet 2009; 18:418-27. [PMID: 18996922 PMCID: PMC2722190 DOI: 10.1093/hmg/ddn369] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 11/04/2008] [Indexed: 01/09/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a clinically heterogeneous developmental disorder characterized by facial dysmorphia, upper limb malformations, growth and cognitive retardation. Mutations in the sister chromatid cohesion factor genes NIPBL, SMC1A and SMC3 are present in approximately 65% of CdLS patients. In addition to their canonical roles in chromosome segregation, the cohesin proteins are involved in other biological processes such as regulation of gene expression, DNA repair and maintenance of genome stability. To gain insights into the molecular basis of CdLS, we analyzed the affinity of mutated SMC1A and SMC3 hinge domains for DNA. Mutated hinge dimers bind DNA with higher affinity than wild-type proteins. SMC1A- and SMC3-mutated CdLS cell lines display genomic instability and sensitivity to ionizing radiation and interstrand crosslinking agents. We propose that SMC1A and SMC3 CdLS mutations affect the dynamic association between SMC proteins and DNA, providing new clues to the underlying molecular cause of CdLS.
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Affiliation(s)
- Ekaterina Revenkova
- Department of Gene and Cell Medicine, Mount Sinai School of Medicine, New York, USA
| | - Maria Luisa Focarelli
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | - Lucia Susani
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | - Marianna Paulis
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | - Maria Teresa Bassi
- Laboratory of Molecular Biology, E. Medea Scientific Institute, Bosisio Parini (LC), Italy
| | - Linda Mannini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Annalisa Frattini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | | | - Ian Krantz
- Division of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia, The University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Paolo Vezzoni
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Dresden University of Technology, Dresden, Germany
| | - Antonio Musio
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa, Italy
- Istituto Toscano Tumori, Florence, Italy
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45
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Ragland RL, Glynn MW, Arlt MF, Glover TW. Stably transfected common fragile site sequences exhibit instability at ectopic sites. Genes Chromosomes Cancer 2008; 47:860-72. [PMID: 18615677 DOI: 10.1002/gcc.20591] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Common fragile sites (CFSs) are loci that are especially prone to forming gaps and breaks on metaphase chromosomes under conditions of replication stress. Although much has been learned about the cellular responses to gaps and breaks at CFSs, less is known about what makes these sites inherently unstable. CFS sequences are highly conserved in mammalian evolution and contain a number of sequence motifs that are hypothesized to contribute to their instability. To examine the role of CFS sequences in chromosome breakage, we stably transfected two BACs containing FRA3B sequences and two nonCFS control BACs containing similar sequence content into HCT116 cells and isolated cell clones with BACs integrated at ectopic sites. Integrated BACs were present at just a few to several hundred contiguous copies. Cell clones containing integrated FRA3B BACs showed a significant, three to sevenfold increase in aphidicolin-induced gaps and breaks at the integration site as compared to control BACs. Furthermore, many FRA3B integration sites displayed additional chromosome rearrangements associated with CFS instability. Clones were examined for replication timing and it was found that the integrated FRA3B sequences were not dependent on late replication for their fragility. This is the first direct evidence in human cells that introduction of CFS sequences into ectopic nonfragile loci is sufficient to recapitulate the instability found at CFSs. These data support the hypothesis that sequences at CFSs are inherently unstable, and are a major factor in the formation of replication stress induced gaps and breaks at CFSs.
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Affiliation(s)
- Ryan L Ragland
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-0618, USA
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46
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Usdin K. The biological effects of simple tandem repeats: lessons from the repeat expansion diseases. Genome Res 2008; 18:1011-9. [PMID: 18593815 DOI: 10.1101/gr.070409.107] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tandem repeats are common features of both prokaryote and eukaryote genomes, where they can be found not only in intergenic regions but also in both the noncoding and coding regions of a variety of different genes. The repeat expansion diseases are a group of human genetic disorders caused by long and highly polymorphic tandem repeats. These disorders provide many examples of the effects that such repeats can have on many biological processes. While repeats in the coding sequence can result in the generation of toxic or malfunctioning proteins, noncoding repeats can also have significant effects including the generation of chromosome fragility, the silencing of the genes in which they are located, the modulation of transcription and translation, and the sequestering of proteins involved in processes such as splicing and cell architecture.
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Affiliation(s)
- Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA.
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47
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An integrative view of dynamic genomic elements influencing human brain evolution and individual neurodevelopment. Med Hypotheses 2008; 71:360-73. [DOI: 10.1016/j.mehy.2008.03.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2008] [Revised: 03/01/2008] [Accepted: 03/06/2008] [Indexed: 11/23/2022]
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48
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Fhit-Deficient Hematopoietic Stem Cells Survive Hydroquinone Exposure Carrying Precancerous Changes. Cancer Res 2008; 68:3662-70. [DOI: 10.1158/0008-5472.can-07-5687] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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The methyl methanesulfonate induced S-phase delay in XRCC1-deficient cells requires ATM and ATR. DNA Repair (Amst) 2008; 7:849-57. [PMID: 18375193 DOI: 10.1016/j.dnarep.2008.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 02/07/2008] [Accepted: 02/11/2008] [Indexed: 11/20/2022]
Abstract
X-ray repair cross-complementing 1 (XRCC1) is required for DNA single-strand break and base excision repair (BER) in human cells. XRCC1-deficient human cells show hypersensitivity to cell killing, increased genetic instability and a significant delay in S-phase progression after exposure to the alkylating agent methyl methanesulfonate (MMS). Using RNAi modulation of XRCC1 levels, we show here that this S-phase delay is associated with significantly increased levels of recombinational repair as visualized by Rad51 focus formation. Using ATM- and ATR-defective cells and an ATM specific kinase inhibitor we demonstrate for the first time that the MMS-induced S-phase checkpoint requires both ATM and ATR. This unique dependency is associated with phosphorylation of ATM/ATR downstream targets or effectors such as SMC1 and Chk1. These results support the hypothesis that after MMS-treatment, the presence of unresolved BER intermediates gives rise to lesions that activate both ATM and ATR and that during the consequent S-phase delay, such intermediates may be repaired by a recombinational pathway which involves the Rad51 protein.
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50
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Pirzio LM, Pichierri P, Bignami M, Franchitto A. Werner syndrome helicase activity is essential in maintaining fragile site stability. ACTA ACUST UNITED AC 2008; 180:305-14. [PMID: 18209099 PMCID: PMC2213598 DOI: 10.1083/jcb.200705126] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
WRN is a member of the RecQ family of DNA helicases implicated in the resolution of DNA structures leading to the stall of replication forks. Fragile sites have been proposed to be DNA regions particularly sensitive to replicative stress. Here, we establish that WRN is a key regulator of fragile site stability. We demonstrate that in response to mild doses of aphidicolin, WRN is efficiently relocalized in nuclear foci in replicating cells and that WRN deficiency is associated with accumulation of gaps and breaks at common fragile sites even under unperturbed conditions. By expressing WRN isoforms impaired in either helicase or exonuclease activity in defective cells, we identified WRN helicase activity as the function required for maintaining the stability of fragile sites. Finally, we find that WRN stabilizes fragile sites acting in a common pathway with the ataxia telangiectasia and Rad3 related replication checkpoint. These findings provide the first evidence of a crucial role for a helicase in protecting cells against chromosome breakage at normally occurring replication fork stalling sites.
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Affiliation(s)
- Livia Maria Pirzio
- Section of Experimental and Computational Carcinogenesis, Istituto Superiore di Sanità, 299-00161 Rome, Italy
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