51
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Dickson KA, Cole AJ, Gill AJ, Clarkson A, Gard GB, Chou A, Kennedy CJ, Henderson BR, Fereday S, Traficante N, Alsop K, Bowtell DD, deFazio A, Clifton-Bligh R, Marsh DJ. The RING finger domain E3 ubiquitin ligases BRCA1 and the RNF20/RNF40 complex in global loss of the chromatin mark histone H2B monoubiquitination (H2Bub1) in cell line models and primary high-grade serous ovarian cancer. Hum Mol Genet 2017; 25:5460-5471. [PMID: 27798111 DOI: 10.1093/hmg/ddw362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/18/2016] [Indexed: 02/07/2023] Open
Abstract
Enzymatic factors driving cancer-associated chromatin remodelling are of increasing interest as the role of the cancer epigenome in gene expression and DNA repair processes becomes elucidated. Monoubiquitination of histone H2B at lysine 120 (H2Bub1) is a central histone modification that functions in histone cross-talk, transcriptional elongation, DNA repair, maintaining centromeric chromatin and replication-dependent histone mRNA 3'-end processing, as well as being required for the differentiation of stem cells. The loss of global H2Bub1 is seen in a number of aggressive malignancies and has been linked to tumour progression and/or a poorer prognosis in some cancers. Here, we analyse a large cohort of high-grade serous ovarian cancers (HGSOC) and show loss of global H2Bub1 in 77% (313 of 407) of tumours. Loss of H2Bub1 was seen at all stages (I-IV) of HGSOC, indicating it is a relatively early epigenomic event in this aggressive malignancy. Manipulation of key H2Bub1 E3 ubiquitin ligases, RNF20, RNF40 and BRCA1, in ovarian cancer cell line models modulated H2Bub1 levels, indicative of the role of these RING finger ligases in monoubiquitination of H2Bub1 in vitro. However, in primary HGSOC, loss of RNF20 protein expression was identified in just 6% of tumours (26 of 424) and did not correlate with global H2Bub1 loss. Similarly, germline mutation of BRCA1 did not show a correlation with the global H2Bub1 loss. We conclude that the regulation of tumour-associated H2Bub1 levels is complex. Aberrant expression of alternative histone-associated 'writer' or 'eraser' enzymes are likely responsible for the global loss of H2Bub1 seen in HGSOC.
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Affiliation(s)
- Kristie-Ann Dickson
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hosptial, University of Sydney, St Leonards, NSW, Australia
| | - Alexander J Cole
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hosptial, University of Sydney, St Leonards, NSW, Australia
| | - Anthony J Gill
- Department of Anatomical Pathology, Royal North Shore Hospital, University of Sydney, Sydney NSW, and Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Adele Clarkson
- Department of Anatomical Pathology, Royal North Shore Hospital, University of Sydney, Sydney NSW, and Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Gregory B Gard
- Department of Obstetrics and Gynaecology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Angela Chou
- Department of Anatomical Pathology, SYDPATH, St Vincents Hospitals, Darlinghurst, NSW, Australia
| | - Catherine J Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Westmead, NSW, Australia.,Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
| | - Beric R Henderson
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
| | | | - Sian Fereday
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Nadia Traficante
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kathryn Alsop
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David D Bowtell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia and.,The Kinghorn Cancer Centre and Garvan Institute, Darlinghurst, NSW, Australia
| | - Anna deFazio
- Department of Gynaecological Oncology, Westmead Hospital, Westmead, NSW, Australia.,Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
| | - Roderick Clifton-Bligh
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hosptial, University of Sydney, St Leonards, NSW, Australia
| | - Deborah J Marsh
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hosptial, University of Sydney, St Leonards, NSW, Australia
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52
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Zhang K, Wang J, Tong TR, Wu X, Nelson R, Yuan YC, Reno T, Liu Z, Yun X, Kim JY, Salgia R, Raz DJ. Loss of H2B monoubiquitination is associated with poor-differentiation and enhanced malignancy of lung adenocarcinoma. Int J Cancer 2017; 141:766-777. [PMID: 28481029 DOI: 10.1002/ijc.30769] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/04/2017] [Accepted: 04/26/2017] [Indexed: 01/01/2023]
Abstract
Deregulated monoubiquitination of histone H2B (H2Bub1), mainly catalyzed by E3 ubiquitin-protein ligase RNF20/RNF40 complex, may play an important role in cancer. Here we investigate potential roles of H2Bub1 and the underlying mechanisms through which it contributes to cancer development and progression in lung adenocarcinoma. We show that downregulation of H2Bub1 through RNF20 knockdown dramatically decreases H3K79 and H3K4 trimethylation in both normal and malignant lung epithelial cell lines. Concurrently, global transcriptional profiling analysis reveals that multiple tumor-associated genes such as CCND3, E2F1/2, HOXA1, Bcl2 modifying factor (BMF), Met, and Myc; and signaling pathways of cellular dedifferentiation, proliferation, adhesion, survival including p53, cadherin, Myc, and anti-apoptotic pathways are differentially expressed or significantly altered in these lung epithelial cells upon downregulation of H2Bub1. Moreover, RNF20 knockdown dramatically suppresses terminal squamous differentiation of cultured bronchial epithelial cells, and significantly enhances proliferation, migration, invasion, and cisplatin resistance of lung cancer cells. Furthermore, immunohistochemistry analysis shows that H2Bub1 is extremely low or undetectable in >70% of 170 lung adenocarcinoma samples. Notably, statistical analysis demonstrates that loss of H2Bub1 is significantly correlated with poor differentiation in lung adenocarcinoma (p = 0.0134). In addition, patients with H2Bub1-negative cancers had a trend towards shorter survival compared with patients with H2Bub1-positive cancers. Taken together, our findings suggest that loss of H2Bub1 may enhance malignancy and promote disease progression in lung adenocarcinoma probably through modulating multiple cancer signaling pathways.
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Affiliation(s)
- Keqiang Zhang
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA
| | - Jinhui Wang
- The Integrative Genomics Core Lab of Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA
| | - Tommy R Tong
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - Xiwei Wu
- The Integrative Genomics Core Lab of Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA
| | - Rebecca Nelson
- Division of Biostatistics, City of Hope National Medical Center, Duarte, CA
| | - Yate-Ching Yuan
- The Bioinformatics Core lab of Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA
| | - Theresa Reno
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA
| | - Zheng Liu
- Division of Biostatistics, City of Hope National Medical Center, Duarte, CA
| | - Xinwei Yun
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA
| | - Jae Y Kim
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA
| | - Ravi Salgia
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA
| | - Dan J Raz
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA
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53
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RNF20 and histone H2B ubiquitylation exert opposing effects in Basal-Like versus luminal breast cancer. Cell Death Differ 2017; 24:694-704. [PMID: 28157208 DOI: 10.1038/cdd.2016.126] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/28/2016] [Accepted: 10/04/2016] [Indexed: 11/09/2022] Open
Abstract
Breast cancer subtypes display distinct biological traits that influence their clinical behavior and response to therapy. Recent studies have highlighted the importance of chromatin structure regulators in tumorigenesis. The RNF20-RNF40 E3 ubiquitin ligase complex monoubiquitylates histone H2B to generate H2Bub1, while the deubiquitinase (DUB) USP44 can remove this modification. We found that RNF20 and RNF40 expression and global H2Bub1 are relatively low, and USP44 expression is relatively high, in basal-like breast tumors compared with luminal tumors. Consistent with a tumor-suppressive role, silencing of RNF20 in basal-like breast cancer cells increased their proliferation and migration, and their tumorigenicity and metastatic capacity, partly through upregulation of inflammatory cytokines. In contrast, in luminal breast cancer cells, RNF20 silencing reduced proliferation, migration and tumorigenic and metastatic capacity, and compromised estrogen receptor transcriptional activity, indicating a tumor-promoting role. Notably, the effects of USP44 silencing on proliferation and migration in both cancer subtypes were opposite to those of RNF20 silencing. Hence, RNF20 and H2Bub1 have contrasting roles in distinct breast cancer subtypes, through differential regulation of key transcriptional programs underpinning the distinctive traits of each subtype.
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54
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He M, Zhou Z, Shah AA, Zou H, Tao J, Chen Q, Wan Y. The emerging role of deubiquitinating enzymes in genomic integrity, diseases, and therapeutics. Cell Biosci 2016; 6:62. [PMID: 28031783 PMCID: PMC5168870 DOI: 10.1186/s13578-016-0127-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/05/2016] [Indexed: 02/05/2023] Open
Abstract
The addition of mono-ubiquitin or poly-ubiquitin chain to signaling proteins in response to DNA damage signal is thought to be a critical event that facilitates the recognition of DNA damage lesion site, the activation of checkpoint function, termination and checkpoint response and the recruitment of DNA repair proteins. Despite the ubiquitin modifiers, removal of ubiquitin from the functional proteins by the deubiquitinating enzymes (DUBs) plays an important role in orchestrating DNA damage response as well as DNA repair processes. Deregulated ubiquitination and deubiquitination could lead to genome instability that in turn causes tumorigenesis. Recent TCGA study has further revealed the connection between mutations in alteration of DUBs and various types of tumors. In addition, emerging drug design based on DUBs provides a new avenue for anti-cancer therapy. In this review, we will summarize the role of deubiquitination and specificity of DUBs, and highlight the recent discoveries of DUBs in the modulation of ubiquitin-mediated DNA damage response and DNA damage repair. We will furthermore discuss the DUBs involved in the tumorigenesis as well as interception of deubiquitination as a novel strategy for anti-cancer therapy.
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Affiliation(s)
- Mingjing He
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA ; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 Sichuan People's Republic of China
| | - Zhuan Zhou
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Anil A Shah
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Haojing Zou
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Jin Tao
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 Sichuan People's Republic of China
| | - Yong Wan
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
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55
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Richard P, Manley JL. R Loops and Links to Human Disease. J Mol Biol 2016; 429:3168-3180. [PMID: 27600412 DOI: 10.1016/j.jmb.2016.08.031] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 12/13/2022]
Abstract
Aberrant R-loop structures are increasingly being realized as an important contributor to human disease. R loops, which are mainly co-transcriptional, abundant RNA/DNA hybrids, form naturally and can indeed be beneficial for transcription regulation at certain loci. However, their unwanted persistence elsewhere or in particular situations can lead to DNA double-strand breaks, chromosome rearrangements, and hypermutation, which are all sources of genomic instability. Mutations in genes involved in R-loop resolution or mutations leading to R-loop formation at specific genes affect the normal physiology of the cell. We discuss here the examples of diseases for which a link with R loops has been described, as well as how disease-causing mutations might participate in the development and/or progression of diseases that include repeat-associated conditions, other neurological disorders, and cancers.
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Affiliation(s)
- Patricia Richard
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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56
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Duan Y, Huo D, Gao J, Wu H, Ye Z, Liu Z, Zhang K, Shan L, Zhou X, Wang Y, Su D, Ding X, Shi L, Wang Y, Shang Y, Xuan C. Ubiquitin ligase RNF20/40 facilitates spindle assembly and promotes breast carcinogenesis through stabilizing motor protein Eg5. Nat Commun 2016; 7:12648. [PMID: 27557628 PMCID: PMC5007379 DOI: 10.1038/ncomms12648] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 07/19/2016] [Indexed: 12/30/2022] Open
Abstract
Whether transcriptional regulators are functionally involved in mitosis is a fundamental question in cell biology. Here we report that the RNF20/40 complex, a major ubiquitin ligase catalysing histone H2B monoubiquitination, interacts with the motor protein Eg5 during mitosis and participates in spindle assembly. We show that the RNF20/40 complex monoubiquitinates and stabilizes Eg5. Loss of RNF20/40 results in spindle assembly defects, cell cycle arrest and apoptosis. Consistently, depletion of either RNF20/40 or Eg5 suppresses breast cancer in vivo. Significantly, RNF20/40 and Eg5 are concurrently upregulated in human breast carcinomas and high Eg5 expression is associated with poorer overall survival of patients with luminal A, or B, breast cancer. Our study uncovers an important spindle assembly role of the RNF20/40 complex, and implicates the RNF20/40-Eg5 axis in breast carcinogenesis, supporting the pursuit of these proteins as potential targets for breast cancer therapeutic interventions. Eg5 has a role in spindle assembly and has been associated with tumorigenesis but it is not clear how its activity is regulated. Here, the authors show that the E3 ligase RNF20/40 regulates mitotic spindle assembly by regulating the stability of Eg5 through mono-ubiquitination of K745.
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Affiliation(s)
- Yang Duan
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Dawei Huo
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Jie Gao
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Heng Wu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zheng Ye
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Zhe Liu
- Department of Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Xing Zhou
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Dongxue Su
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Xiang Ding
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Yan Wang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Chenghao Xuan
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
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57
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Tarcic O, Pateras IS, Cooks T, Shema E, Kanterman J, Ashkenazi H, Boocholez H, Hubert A, Rotkopf R, Baniyash M, Pikarsky E, Gorgoulis VG, Oren M. RNF20 Links Histone H2B Ubiquitylation with Inflammation and Inflammation-Associated Cancer. Cell Rep 2016; 14:1462-1476. [PMID: 26854224 PMCID: PMC4761112 DOI: 10.1016/j.celrep.2016.01.020] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/24/2015] [Accepted: 01/01/2016] [Indexed: 02/07/2023] Open
Abstract
Factors linking inflammation and cancer are of great interest. We now report that the chromatin-targeting E3 ubiquitin ligase RNF20/RNF40, driving histone H2B monoubiquitylation (H2Bub1), modulates inflammation and inflammation-associated cancer in mice and humans. Downregulation of RNF20 and H2Bub1 favors recruitment of p65-containing nuclear factor κB (NF-κB) dimers over repressive p50 homodimers and decreases the heterochromatin mark H3K9me3 on a subset of NF-κB target genes to augment their transcription. Concordantly, RNF20(+/-) mice are predisposed to acute and chronic colonic inflammation and inflammation-associated colorectal cancer, with excessive myeloid-derived suppressor cells (MDSCs) that may quench antitumoral T cell activity. Notably, colons of human ulcerative colitis patients, as well as colorectal tumors, reveal downregulation of RNF20/RNF40 and H2Bub1 in both epithelium and stroma, supporting the clinical relevance of our tissue culture and mouse model findings.
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Affiliation(s)
- Ohad Tarcic
- Department of Molecular Cell Biology, The Weizmann Institute, Rehovot 7610001, Israel
| | - Ioannis S Pateras
- Molecular Carcinogenesis Group, Department of Histology-Embryology, School of Medicine, University of Athens, 11527 Athens, Greece
| | - Tomer Cooks
- Department of Molecular Cell Biology, The Weizmann Institute, Rehovot 7610001, Israel
| | - Efrat Shema
- Department of Molecular Cell Biology, The Weizmann Institute, Rehovot 7610001, Israel
| | - Julia Kanterman
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Hadas Ashkenazi
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Hana Boocholez
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Ayala Hubert
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem 91120, Israel
| | - Ron Rotkopf
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Baniyash
- The Lautenberg Center for General and Tumor Immunology, Israel-Canada Medical Research Institute, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Eli Pikarsky
- Department of Immunology and Cancer Research, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; Department of Pathology, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology-Embryology, School of Medicine, University of Athens, 11527 Athens, Greece; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; Faculty Institute for Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Moshe Oren
- Department of Molecular Cell Biology, The Weizmann Institute, Rehovot 7610001, Israel.
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58
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Fahrenkrog B. Histone modifications as regulators of life and death in Saccharomyces cerevisiae. MICROBIAL CELL 2015; 3:1-13. [PMID: 28357312 PMCID: PMC5354586 DOI: 10.15698/mic2016.01.472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Apoptosis or programmed cell death is an integrated, genetically controlled
suicide program that not only regulates tissue homeostasis of multicellular
organisms, but also the fate of damaged and aged cells of lower eukaryotes, such
as the yeast Saccharomyces cerevisiae. Recent years have
revealed key apoptosis regulatory proteins in yeast that play similar roles in
mammalian cells. Apoptosis is a process largely defined by characteristic
structural rearrangements in the dying cell that include chromatin condensation
and DNA fragmentation. The mechanism by which chromosomes restructure during
apoptosis is still poorly understood, but it is becoming increasingly clear that
altered epigenetic histone modifications are fundamental parameters that
influence the chromatin state and the nuclear rearrangements within apoptotic
cells. The present review will highlight recent work on the epigenetic
regulation of programmed cell death in budding yeast.
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Affiliation(s)
- Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Rue Profs. Jeener et Brachet 12; 6041 Charleroi, Belgium
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59
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Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC. The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast. Nucleic Acids Res 2015; 44:1703-17. [PMID: 26682798 PMCID: PMC4770224 DOI: 10.1093/nar/gkv1473] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 12/03/2015] [Indexed: 01/07/2023] Open
Abstract
The formation of RNA–DNA hybrids, referred to as R-loops, can promote genome instability and cancer development. Yet the mechanisms by which R-loops compromise genome instability are poorly understood. Here, we establish roles for the evolutionarily conserved Nrl1 protein in pre-mRNA splicing regulation, R-loop suppression and in maintaining genome stability. nrl1Δ mutants exhibit endogenous DNA damage, are sensitive to exogenous DNA damage, and have defects in homologous recombination (HR) repair. Concomitantly, nrl1Δ cells display significant changes in gene expression, similar to those induced by DNA damage in wild-type cells. Further, we find that nrl1Δ cells accumulate high levels of R-loops, which co-localize with HR repair factors and require Rad51 and Rad52 for their formation. Together, our findings support a model in which R-loop accumulation and subsequent DNA damage sequesters HR factors, thereby compromising HR repair at endogenously or exogenously induced DNA damage sites, leading to genome instability.
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Affiliation(s)
- Lucia Aronica
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna A-1030, Austria Department of Oncology, Stanford University, Stanford 94305, USA
| | - Torben Kasparek
- CRUK/MRC Oxford Institute for Radiation Oncology, Oxford OX37DQ , UK
| | - David Ruchman
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna A-1030, Austria
| | - Yamile Marquez
- Department of Medical Biochemistry, Max F. Perutz Laboratories,Medical University of Vienna, Vienna A-1030, Austria
| | - Lubos Cipak
- Cancer Research Institute, Slovak Academy of Sciences, Bratislava 81438, Slovakia
| | - Ingrid Cipakova
- Cancer Research Institute, Slovak Academy of Sciences, Bratislava 81438, Slovakia
| | - Dorothea Anrather
- Max F. Perutz Laboratories, Mass Spectrometry Facility, Vienna A-1030, Austria
| | - Barbora Mikolaskova
- Cancer Research Institute, Slovak Academy of Sciences, Bratislava 81438, Slovakia
| | - Maximilian Radtke
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna A-1030, Austria
| | - Sovan Sarkar
- CRUK/MRC Oxford Institute for Radiation Oncology, Oxford OX37DQ , UK
| | - Chen-Chun Pai
- CRUK/MRC Oxford Institute for Radiation Oncology, Oxford OX37DQ , UK
| | | | - Carol Walker
- CRUK/MRC Oxford Institute for Radiation Oncology, Oxford OX37DQ , UK
| | - Kuo-Fang Shen
- University of Southern California, Los Angeles 90089-0911, USA
| | - Renee Schroeder
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna A-1030, Austria
| | - Andrea Barta
- Department of Medical Biochemistry, Max F. Perutz Laboratories,Medical University of Vienna, Vienna A-1030, Austria
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60
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Herr P, Lundin C, Evers B, Ebner D, Bauerschmidt C, Kingham G, Palmai-Pallag T, Mortusewicz O, Frings O, Sonnhammer E, Helleday T. A genome-wide IR-induced RAD51 foci RNAi screen identifies CDC73 involved in chromatin remodeling for DNA repair. Cell Discov 2015; 1:15034. [PMID: 27462432 PMCID: PMC4860774 DOI: 10.1038/celldisc.2015.34] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022] Open
Abstract
To identify new regulators of homologous recombination repair, we carried out a genome-wide short-interfering RNA screen combined with ionizing irradiation using RAD51 foci formation as readout. All candidates were confirmed by independent short-interfering RNAs and validated in secondary assays like recombination repair activity and RPA foci formation. Network analysis of the top modifiers identified gene clusters involved in recombination repair as well as components of the ribosome, the proteasome and the spliceosome, which are known to be required for effective DNA repair. We identified and characterized the RNA polymerase II-associated protein CDC73/Parafibromin as a new player in recombination repair and show that it is critical for genomic stability. CDC73 interacts with components of the SCF/Cullin and INO80/NuA4 chromatin-remodeling complexes to promote Histone ubiquitination. Our findings indicate that CDC73 is involved in local chromatin decondensation at sites of DNA damage to promote DNA repair. This function of CDC73 is related to but independent of its role in transcriptional elongation.
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Affiliation(s)
- Patrick Herr
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden
| | - Cecilia Lundin
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden
| | - Bastiaan Evers
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden
| | - Daniel Ebner
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Headington, UK
| | - Christina Bauerschmidt
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Headington, UK
| | - Guy Kingham
- CR-UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford , Oxford, UK
| | | | - Oliver Mortusewicz
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden
| | - Oliver Frings
- Science for Life Laboratory, Bioinformatics Centre Stockholm, Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - Erik Sonnhammer
- Science for Life Laboratory, Bioinformatics Centre Stockholm, Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden
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Upadhyay A, Amanullah A, Chhangani D, Mishra R, Mishra A. Selective multifaceted E3 ubiquitin ligases barricade extreme defense: Potential therapeutic targets for neurodegeneration and ageing. Ageing Res Rev 2015; 24:138-59. [PMID: 26247845 DOI: 10.1016/j.arr.2015.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/24/2015] [Accepted: 07/30/2015] [Indexed: 12/24/2022]
Abstract
Efficient and regular performance of Ubiquitin Proteasome System and Autophagy continuously eliminate deleterious accumulation of nonnative protiens. In cellular quality control system, E3 ubiquitin ligases are significant employees for defense mechanism against abnormal toxic proteins. Few findings indicate that lack of functions of E3 ubiquitin ligases can be a causative factor of neurodevelopmental disorders, neurodegeneration, cancer and ageing. However, the detailed molecular pathomechanism implying E3 ubiquitin ligases in cellular functions in multifactorial disease conditions are not well understood. This article systematically represents the unique characteristics, molecular nature, and recent developments in the knowledge of neurobiological functions of few crucial E3 ubiquitin ligases. Here, we review recent literature on the roles of E6-AP, HRD1 and ITCH E3 ubiquitin ligases in the neuro-pathobiological mechanisms, with precise focus on the processes of neurodegeneration, and thereby propose new lines of potential targets for therapeutic interventions.
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Belo H, Silva G, Cardoso BA, Porto B, Minguillon J, Barbot J, Coutinho J, Casado JA, Benedito M, Saturnino H, Costa E, Bueren JA, Surralles J, Almeida A. Epigenetic Alterations in Fanconi Anaemia: Role in Pathophysiology and Therapeutic Potential. PLoS One 2015; 10:e0139740. [PMID: 26466379 PMCID: PMC4605638 DOI: 10.1371/journal.pone.0139740] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/15/2015] [Indexed: 01/23/2023] Open
Abstract
Fanconi anaemia (FA) is an inherited disorder characterized by chromosomal instability. The phenotype is variable, which raises the possibility that it may be affected by other factors, such as epigenetic modifications. These play an important role in oncogenesis and may be pharmacologically manipulated. Our aim was to explore whether the epigenetic profiles in FA differ from non-FA individuals and whether these could be manipulated to alter the disease phenotype. We compared expression of epigenetic genes and DNA methylation profile of tumour suppressor genes between FA and normal samples. FA samples exhibited decreased expression levels of genes involved in epigenetic regulation and hypomethylation in the promoter regions of tumour suppressor genes. Treatment of FA cells with histone deacetylase inhibitor Vorinostat increased the expression of DNM3Tβ and reduced the levels of CIITA and HDAC9, PAK1, USP16, all involved in different aspects of epigenetic and immune regulation. Given the ability of Vorinostat to modulate epigenetic genes in FA patients, we investigated its functional effects on the FA phenotype. This was assessed by incubating FA cells with Vorinostat and quantifying chromosomal breaks induced by DNA cross-linking agents. Treatment of FA cells with Vorinostat resulted in a significant reduction of aberrant cells (81% on average). Our results suggest that epigenetic mechanisms may play a role in oncogenesis in FA. Epigenetic agents may be helpful in improving the phenotype of FA patients, potentially reducing tumour incidence in this population.
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Affiliation(s)
- Hélio Belo
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, E.P.E., Lisboa, Portugal
- CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Gabriela Silva
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, E.P.E., Lisboa, Portugal
- CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Bruno A. Cardoso
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, E.P.E., Lisboa, Portugal
- CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Beatriz Porto
- Laboratório de Citogenética do Instituto de Ciências Biomédicas de Abel Salazar, Porto, Portugal
| | - Jordi Minguillon
- Center for Biomedical Network Research on Rare Diseases (CIBERER) and Department of Genetics and Microbiology, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - José Barbot
- Unidade de Hematologia Pediátrica do Centro Hospitalar do Porto, Porto, Portugal
| | - Jorge Coutinho
- Unidade de Hematologia Pediátrica do Centro Hospitalar do Porto, Porto, Portugal
| | - Jose A. Casado
- Hematopoiesis and Gene Therapy Division, CIEMAT, Madrid, Spain
| | - Manuela Benedito
- Serviço de hematologia do Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Hema Saturnino
- Serviço de hematologia do Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Emília Costa
- Unidade de Hematologia Pediátrica do Centro Hospitalar do Porto, Porto, Portugal
| | - Juan A. Bueren
- Unidade de Hematologia Pediátrica do Centro Hospitalar do Porto, Porto, Portugal
| | - Jordi Surralles
- Center for Biomedical Network Research on Rare Diseases (CIBERER) and Department of Genetics and Microbiology, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Antonio Almeida
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, E.P.E., Lisboa, Portugal
- CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
- * E-mail:
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Santos-Pereira JM, Aguilera A. R loops: new modulators of genome dynamics and function. Nat Rev Genet 2015; 16:583-97. [PMID: 26370899 DOI: 10.1038/nrg3961] [Citation(s) in RCA: 511] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
R loops are nucleic acid structures composed of an RNA-DNA hybrid and a displaced single-stranded DNA. Recently, evidence has emerged that R loops occur more often in the genome and have greater physiological relevance, including roles in transcription and chromatin structure, than was previously predicted. Importantly, however, R loops are also a major threat to genome stability. For this reason, several DNA and RNA metabolism factors prevent R-loop formation in cells. Dysfunction of these factors causes R-loop accumulation, which leads to replication stress, genome instability, chromatin alterations or gene silencing, phenomena that are frequently associated with cancer and a number of genetic diseases. We review the current knowledge of the mechanisms controlling R loops and their putative relationship with disease.
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Affiliation(s)
- José M Santos-Pereira
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Av. Américo Vespucio s/n, Seville 41092, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Av. Américo Vespucio s/n, Seville 41092, Spain
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Replication Stress: A Lifetime of Epigenetic Change. Genes (Basel) 2015; 6:858-77. [PMID: 26378584 PMCID: PMC4584333 DOI: 10.3390/genes6030858] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/04/2015] [Accepted: 09/08/2015] [Indexed: 12/29/2022] Open
Abstract
DNA replication is essential for cell division. Challenges to the progression of DNA polymerase can result in replication stress, promoting the stalling and ultimately collapse of replication forks. The latter involves the formation of DNA double-strand breaks (DSBs) and has been linked to both genome instability and irreversible cell cycle arrest (senescence). Recent technological advances have elucidated many of the factors that contribute to the sensing and repair of stalled or broken replication forks. In addition to bona fide repair factors, these efforts highlight a range of chromatin-associated changes at and near sites of replication stress, suggesting defects in epigenome maintenance as a potential outcome of aberrant DNA replication. Here, we will summarize recent insight into replication stress-induced chromatin-reorganization and will speculate on possible adverse effects for gene expression, nuclear integrity and, ultimately, cell function.
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Loss of H2Bub1 Expression is Linked to Poor Prognosis in Nodal Negative Colorectal Cancers. Pathol Oncol Res 2015; 22:95-102. [PMID: 26347467 DOI: 10.1007/s12253-015-9977-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Abstract
To correlate H2Bub1 expression with outcome in colorectal cancer, H2Bub1 expression was analyzed by immunohistochemistry on a tissue microarray containing 1800 colorectal cancers. Results were compared to clinicopathological parameters.H2Bub1 IHC was seen in 1256 (79.3%) of 1584 interpretable CRC and was considered weak in 26.2% and strong in 53.1% of cancers. H2Bub1 expression was completely lost in 20.7% of the cases. Loss of H2Bub1 expression was associated with high tumor grade (p = 0.0211), high tumor stage (p = 0.0003), positive nodal status (p = 0.0139) and histological tumor type (p = 0.0202). No link was found between H2Bub1 expression and tumor localization (p = 0.1262), peritumoral lymphocytic infiltration (p = 0.2523) or vascular invasion (p = 0.5970).Loss of H2Bub1 expression in CRC was strongly associated with poor patient survival (p = 0.0006). This observation held true also in a subset survival analysis of nodal negative (N0) and nodal positive (N1) cancers (p = 0.0296 and p = 0.0197, respectively). In the subgroup of p53 negative cancers no prognostic impact of H2Bub1 staining was seen (p = 0.1924), whereas in p53 positive CRC H2Bub1 expression loss was associated with poor prognosis (p = 0.0031). Strikingly worsened outcome was found for nodal negative cancers presenting with accumulation of p53 when H2Bub1 expression was lost (p = 0.0006).Our data demonstrate that a reduced H2Bub1 expression is a strong prognostic biomarker both in nodal negative and nodal positive CRC. H2Bub1 expression measurement might help to select nodal negative CRC patients that may benefit from adjuvant therapy.
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Liu T, Sun B, Zhao X, Li Y, Zhao X, Liu Y, Yao Z, Gu Q, Dong X, Shao B, Lin X, Liu F, An J. USP44+ Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry. Mol Cancer Ther 2015; 14:2121-31. [PMID: 26232424 DOI: 10.1158/1535-7163.mct-15-0114-t] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 06/10/2015] [Indexed: 11/16/2022]
Abstract
Vasculogenic mimicry (VM), a newly defined pattern of tumor blood supply, describes the functional plasticity of aggressive cancer cells that form vascular networks. In our previous study, breast cancer stem cells (CSC) were shown to potentially participate in VM formation. In this study, breast CSCs presented centrosome amplification (CA) phenotype and ubiquitin-specific protease 44 (USP44) upregulation. USP44 expression contributed to the establishment of bipolar spindles in breast CSCs with supernumerary centrosomes by localizing at pole-associated centrosomes. The bipolar spindle patterns of breast CSCs with CA, including planar-like and apico-basal-like, functioned differently during the VM process of CSCs. Moreover, the ability of transendothelial migration in VM-forming cells was increased. In vivo experiment results showed that CSC xenografts presented linearly patterned programmed cell necrosis, which provided a spatial foundation for VM formation as well as angiogenesis. Breast CSCs further showed increased levels of IL6 and IL8. However, USP44 silencing induced spindle multipolarity, abated VM, reduced transendothelial migration, and consequently decreased IL6 and IL8 levels in breast CSCs. Finally, USP44(+) CSC subclones (ALDH1(+)/USP44(+)/IL6(+)/IL8(+)) were identified in breast cancer specimens through consecutive sections scanning. The subclones were related not only to CA, but also to VM. Statistical analysis suggested that USP44(+) CSC subclones could be used as an independent prognostic biomarker of poor clinical outcomes in patients with breast cancer. Collectively, the identification of USP44(+) CSC subclones may contribute to the prediction of VM formation and aggressive behavior. This study provides novel insights into the therapy for advanced breast cancer.
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Affiliation(s)
- Tieju Liu
- Department of Pathology, Tianjin Medical University, Tianjin, China. Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Baocun Sun
- Department of Pathology, Tianjin Medical University, Tianjin, China. Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China. Department of Pathology, Tianjin Cancer Hospital, Tianjin Medical University, Tianjin, China.
| | - Xiulan Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, China. Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Yanlei Li
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Xueming Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Ying Liu
- Department of Pathology, Tianjin Medical University, Tianjin, China. Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Zhi Yao
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Qiang Gu
- Department of Pathology, Tianjin Medical University, Tianjin, China. Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Xueyi Dong
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Bing Shao
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Xian Lin
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Fang Liu
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Jindan An
- Department of Pathology, Tianjin Medical University, Tianjin, China
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Wu Y, Chen P, Jing Y, Wang C, Men YL, Zhan W, Wang Q, Gan Z, Huang J, Xie K, Mi J, Yu C, Yu X, Chen PC, Chang JF, Cai F, Chen S. Microarray Analysis Reveals Potential Biological Functions of Histone H2B Monoubiquitination. PLoS One 2015; 10:e0133444. [PMID: 26177367 PMCID: PMC4503354 DOI: 10.1371/journal.pone.0133444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/26/2015] [Indexed: 11/19/2022] Open
Abstract
Histone H2B monoubiquitination is a key histone modification that has significant effects on chromatin higher-order structure and gene transcription. Multiple biological processes have been suggested to be tightly related to the dynamics of H2B monoubiquitination. However, a comprehensive understanding of biological roles of H2B monoubiquitination is still poorly understood. In the present study, we developed an efficient tool to disrupt endogenous H2B monoubiquitination levels by using an H2BK120R mutant construct expressed in human cells. Genome-wide microarray analysis of these cells revealed a potential global view of biological functions of H2B monoubiquitination. Bioinformatics analysis of our data demonstrated that while H2B monoubiquitination expectedly affected a number of previously reported biological pathways, we also uncovered the influence of this histone modification on many novel biological processes. Therefore, our work provided valuable information for understanding the role of H2B monoubiquitination and indicated potential directions for its further studies.
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Affiliation(s)
- You Wu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Ping Chen
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Yuanya Jing
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Chen Wang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Yu-Long Men
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Wang Zhan
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Qiang Wang
- Department of Nephrology and Rheumatology of Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200092, P. R. China
| | - Zhixue Gan
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Jin Huang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Kun Xie
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Jiangsheng Mi
- Department of Science and Education, People’s Hospital of Zunhua, Tangshan, Hebei 064200, P. R. China
| | - Chenghua Yu
- Department of Science and Education, People’s Hospital of Zunhua, Tangshan, Hebei 064200, P. R. China
| | - Xiuqing Yu
- Department of Science and Education, People’s Hospital of Zunhua, Tangshan, Hebei 064200, P. R. China
| | - Pei-Chao Chen
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, P. R. China
| | - Jian-Feng Chang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
| | - Fengfeng Cai
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
- * E-mail: (SC); (FC)
| | - Su Chen
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Tongji University, Shanghai 200092, P. R. China
- Department of Science and Education, People’s Hospital of Zunhua, Tangshan, Hebei 064200, P. R. China
- * E-mail: (SC); (FC)
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Wang Z, Zhu L, Guo T, Wang Y, Yang J. Decreased H2B monoubiquitination and overexpression of ubiquitin-specific protease enzyme 22 in malignant colon carcinoma. Hum Pathol 2015; 46:1006-14. [DOI: 10.1016/j.humpath.2015.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 02/07/2023]
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Javadekar SM, Raghavan SC. Snaps and mends: DNA breaks and chromosomal translocations. FEBS J 2015; 282:2627-45. [PMID: 25913527 DOI: 10.1111/febs.13311] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/29/2015] [Accepted: 04/23/2015] [Indexed: 01/11/2023]
Abstract
Integrity in entirety is the preferred state of any organism. The temporal and spatial integrity of the genome ensures continued survival of a cell. DNA breakage is the first step towards creation of chromosomal translocations. In this review, we highlight the factors contributing towards the breakage of chromosomal DNA. It has been well-established that the structure and sequence of DNA play a critical role in selective fragility of the genome. Several non-B-DNA structures such as Z-DNA, cruciform DNA, G-quadruplexes, R loops and triplexes have been implicated in generation of genomic fragility leading to translocations. Similarly, specific sequences targeted by proteins such as Recombination Activating Genes and Activation Induced Cytidine Deaminase are involved in translocations. Processes that ensure the integrity of the genome through repair may lead to persistence of breakage and eventually translocations if their actions are anomalous. An insufficient supply of nucleotides and chromatin architecture may also play a critical role. This review focuses on a range of events with the potential to threaten the genomic integrity of a cell, leading to cancer.
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Affiliation(s)
- Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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70
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Sen R, Bhaumik SR. Transcriptional stimulatory and repressive functions of histone H2B ubiquitin ligase. Transcription 2015; 4:221-6. [PMID: 24135701 DOI: 10.4161/trns.26623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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71
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Abstract
Ubiquitination has traditionally been viewed in the context of polyubiquitination that is essential for marking proteins for degradation via the proteasome. Recent discoveries have shed light on key cellular roles for monoubiquitination, including as a post-translational modification (PTM) of histones such as histone H2B. Monoubiquitination plays a significant role as one of the largest histone PTMs, alongside smaller, better-studied modifications such as methylation, acetylation and phosphorylation. Monoubiquitination of histone H2B at lysine 120 (H2Bub1) has been shown to have key roles in transcription, the DNA damage response and stem cell differentiation. The H2Bub1 enzymatic cascade involves E3 RING finger ubiquitin ligases, with the main E3 generally accepted to be the RNF20-RNF40 complex, and deubiquitinases including ubiquitin-specific protease 7 (USP7), USP22 and USP44. H2Bub1 has been shown to physically disrupt chromatin strands, fostering a more open chromatin structure accessible to transcription factors and DNA repair proteins. It also acts as a recruiting signal, actively attracting proteins with roles in transcription and DNA damage. H2Bub1 also appears to play central roles in histone cross-talk, influencing methylation events on histone H3, including H3K4 and H3K79. Most significantly, global levels of H2Bub1 are low to absent in advanced cancers including breast, colorectal, lung and parathyroid, marking H2Bub1 and the enzymes that regulate it as key molecules of interest as possible new therapeutic targets for the treatment of cancer. This review offers an overview of current knowledge regarding H2Bub1 and highlights links between dysregulation of H2Bub1-associated enzymes, stem cells and malignancy.
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Affiliation(s)
- Alexander J Cole
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Roderick Clifton-Bligh
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Deborah J Marsh
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
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Mitotic accumulation of dimethylated lysine 79 of histone H3 is important for maintaining genome integrity during mitosis in human cells. Genetics 2014; 199:423-33. [PMID: 25533199 PMCID: PMC4317652 DOI: 10.1534/genetics.114.172874] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The loss of genome stability is an early event that drives the development and progression of virtually all tumor types. Recent studies have revealed that certain histone post-translational modifications exhibit dynamic and global increases in abundance that coincide with mitosis and exhibit essential roles in maintaining genomic stability. Histone H2B ubiquitination at lysine 120 (H2Bub1) is regulated by RNF20, an E3 ubiquitin ligase that is altered in many tumor types. Through an evolutionarily conserved trans-histone pathway, H2Bub1 is an essential prerequisite for subsequent downstream dimethylation events at lysines 4 (H3K4me2) and 79 (H3K79me2) of histone H3. Although the role that RNF20 plays in tumorigenesis has garnered much attention, the downstream components of the trans-histone pathway, H3K4me2 and H3K79me2, and their potential contributions to genome stability remain largely overlooked. In this study, we employ single-cell imaging and biochemical approaches to investigate the spatial and temporal patterning of RNF20, H2Bub1, H3K4me2, and H3K79me2 throughout the cell cycle, with a particular focus on mitosis. We show that H2Bub1, H3K4me2, and H3K79me2 exhibit distinct temporal progression patterns throughout the cell cycle. Most notably, we demonstrate that H3K79me2 is a highly dynamic histone post-translational modification that reaches maximal abundance during mitosis in an H2Bub1-independent manner. Using RNAi and chemical genetic approaches, we identify DOT1L as a histone methyltransferase required for the mitotic-associated increases in H3K79me2. We also demonstrate that the loss of mitotic H3K79me2 levels correlates with increases in chromosome numbers and increases in mitotic defects. Collectively, these data suggest that H3K79me2 dynamics during mitosis are normally required to maintain genome stability and further implicate the loss of H3K79me2 during mitosis as a pathogenic event that contributes to the development and progression of tumors.
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Shchebet A, Karpiuk O, Kremmer E, Eick D, Johnsen SA. Phosphorylation by cyclin-dependent kinase-9 controls ubiquitin-conjugating enzyme-2A function. Cell Cycle 2014; 11:2122-7. [DOI: 10.4161/cc.20548] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Abstract
R-loops are cellular structures composed of an RNA/DNA hybrid, which is formed when the RNA hybridises to a complementary DNA strand and a displaced single-stranded DNA. R-loops have been detected in various organisms from bacteria to mammals and play crucial roles in regulating gene expression, DNA and histone modifications, immunoglobulin class switch recombination, DNA replication, and genome stability. Recent evidence suggests that R-loops are also involved in molecular mechanisms of neurological diseases and cancer. In addition, mutations in factors implicated in R-loop biology, such as RNase H and SETX (senataxin), lead to devastating human neurodegenerative disorders, highlighting the importance of correctly regulating the level of R-loops in human cells. In this review we summarise current advances in this field, with a particular focus on diseases associated with dysregulation of R-loop structures. We also discuss potential therapeutic approaches for such diseases and highlight future research directions.
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Affiliation(s)
- Matthias Groh
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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The oncogenic polycomb histone methyltransferase EZH2 methylates lysine 120 on histone H2B and competes ubiquitination. Neoplasia 2014; 15:1251-61. [PMID: 24339737 DOI: 10.1593/neo.131436] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/16/2013] [Accepted: 10/21/2013] [Indexed: 11/18/2022] Open
Abstract
The histone methyltransferase enhancer of zeste 2 (EZH2) is known to be a polycomb protein homologous to Drosophila enhancer of zeste and catalyzes the addition of methyl groups to histone H3 at lysine 27 (H3K27). We previously reported that EZH2 was overexpressed in various types of cancer and plays a crucial role in the cell cycle regulation of cancer cells. In the present study, we demonstrated that EZH2 has the function to monomethylate lysine 120 on histone H2B (H2BK120). EZH2-dependent H2BK120 methylation in cancer cells was confirmed with an H2BK120 methylation-specific antibody. Overexpression of EZH2 significantly attenuated the ubiquitination of H2BK120, a key posttranslational modification of histones for transcriptional regulation. Concordantly, knockdown of EZH2 increased the ubiquitination level of H2BK120, suggesting that the methylation of H2BK120 by EZH2 may competitively inhibit the ubiquitination of H2BK120. Subsequent chromatin immunoprecipitation-Seq and microarray analyses identified downstream candidate genes regulated by EZH2 through the methylation of H2BK120. This is the first report to describe a novel substrate of EZH2, H2BK120, unveiling a new aspect of EZH2 functions in human carcinogenesis.
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76
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GOV ESRA, ARGA KAZIMYALCIN. GENETIC MUTATIONS ARE CHARACTERIZED BY INCREASE IN ENTROPY AT THE TRANSCRIPTIONAL LEVEL. J BIOL SYST 2014. [DOI: 10.1142/s0218339014500132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Predicting the genomic and phenotypic re-programming in organisms undergoing genetic perturbations is a challenging task in modern biology. It is hypothesized that genomic alterations perturb the dynamics of biological information flow. In the present study, a statistical data analysis framework was designed and the network entropy concept was employed to quantify the level of disorder at the transcriptional level as a result of the genomic re-programming of S. cerevisiae cells under genetic perturbations. The customized re-programming in transcription levels to different genetic modifications was observed and genetic mutations were characterized by enhanced network entropies, which revealed higher degree of randomness in mRNA expression levels. To our knowledge, this study constitutes the first numerical demonstration on the conservative energetic state of the microorganisms against genetic perturbations.
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Affiliation(s)
- ESRA GOV
- Department of Bioengineering, Faculty of Engineering, Marmara University, 34722 Göztepe, Istanbul, Turkey
| | - KAZIM YALCIN ARGA
- Department of Bioengineering, Faculty of Engineering, Marmara University, 34722 Göztepe, Istanbul, Turkey
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77
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The potential role of O-GlcNAc modification in cancer epigenetics. Cell Mol Biol Lett 2014; 19:438-60. [PMID: 25141978 PMCID: PMC6275943 DOI: 10.2478/s11658-014-0204-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/01/2014] [Indexed: 12/20/2022] Open
Abstract
There is no doubt that cancer is not only a genetic disease but that it can also occur due to epigenetic abnormalities. Diet and environmental factors can alter the scope of epigenetic regulation. The results of recent studies suggest that O-GlcNAcylation, which involves the addition of N-acetylglucosamine on the serine or threonine residues of proteins, may play a key role in the regulation of the epigenome in response to the metabolic status of the cell. Two enzymes are responsible for cyclic O-GlcNAcylation: O-GlcNAc transferase (OGT), which catalyzes the addition of the GlcNAc moiety to target proteins; and O-GlcNAcase (OGA), which removes the sugar moiety from proteins. Aberrant expression of O-GlcNAc cycling enzymes, especially OGT, has been found in all studied human cancers. OGT can link the cellular metabolic state and the epigenetic status of cancer cells by interacting with and modifying many epigenetic factors, such as HCF-1, TET, mSin3A, HDAC, and BAP1. A growing body of evidence from animal model systems also suggests an important role for OGT in polycomb-dependent repression of genes activity. Moreover, O-GlcNAcylation may be a part of the histone code: O-GlcNAc residues are found on all core histones.
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78
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Gole B, Baumann C, Mian E, Ireno CI, Wiesmüller L. Endonuclease G initiates DNA rearrangements at the MLL breakpoint cluster upon replication stress. Oncogene 2014; 34:3391-401. [PMID: 25132265 DOI: 10.1038/onc.2014.268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 07/02/2014] [Accepted: 07/14/2014] [Indexed: 12/31/2022]
Abstract
MLL (myeloid/lymphoid or mixed-lineage leukemia) rearrangements are frequent in therapy-related and childhood acute leukemia, and are associated with poor prognosis. The majority of the rearrangements fall within a 7.3-kb MLL breakpoint cluster region (MLLbcr), particularly in a 0.4-kb hotspot at the intron11-exon12 boundary. The underlying mechanisms are poorly understood, though multiple pathways including early apoptotic signaling, accompanied by high-order DNA fragmentation, have been implicated. We introduced the MLLbcr hotspot in an EGFP-based recombination reporter system and demonstrated enhancement of both spontaneous and genotoxic treatment-induced DNA recombination by the MLLbcr in various human cell types. We identified Endonuclease G (EndoG), an apoptotic nuclease, as an essential factor for MLLbcr-specific DNA recombination after induction of replication stress. We provide evidence for replication stress-induced nuclear accumulation of EndoG, DNA binding by EndoG as well as cleavage of the chromosomal MLLbcr locus in a manner requiring EndoG. We demonstrate additional dependency of MLLbcr breakage on ATM signaling to histone H2B monoubiquitinase RNF20, involved in chromatin relaxation. Altogether our findings provide a novel mechanism underlying MLLbcr destabilization in the cells of origin of leukemogenesis, with replication stress-activated, EndoG-mediated cleavage at the MLLbcr, which may serve resolution of the stalled forks via recombination repair, however, also permits MLL rearrangements.
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Affiliation(s)
- B Gole
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - C Baumann
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - E Mian
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - C I Ireno
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - L Wiesmüller
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
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79
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Durairaj G, Sen R, Uprety B, Shukla A, Bhaumik SR. Sus1p facilitates pre-initiation complex formation at the SAGA-regulated genes independently of histone H2B de-ubiquitylation. J Mol Biol 2014; 426:2928-2941. [PMID: 24911582 DOI: 10.1016/j.jmb.2014.05.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/29/2014] [Accepted: 05/31/2014] [Indexed: 12/23/2022]
Abstract
Sus1p is a common component of transcriptional co-activator, SAGA (Spt-Ada-Gcn5-Acetyltransferase), and mRNA export complex, TREX-2 (Transcription-export 2), and is involved in promoting transcription and mRNA export. However, it is not clearly understood how Sus1p promotes transcription. Here, we show that Sus1p is predominantly recruited to the upstream activating sequence of a SAGA-dependent gene, GAL1, under transcriptionally active conditions as a component of SAGA to promote the formation of pre-initiation complex (PIC) at the core promoter and, consequently, transcriptional initiation. Likewise, Sus1p promotes the PIC formation at other SAGA-dependent genes and hence transcriptional initiation. Such function of Sus1p in promoting PIC formation and transcriptional initiation is not mediated via its role in regulation of SAGA's histone H2B de-ubiquitylation activity. However, Sus1p's function in regulation of histone H2B ubiquitylation is associated with transcriptional elongation, DNA repair and replication. Collectively, our results support that Sus1p promotes PIC formation (and hence transcriptional initiation) at the SAGA-regulated genes independently of histone H2B de-ubiquitylation and further controls transcriptional elongation, DNA repair and replication via orchestration of histone H2B ubiquitylation, thus providing distinct functional insights of Sus1p in regulation of DNA transacting processes.
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Affiliation(s)
- Geetha Durairaj
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
| | - Rwik Sen
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
| | - Bhawana Uprety
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
| | - Abhijit Shukla
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
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80
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Mechanisms of genome instability induced by RNA-processing defects. Trends Genet 2014; 30:245-53. [PMID: 24794811 DOI: 10.1016/j.tig.2014.03.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/20/2022]
Abstract
The role of normal transcription and RNA processing in maintaining genome integrity is becoming increasingly appreciated in organisms ranging from bacteria to humans. Several mutations in RNA biogenesis factors have been implicated in human cancers, but the mechanisms and potential connections to tumor genome instability are not clear. Here, we discuss how RNA-processing defects could destabilize genomes through mutagenic R-loop structures and by altering expression of genes required for genome stability. A compelling body of evidence now suggests that researchers should be directly testing these mechanisms in models of human cancer.
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81
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Chan YA, Aristizabal MJ, Lu PYT, Luo Z, Hamza A, Kobor MS, Stirling PC, Hieter P. Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip. PLoS Genet 2014; 10:e1004288. [PMID: 24743342 PMCID: PMC3990523 DOI: 10.1371/journal.pgen.1004288] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/21/2014] [Indexed: 12/17/2022] Open
Abstract
DNA:RNA hybrid formation is emerging as a significant cause of genome instability in biological systems ranging from bacteria to mammals. Here we describe the genome-wide distribution of DNA:RNA hybrid prone loci in Saccharomyces cerevisiae by DNA:RNA immunoprecipitation (DRIP) followed by hybridization on tiling microarray. These profiles show that DNA:RNA hybrids preferentially accumulated at rDNA, Ty1 and Ty2 transposons, telomeric repeat regions and a subset of open reading frames (ORFs). The latter are generally highly transcribed and have high GC content. Interestingly, significant DNA:RNA hybrid enrichment was also detected at genes associated with antisense transcripts. The expression of antisense-associated genes was also significantly altered upon overexpression of RNase H, which degrades the RNA in hybrids. Finally, we uncover mutant-specific differences in the DRIP profiles of a Sen1 helicase mutant, RNase H deletion mutant and Hpr1 THO complex mutant compared to wild type, suggesting different roles for these proteins in DNA:RNA hybrid biology. Our profiles of DNA:RNA hybrid prone loci provide a resource for understanding the properties of hybrid-forming regions in vivo, extend our knowledge of hybrid-mitigating enzymes, and contribute to models of antisense-mediated gene regulation. A summary of this paper was presented at the 26th International Conference on Yeast Genetics and Molecular Biology, August 2013.
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Affiliation(s)
- Yujia A. Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Maria J. Aristizabal
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada
| | - Phoebe Y. T. Lu
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada
| | - Zongli Luo
- Wine Research Centre, University of British Columbia, Vancouver, Canada
| | - Akil Hamza
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C. Stirling
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
- * E-mail: (PCS); (PH)
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- * E-mail: (PCS); (PH)
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82
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Koso H, Tsuhako A, Lyons E, Ward JM, Rust AG, Adams DJ, Jenkins NA, Copeland NG, Watanabe S. Identification of FoxR2 as an oncogene in medulloblastoma. Cancer Res 2014; 74:2351-61. [PMID: 24599127 DOI: 10.1158/0008-5472.can-13-1523] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Medulloblastoma is the most common pediatric brain tumor, and in ∼25% of cases, it is driven by aberrant activation of the Sonic Hedgehog (SHH) pathway in granule neuron precursor (GNP) cells. In this study, we identified novel medulloblastoma driver genes through a transposon mutagenesis screen in the developing brain of wild-type and Trp53 mutant mice. Twenty-six candidates were identified along with established driver genes such as Gli1 and Crebbp. The transcription factor FoxR2, the most frequent gene identified in the screen, is overexpressed in a small subset of human medulloblastoma of the SHH subtype. Tgif2 and Alx4, 2 new putative oncogenes identified in the screen, are strongly expressed in the SHH subtype of human medulloblastoma. Mutations in these two genes were mutually exclusive with mutations in Gli1 and tended to cooccur, consistent with involvement in the SHH pathway. Notably, Foxr2, Tgif2, and Alx4 activated Gli-binding sites in cooperation with Gli1, strengthening evidence that they function in SHH signaling. In support of an oncogenic function, Foxr2 overexpression transformed NIH3T3 cells and promoted proliferation of GNPs, the latter of which was also observed for Tgif2 and Alx4. These findings offer forward genetic and functional evidence associating Foxr2, Tgif2, and Alx4 with SHH subtype medulloblastoma.
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Affiliation(s)
- Hideto Koso
- Authors' Affiliations: Division of Molecular and Developmental Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Division of Genetics and Genomics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore; Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom; and Cancer Research Program, The Methodist Hospital Research Institute, Houston, Texas
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83
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Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity. Nat Struct Mol Biol 2014; 21:236-43. [PMID: 24531659 DOI: 10.1038/nsmb.2776] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/22/2014] [Indexed: 01/06/2023]
Abstract
Functional centromeres are essential for proper cell division. Centromeres are established largely by epigenetic processes resulting in incorporation of the histone H3 variant CENP-A. Here, we demonstrate the direct involvement of H2B monoubiquitination, mediated by RNF20 in humans or Brl1 in Schizosaccharomyces pombe, in centromeric chromatin maintenance. Monoubiquinated H2B (H2Bub1) is needed for this maintenance, promoting noncoding transcription, centromere integrity and accurate chromosomal segregation. A transient pulse of centromeric H2Bub1 leads to RNA polymerase II-mediated transcription of the centromere's central domain, coupled to decreased H3 stability. H2Bub1-deficient cells have centromere cores that, despite their intact centromeric heterochromatin barriers, exhibit characteristics of heterochromatin, such as silencing histone modifications, reduced nucleosome turnover and reduced levels of transcription. In the H2Bub1-deficient cells, centromere functionality is hampered, thus resulting in unequal chromosome segregation. Therefore, centromeric H2Bub1 is essential for maintaining active centromeric chromatin.
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84
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Kim W, Choi M, Kim JE. The histone methyltransferase Dot1/DOT1L as a critical regulator of the cell cycle. Cell Cycle 2014; 13:726-38. [PMID: 24526115 PMCID: PMC3979909 DOI: 10.4161/cc.28104] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Dot1/DOT1L catalyzes the methylation of histone H3 lysine 79 (H3K79), which regulates diverse cellular processes, such as development, reprogramming, differentiation, and proliferation. In regards to these processes, studies of Dot1/DOT1L-dependent H3K79 methylation have mainly focused on the transcriptional regulation of specific genes. Although the gene transcription mediated by Dot1/DOT1L during the cell cycle is not fully understood, H3K79 methylation plays a critical role in the progression of G 1 phase, S phase, mitosis, and meiosis. This modification may contribute to the chromatin structure that controls gene expression, replication initiation, DNA damage response, microtubule reorganization, chromosome segregation, and heterochromatin formation. Overall, Dot1/DOT1L is required to maintain genomic and chromosomal stability. This review summarizes the several functions of Dot1/DOT1L and highlights its role in cell cycle regulation.
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Affiliation(s)
- Wootae Kim
- Department of Pharmacology; School of Medicine; Kyung Hee University; Seoul, Republic of Korea; Department of Biomedical Science; Graduate School; Kyung Hee University; Seoul, Republic of Korea
| | - Minji Choi
- Department of Pharmacology; School of Medicine; Kyung Hee University; Seoul, Republic of Korea; Department of Biomedical Science; Graduate School; Kyung Hee University; Seoul, Republic of Korea
| | - Ja-Eun Kim
- Department of Pharmacology; School of Medicine; Kyung Hee University; Seoul, Republic of Korea; Department of Biomedical Science; Graduate School; Kyung Hee University; Seoul, Republic of Korea
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85
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Fuchs G, Oren M. Writing and reading H2B monoubiquitylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:694-701. [PMID: 24412854 DOI: 10.1016/j.bbagrm.2014.01.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/01/2014] [Accepted: 01/02/2014] [Indexed: 01/27/2023]
Abstract
Monoubiquitylation of histone H2B (H2Bub1), catalyzed by the heterodimeric ubiquitin ligase complex RNF20/40, regulates multiple molecular and biological processes. The addition of a large ubiquitin moiety to the small H2B is believed to change the biochemical features of the chromatin. H2B monoubiquitylation alters nucleosome stability, nucleosome reassembly and higher order compaction of the chromatin. While these effects explain some of the direct roles of H2Bub1, there is growing evidence that H2Bub1 can also regulate multiple DNA-templated processes indirectly, by recruitment of specific factors ("readers") to the chromatin. H2Bub1 readers mediate much of the effect of H2Bub1 on histone crosstalk, transcriptional outcome and probably other chromatin-related activities. Here we summarize the current knowledge about H2Bub1-specific readers and their role in various biological processes. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Gilad Fuchs
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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86
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Nakachi I, Rice JL, Coldren CD, Edwards MG, Stearman RS, Glidewell SC, Varella-Garcia M, Franklin WA, Keith RL, Lewis MT, Gao B, Merrick DT, Miller YE, Geraci MW. Application of SNP microarrays to the genome-wide analysis of chromosomal instability in premalignant airway lesions. Cancer Prev Res (Phila) 2013; 7:255-65. [PMID: 24346345 DOI: 10.1158/1940-6207.capr-12-0485] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chromosomal instability is central to the process of carcinogenesis. The genome-wide detection of somatic chromosomal alterations (SCA) in small premalignant lesions remains challenging because sample heterogeneity dilutes the aberrant cell information. To overcome this hurdle, we focused on the B allele frequency data from single-nucleotide polymorphism microarrays (SNP arrays). The difference of allelic fractions between paired tumor and normal samples from the same patient (delta-θ) provides a simple but sensitive detection of SCA in the affected tissue. We applied the delta-θ approach to small, heterogeneous clinical specimens, including endobronchial biopsies and brushings. Regions identified by delta-θ were validated by FISH and quantitative PCR in heterogeneous samples. Distinctive genomic variations were successfully detected across the whole genome in all invasive cancer cases (6 of 6), carcinoma in situ (3 of 3), and high-grade dysplasia (severe or moderate; 3 of 11). Not only well-described SCAs in lung squamous cell carcinoma, but also several novel chromosomal alterations were frequently found across the preinvasive dysplastic cases. Within these novel regions, losses of putative tumor suppressors (RNF20 and SSBP2) and an amplification of RASGRP3 gene with oncogenic activity were observed. Widespread sampling of the airway during bronchoscopy demonstrated that field cancerization reflected by SCAs at multiple sites was detectable. SNP arrays combined with delta-θ analysis can detect SCAs in heterogeneous clinical sample and expand our ability to assess genomic instability in the airway epithelium as a biomarker of lung cancer risk.
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Affiliation(s)
- Ichiro Nakachi
- University of Colorado, Anschutz Medical Campus, 12700, East 19th Avenue, RC2 9th Floor, Aurora, CO 80045.
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87
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Sen R, Lahudkar S, Durairaj G, Bhaumik SR. Functional analysis of Bre1p, an E3 ligase for histone H2B ubiquitylation, in regulation of RNA polymerase II association with active genes and transcription in vivo. J Biol Chem 2013; 288:9619-9633. [PMID: 23417674 DOI: 10.1074/jbc.m113.450403] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
H2B ubiquitylation is carried out by Bre1p, an E3 ligase, along with an E2 conjugase, Rad6p. H2B ubiquitylation has been previously implicated in promoting the association of RNA polymerase II with the coding sequence of the active GAL1 gene, and hence transcriptional elongation. Intriguingly, we find here that the association of RNA polymerase II with the active GAL1 coding sequence is not decreased in Δbre1, although it is required for H2B ubiquitylation. In contrast, the loss of Rad6p significantly impairs the association of RNA polymerase II with GAL1. Likewise, the point mutation of lysine 123 (ubiquitylation site) to arginine of H2B (H2B-K123R) also lowers the association of RNA polymerase II with GAL1, consistent with the role of H2B ubiquitylation in promoting RNA polymerase II association. Surprisingly, unlike the Δrad6 and H2B-K123R strains, complete deletion of BRE1 does not impair the association of RNA polymerase II with GAL1. However, deletion of the RING domain of Bre1p (that is essential for H2B ubiquitylation) impairs RNA polymerase II association with GAL1. These results imply that a non-RING domain of Bre1p counteracts the stimulatory role of the RING domain in regulating the association of RNA polymerase II with GAL1, and hence RNA polymerase II occupancy is not impaired in Δbre1. Consistently, GAL1 transcription is impaired in the absence of the RING domain of Bre1p, but not in Δbre1. Similar results are also obtained at other genes. Collectively, our results implicate both the stimulatory and repressive roles of Bre1p in regulation of RNA polymerase II association with active genes (and hence transcription) in vivo.
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Affiliation(s)
- Rwik Sen
- Department of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
| | - Shweta Lahudkar
- Department of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
| | - Geetha Durairaj
- Department of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901.
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88
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Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia. Proc Natl Acad Sci U S A 2013; 110:3901-6. [PMID: 23412334 DOI: 10.1073/pnas.1301045110] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mixed-lineage leukemia (MLL) fusions are potent oncogenes that initiate aggressive forms of acute leukemia. As aberrant transcriptional regulators, MLL-fusion proteins alter gene expression in hematopoietic cells through interactions with the histone H3 lysine 79 (H3K79) methyltransferase DOT1L. Notably, interference with MLL-fusion cofactors like DOT1L is an emerging therapeutic strategy in this disease. Here, we identify the histone H2B E3 ubiquitin ligase ring finger protein 20 (RNF20) as an additional chromatin regulator that is necessary for MLL-fusion-mediated leukemogenesis. Suppressing the expression of Rnf20 in diverse models of MLL-rearranged leukemia leads to inhibition of cell proliferation, under tissue culture conditions as well as in vivo. Rnf20 knockdown leads to reduced expression of MLL-fusion target genes, effects resembling Dot1l inhibition. Using ChIP-seq, we found that H2B ubiquitination is enriched in the body of MLL-fusion target genes, correlating with sites of H3K79 methylation and transcription elongation. Furthermore, Rnf20 is required to maintain local levels of H3K79 methylation by Dot1l at Hoxa9 and Meis1. These findings support a model whereby cotranscriptional recruitment of Rnf20 at MLL-fusion target genes leads to amplification of Dot1l-mediated H3K79 methylation, thereby rendering leukemia cells dependent on Rnf20 to maintain their oncogenic transcriptional program.
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89
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Johnson DG, Dent SYR. Chromatin: receiver and quarterback for cellular signals. Cell 2013; 152:685-9. [PMID: 23375745 DOI: 10.1016/j.cell.2013.01.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/28/2012] [Accepted: 01/08/2013] [Indexed: 12/21/2022]
Abstract
Signal transduction pathways converge upon sequence-specific DNA binding factors to reprogram gene expression. Transcription factors, in turn, team up with chromatin modifying activities. However, chromatin is not simply an endpoint for signaling pathways. Histone modifications relay signals to other proteins to trigger more immediate responses than can be achieved through altered gene transcription, which might be especially important to time-urgent processes such as the execution of cell-cycle check points, chromosome segregation, or exit from mitosis. In addition, histone-modifying enzymes often have multiple nonhistone substrates, and coordination of activity toward different targets might direct signals both to and from chromatin.
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Affiliation(s)
- David G Johnson
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA
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90
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Gospodinov A, Herceg Z. Shaping chromatin for repair. Mutat Res 2012; 752:45-60. [PMID: 23085398 DOI: 10.1016/j.mrrev.2012.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 10/08/2012] [Accepted: 10/09/2012] [Indexed: 12/19/2022]
Abstract
To counteract the adverse effects of various DNA lesions, cells have evolved an array of diverse repair pathways to restore DNA structure and to coordinate repair with cell cycle regulation. Chromatin changes are an integral part of the DNA damage response, particularly with regard to the types of repair that involve assembly of large multiprotein complexes such as those involved in double strand break (DSB) repair and nucleotide excision repair (NER). A number of phosphorylation, acetylation, methylation, ubiquitylation and chromatin remodeling events modulate chromatin structure at the lesion site. These changes demarcate chromatin neighboring the lesion, afford accessibility and binding surfaces to repair factors and provide on-the-spot means to coordinate repair and damage signaling. Thus, the hierarchical assembly of repair factors at a double strand break is mostly due to their regulated interactions with posttranslational modifications of histones. A large number of chromatin remodelers are required at different stages of DSB repair and NER. Remodelers physically interact with proteins involved in repair processes, suggesting that chromatin remodeling is a requisite for repair factors to access the damaged site. Together, recent findings define the roles of histone post-translational modifications and chromatin remodeling in the DNA damage response and underscore possible differences in the requirements for these events in relation to the chromatin context.
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Affiliation(s)
- Anastas Gospodinov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. 21, 1113 Sofia, Bulgaria
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France.
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91
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Friedl AA, Mazurek B, Seiler DM. Radiation-induced alterations in histone modification patterns and their potential impact on short-term radiation effects. Front Oncol 2012; 2:117. [PMID: 23050241 PMCID: PMC3445916 DOI: 10.3389/fonc.2012.00117] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 08/28/2012] [Indexed: 12/12/2022] Open
Abstract
Detection and repair of radiation-induced DNA damage occur in the context of chromatin. An intricate network of mechanisms defines chromatin structure, including DNA methylation, incorporation of histone variants, histone modifications, and chromatin remodeling. In the last years it became clear that the cellular response to radiation-induced DNA damage involves all of these mechanisms. Here we focus on the current knowledge on radiation-induced alterations in post-translational histone modification patterns and their effect on the chromatin accessibility, transcriptional regulation and chromosomal stability.
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Affiliation(s)
- Anna A Friedl
- Department of Radiation Oncology, Ludwig-Maximilians-University Munich, Germany
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92
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Fuchs G, Shema E, Vesterman R, Kotler E, Wolchinsky Z, Wilder S, Golomb L, Pribluda A, Zhang F, Haj-Yahya M, Feldmesser E, Brik A, Yu X, Hanna J, Aberdam D, Domany E, Oren M. RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation. Mol Cell 2012; 46:662-73. [PMID: 22681888 DOI: 10.1016/j.molcel.2012.05.023] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 03/06/2012] [Accepted: 05/17/2012] [Indexed: 11/17/2022]
Abstract
Embryonic stem cells (ESCs) maintain high genomic plasticity, which is essential for their capacity to enter diverse differentiation pathways. Posttranscriptional modifications of chromatin histones play a pivotal role in maintaining this plasticity. We now report that one such modification, monoubiquitylation of histone H2B on lysine 120 (H2Bub1), catalyzed by the E3 ligase RNF20, increases during ESC differentiation and is required for efficient execution of this process. This increase is particularly important for the transcriptional induction of relatively long genes during ESC differentiation. Furthermore, we identify the deubiquitinase USP44 as a negative regulator of H2B ubiquitylation, whose downregulation during ESC differentiation contributes to the increase in H2Bub1. Our findings suggest that optimal ESC differentiation requires dynamic changes in H2B ubiquitylation patterns, which must occur in a timely and well-coordinated manner.
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Affiliation(s)
- Gilad Fuchs
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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93
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Chernikova SB, Brown JM. R-loops and genomic instability in Bre1 (RNF20/40)-deficient cells. Cell Cycle 2012; 11:2980-4. [PMID: 22825248 DOI: 10.4161/cc.21090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have proposed that maintenance of genomic stability may constitute the basis for the tumor-suppressing activity of the Bre1 (RNF20/RNF40) complex. Revisiting the evidence we presented in our recent publication, we discuss the mechanism by which maintenance of genomic stability by the Bre1 complex is achieved through coordination of events during transcription. Among many functions of Bre1, we focus on the two that, when defective, could lead to the formation of R-loops, the RNA:DNA hybrid structures regarded as a major source of genomic instability. Specifically, we discuss the role of Bre1-mediated H2B ubiquitination in the 3'-end processing of replication-associated histone mRNA and in heterochromatic gene silencing and show how disturbance of these two functions may result in the specific pattern of chromosomal abnormalities we observe in the Bre1-depleted cells.
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94
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R loops: from transcription byproducts to threats to genome stability. Mol Cell 2012; 46:115-24. [PMID: 22541554 DOI: 10.1016/j.molcel.2012.04.009] [Citation(s) in RCA: 717] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/03/2012] [Accepted: 04/06/2012] [Indexed: 12/17/2022]
Abstract
RNA:DNA hybrid structures known as R loops were thought to be rare byproducts of transcription. In the last decade, however, accumulating evidence has pointed to a new view in which R loops form more frequently, impacting transcription and threatening genome integrity as a source of chromosome fragility and a potential cause of disease. Not surprisingly, cells have evolved mechanisms to prevent cotranscriptional R loop formation. Here we discuss the factors and cellular processes that control R loop formation and the mechanisms by which R loops may influence gene expression and the integrity of the genome.
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95
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Johnsen SA. The enigmatic role of H2Bub1 in cancer. FEBS Lett 2012; 586:1592-601. [PMID: 22564770 DOI: 10.1016/j.febslet.2012.04.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 04/02/2012] [Accepted: 04/03/2012] [Indexed: 12/19/2022]
Abstract
The post-translational modification of histone proteins plays an important role in controlling cell fate by directing essentially all DNA-associated nuclear processes. Misregulation and mutation of histone modifying enzymes is a hallmark of tumorigenesis. However, how these different epigenetic modifications lead to tumor initiation and/or progression remains poorly understood. Recent studies have uncovered a potential tumor suppressor role for histone H2B monoubiquitination (H2Bub1). Like many other histone modifications, H2Bub1 has diverse functions and plays roles both in transcriptional activation and repression as well as in controlling mRNA processing and directing DNA repair processes. Notably, H2Bub1 has been linked to transcriptional elongation and is preferentially found in the transcribed region of active genes. Its activity is intimately connected to active transcription and the transcriptional elongation regulatory protein cyclin-dependent kinase-9 (CDK9) and the facilitates chromatin transcription (FACT) complex. This review provides an overview of the current understanding of H2Bub1 function in mammalian systems with a particular emphasis on its role in cancer and potential options for exploiting this knowledge for the treatment of cancer.
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Affiliation(s)
- Steven A Johnsen
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.
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