51
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Wu PS, Enervald E, Joelsson A, Palmberg C, Rutishauser D, Hällberg BM, Ström L. Post-translational Regulation of DNA Polymerase η, a Connection to Damage-Induced Cohesion in Saccharomyces cerevisiae. Genetics 2020; 216:1009-1022. [PMID: 33033113 PMCID: PMC7768261 DOI: 10.1534/genetics.120.303494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Double-strand breaks that are induced postreplication trigger establishment of damage-induced cohesion in Saccharomyces cerevisiae, locally at the break site and genome-wide on undamaged chromosomes. The translesion synthesis polymerase, polymerase η, is required for generation of damage-induced cohesion genome-wide. However, its precise role and regulation in this process is unclear. Here, we investigated the possibility that the cyclin-dependent kinase Cdc28 and the acetyltransferase Eco1 modulate polymerase η activity. Through in vitro phosphorylation and structure modeling, we showed that polymerase η is an attractive substrate for Cdc28 Mutation of the putative Cdc28-phosphorylation site Ser14 to Ala not only affected polymerase η protein level, but also prevented generation of damage-induced cohesion in vivo We also demonstrated that Eco1 acetylated polymerase η in vitro Certain nonacetylatable polymerase η mutants showed reduced protein level, deficient nuclear accumulation, and increased ultraviolet irradiation sensitivity. In addition, we found that both Eco1 and subunits of the cohesin network are required for cell survival after ultraviolet irradiation. Our findings support functionally important Cdc28-mediated phosphorylation, as well as post-translational modifications of multiple lysine residues that modulate polymerase η activity, and provide new insights into understanding the regulation of polymerase η for damage-induced cohesion.
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Affiliation(s)
- Pei-Shang Wu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Elin Enervald
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Angelica Joelsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Carina Palmberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Dorothea Rutishauser
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Lena Ström
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
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52
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Sabbatino F, Liguori L, Malapelle U, Schiavi F, Tortora V, Conti V, Filippelli A, Tortora G, Ferrone CR, Pepe S. Case Report: BAP1 Mutation and RAD21 Amplification as Predictive Biomarkers to PARP Inhibitor in Metastatic Intrahepatic Cholangiocarcinoma. Front Oncol 2020; 10:567289. [PMID: 33330039 PMCID: PMC7728995 DOI: 10.3389/fonc.2020.567289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction Intrahepatic cholangiocarcinoma (ICC) is a rare hepatobiliary cancer characterized by a poor prognosis and a limited response to conventional therapies. Currently chemotherapy is the only therapeutic option for patients with Stage IV ICC. Due to the poor response rate, there is an urgent need to identify novel molecular targets to develop novel effective therapies. Precision oncology tests utilizing targeted next-generation sequencing (NGS) platforms have rapidly entered into clinical practice. Profiling the genome and transcriptome of cancer to identify potentially targetable oncogenic pathways may guide the clinical care of the patient. Case presentation We present a 56-year-old male patient affected with metastatic ICC, whose cancer underwent several precision oncology tests by different NGS platforms. A novel BAP1 mutation (splice site c.581-17_585del22) and a RAD21 amplification were identified by a commercial available platform on a metastatic lesion. No germline BAP1 mutations were identified. Several lines of evidences indicate that PARP inhibitor administration might be an effective treatment in presence of BAP1 and/or RAD21 alterations since both BAP1 and RAD21 are involved in the DNA repair pathway, BAP1 interacts with BRCA1 and BRCA1-mediated DNA repair pathway alterations enhance the sensitivity to PARP inhibitor administration. In this case, after failing conventional therapies, patient was treated with PARP inhibitor olaparib. The patient had a partial response according to RECIST criteria with an overall survival of 37.2 months from the time of diagnosis of his ICC. Following 11.0 months on olaparib treatment, sustained stable disease control is ongoing. The patient is still being treated with olaparib and no significant toxicity has been reported. Conclusion These findings have clinical relevance since we have shown PARP inhibitor as a potential treatment for ICC patients harboring BAP1 deletion and RAD21 amplification. We have also highlighted the utility of NGS platforms to identify targetable mutations within a cancer.
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Affiliation(s)
- Francesco Sabbatino
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy.,Oncology Unit, University Hospital San Giovanni di Dio e Ruggi D'Aragona, Salerno, Italy
| | - Luigi Liguori
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, Italy
| | | | - Francesca Schiavi
- Familial Cancer Clinic and Oncoendocrinology, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Vincenzo Tortora
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, Italy
| | - Valeria Conti
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy.,Clinical Pharmacology and Pharmacogenetics Unit, University Hospital "San Giovanni di Dio e Ruggi D'Aragona", Salerno, Italy
| | - Amelia Filippelli
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy.,Clinical Pharmacology and Pharmacogenetics Unit, University Hospital "San Giovanni di Dio e Ruggi D'Aragona", Salerno, Italy
| | - Giampaolo Tortora
- Oncologia Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica Del Sacro Cuore, Roma, Italy
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Stefano Pepe
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy.,Oncology Unit, University Hospital San Giovanni di Dio e Ruggi D'Aragona, Salerno, Italy
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53
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Kurokawa Y, Murayama Y. DNA Binding by the Mis4 Scc2 Loader Promotes Topological DNA Entrapment by the Cohesin Ring. Cell Rep 2020; 33:108357. [PMID: 33176147 DOI: 10.1016/j.celrep.2020.108357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Cohesin, a critical mediator of genome organization including sister chromatid cohesion, is a ring-shaped multi-subunit ATPase that topologically embraces DNA. Its loading and function on chromosomes require the Scc2-Scc4 loader. Using biochemical reconstitution, we show here that the ability of the loader to bind DNA plays a critical role in promoting cohesin loading. Two distinct sites within the Mis4Scc2 subunit are found to cooperatively bind DNA. Mis4Scc2 initially forms a tertiary complex with cohesin on DNA and promotes subsequent topological DNA entrapment by cohesin through its DNA binding activity, a process that requires an additional DNA binding surface provided by Psm3Smc3, the ATPase domain of cohesin. Furthermore, we show that mutations in the two DNA binding sites of Mis4 impair the chromosomal loading of cohesin. These observations demonstrate the physiological importance of DNA binding by the loader and provide mechanistic insights into the process of topological cohesin loading.
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Affiliation(s)
- Yumiko Kurokawa
- Center for Frontier Research, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yasuto Murayama
- Center for Frontier Research, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111, Yata, Mishima, Shizuoka 411-8540, Japan.
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54
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Tao H, Lambert JP, Yung TM, Zhu M, Hahn NA, Li D, Lau K, Sturgeon K, Puviindran V, Zhang X, Gong W, Chen XX, Anderson G, Garry DJ, Henkelman RM, Sun Y, Iulianella A, Kawakami Y, Gingras AC, Hui CC, Hopyan S. IRX3/5 regulate mitotic chromatid segregation and limb bud shape. Development 2020; 147:dev.180042. [PMID: 32907847 DOI: 10.1242/dev.180042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/25/2020] [Indexed: 01/19/2023]
Abstract
Pattern formation is influenced by transcriptional regulation as well as by morphogenetic mechanisms that shape organ primordia, although factors that link these processes remain under-appreciated. Here we show that, apart from their established transcriptional roles in pattern formation, IRX3/5 help to shape the limb bud primordium by promoting the separation and intercalation of dividing mesodermal cells. Surprisingly, IRX3/5 are required for appropriate cell cycle progression and chromatid segregation during mitosis, possibly in a nontranscriptional manner. IRX3/5 associate with, promote the abundance of, and share overlapping functions with co-regulators of cell division such as the cohesin subunits SMC1, SMC3, NIPBL and CUX1. The findings imply that IRX3/5 coordinate early limb bud morphogenesis with skeletal pattern formation.
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Affiliation(s)
- Hirotaka Tao
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Theodora M Yung
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Min Zhu
- Department of Mechanical and Industrial Engineering, University of Toronto, ON M5S 3G8, Canada
| | - Noah A Hahn
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Danyi Li
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kimberly Lau
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kendra Sturgeon
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Vijitha Puviindran
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Xiaoyun Zhang
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Wuming Gong
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiao Xiao Chen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory Anderson
- Mouse Imaging Centre, Hospital for Sick Children, Toronto Centre for Phenogenomics, Department of Medical Biophysics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto Centre for Phenogenomics, Department of Medical Biophysics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, University of Toronto, ON M5S 3G8, Canada
| | - Angelo Iulianella
- Department of Medical Neuroscience, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sevan Hopyan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Division of Orthopaedic Surgery, Hospital for Sick Children and University of Toronto, Toronto M5G 1X8, Canada
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55
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Muñoz S, Passarelli F, Uhlmann F. Conserved roles of chromatin remodellers in cohesin loading onto chromatin. Curr Genet 2020; 66:951-956. [PMID: 32277274 PMCID: PMC7497338 DOI: 10.1007/s00294-020-01075-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 12/23/2022]
Abstract
Cohesin is a conserved, ring-shaped protein complex that topologically entraps DNA. This ability makes this member of the structural maintenance of chromosomes (SMC) complex family a central hub of chromosome dynamics regulation. Besides its essential role in sister chromatid cohesion, cohesin shapes the interphase chromatin domain architecture and plays important roles in transcriptional regulation and DNA repair. Cohesin is loaded onto chromosomes at centromeres, at the promoters of highly expressed genes, as well as at DNA replication forks and sites of DNA damage. However, the features that determine these binding sites are still incompletely understood. We recently described a role of the budding yeast RSC chromatin remodeler in cohesin loading onto chromosomes. RSC has a dual function, both as a physical chromatin receptor of the Scc2/Scc4 cohesin loader complex, as well as by providing a nucleosome-free template for cohesin loading. Here, we show that the role of RSC in sister chromatid cohesion is conserved in fission yeast. We discuss what is known about the broader conservation of the contribution of chromatin remodelers to cohesin loading onto chromatin.
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Affiliation(s)
- Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
| | | | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
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56
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Abstract
Mutations of the cohesin complex in human cancer were first discovered ~10 years ago. Since then, researchers worldwide have demonstrated that cohesin is among the most commonly mutated protein complexes in cancer. Inactivating mutations in genes encoding cohesin subunits are common in bladder cancers, paediatric sarcomas, leukaemias, brain tumours and other cancer types. Also in those 10 years, the prevailing view of the functions of cohesin in cell biology has undergone a revolutionary transformation. Initially, the predominant view of cohesin was as a ring that encircled and cohered replicated chromosomes until its cleavage triggered the metaphase-to-anaphase transition. As such, early studies focused on the role of tumour-derived cohesin mutations in the fidelity of chromosome segregation and aneuploidy. However, over the past 5 years the cohesin field has shifted dramatically, and research now focuses on the primary role of cohesin in generating, maintaining and regulating the intra-chromosomal DNA looping events that modulate 3D genome organization and gene expression. This Review focuses on recent discoveries in the cohesin field that provide insight into the role of cohesin inactivation in cancer pathogenesis, and opportunities for exploiting these findings for the clinical benefit of patients with cohesin-mutant cancers.
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Affiliation(s)
- Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC, USA.
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57
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Shi D, Zhao S, Zuo MQ, Zhang J, Hou W, Dong MQ, Cao Q, Lou H. The acetyltransferase Eco1 elicits cohesin dimerization during S phase. J Biol Chem 2020; 295:7554-7565. [PMID: 32312753 PMCID: PMC7261783 DOI: 10.1074/jbc.ra120.013102] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/09/2020] [Indexed: 01/26/2023] Open
Abstract
Cohesin is a DNA-associated protein complex that forms a tripartite ring controlling sister chromatid cohesion, chromosome segregation and organization, DNA replication, and gene expression. Sister chromatid cohesion is established by the protein acetyltransferase Eco1, which acetylates two conserved lysine residues on the cohesin subunit Smc3 and thereby ensures correct chromatid separation in yeast (Saccharomyces cerevisiae) and other eukaryotes. However, the consequence of Eco1-catalyzed cohesin acetylation is unknown, and the exact nature of the cohesive state of chromatids remains controversial. Here, we show that self-interactions of the cohesin subunits Scc1/Rad21 and Scc3 occur in a DNA replication-coupled manner in both yeast and human cells. Using cross-linking MS-based and in vivo disulfide cross-linking analyses of purified cohesin, we show that a subpopulation of cohesin may exist as dimers. Importantly, upon temperature-sensitive and auxin-induced degron-mediated Eco1 depletion, the cohesin-cohesin interactions became significantly compromised, whereas deleting either the deacetylase Hos1 or the Eco1 antagonist Wpl1/Rad61 increased cohesin dimer levels by ∼20%. These results indicate that cohesin dimerizes in the S phase and monomerizes in mitosis, processes that are controlled by Eco1, Wpl1, and Hos1 in the sister chromatid cohesion-dissolution cycle. These findings suggest that cohesin dimerization is controlled by the cohesion cycle and support the notion that a double-ring cohesin model operates in sister chromatid cohesion.
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Affiliation(s)
- Di Shi
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Shuaijun Zhao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Mei-Qing Zuo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jingjing Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Wenya Hou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No. 2 Yuan-Ming-Yuan West Road, Beijing 100193, China
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58
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Liu HW, Bouchoux C, Panarotto M, Kakui Y, Patel H, Uhlmann F. Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment. Mol Cell 2020; 78:725-738.e4. [PMID: 32277910 PMCID: PMC7242910 DOI: 10.1016/j.molcel.2020.03.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/17/2019] [Accepted: 03/10/2020] [Indexed: 01/26/2023]
Abstract
Concomitant with DNA replication, the chromosomal cohesin complex establishes cohesion between newly replicated sister chromatids. Several replication-fork-associated "cohesion establishment factors," including the multifunctional Ctf18-RFC complex, aid this process in as yet unknown ways. Here, we show that Ctf18-RFC's role in sister chromatid cohesion correlates with PCNA loading but is separable from its role in the replication checkpoint. Ctf18-RFC loads PCNA with a slight preference for the leading strand, which is dispensable for DNA replication. Conversely, the canonical Rfc1-RFC complex preferentially loads PCNA onto the lagging strand, which is crucial for DNA replication but dispensable for sister chromatid cohesion. The downstream effector of Ctf18-RFC is cohesin acetylation, which we place toward a late step during replication maturation. Our results suggest that Ctf18-RFC enriches and balances PCNA levels at the replication fork, beyond the needs of DNA replication, to promote establishment of sister chromatid cohesion and possibly other post-replicative processes.
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Affiliation(s)
- Hon Wing Liu
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mélanie Panarotto
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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59
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Silva MC, Powell S, Ladstätter S, Gassler J, Stocsits R, Tedeschi A, Peters JM, Tachibana K. Wapl releases Scc1-cohesin and regulates chromosome structure and segregation in mouse oocytes. J Cell Biol 2020; 219:e201906100. [PMID: 32328639 PMCID: PMC7147110 DOI: 10.1083/jcb.201906100] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 11/22/2019] [Accepted: 02/10/2020] [Indexed: 12/21/2022] Open
Abstract
Cohesin is essential for genome folding and inheritance. In somatic cells, these functions are both mediated by Scc1-cohesin, which in mitosis is released from chromosomes by Wapl and separase. In mammalian oocytes, cohesion is mediated by Rec8-cohesin. Scc1 is expressed but neither required nor sufficient for cohesion, and its function remains unknown. Likewise, it is unknown whether Wapl regulates one or both cohesin complexes and chromosome segregation in mature oocytes. Here, we show that Wapl is required for accurate meiosis I chromosome segregation, predominantly releases Scc1-cohesin from chromosomes, and promotes production of euploid eggs. Using single-nucleus Hi-C, we found that Scc1 is essential for chromosome organization in oocytes. Increasing Scc1 residence time on chromosomes by Wapl depletion leads to vermicelli formation and intra-loop structures but, unlike in somatic cells, does not increase loop size. We conclude that distinct cohesin complexes generate loops and cohesion in oocytes and propose that the same principle applies to all cell types and species.
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Affiliation(s)
- Mariana C.C. Silva
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Sean Powell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Sabrina Ladstätter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Johanna Gassler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Roman Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Antonio Tedeschi
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Kikuë Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Department of Totipotency, Max Planck Institute of Biochemistry, Martinsried, Germany
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60
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Eksi SE, Saldivar JC. Cohesin Is Out for Stalled Replication Fork Restart. Dev Cell 2020; 52:675-676. [PMID: 32208158 DOI: 10.1016/j.devcel.2020.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Replication stress underlies many genomic alterations in cancer cells. In this issue of Developmental Cell, Benedict et al. show that WAPL-dependent cohesin removal is needed to restart DNA synthesis at stalled forks and promote survival following replication stress, uncovering an unexpected link between stress and sister chromatid cohesion loss.
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Affiliation(s)
- Sebnem Ece Eksi
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Joshua C Saldivar
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA.
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61
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Benedict B, van Schie JJM, Oostra AB, Balk JA, Wolthuis RMF, Riele HT, de Lange J. WAPL-Dependent Repair of Damaged DNA Replication Forks Underlies Oncogene-Induced Loss of Sister Chromatid Cohesion. Dev Cell 2020; 52:683-698.e7. [PMID: 32084359 DOI: 10.1016/j.devcel.2020.01.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/19/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
Premature loss of sister chromatid cohesion at metaphase is a diagnostic marker for different cohesinopathies. Here, we report that metaphase spreads of many cancer cell lines also show premature loss of sister chromatid cohesion. Cohesion loss occurs independently of mutations in cohesion factors including SA2, a cohesin subunit frequently inactivated in cancer. In untransformed cells, induction of DNA replication stress by activation of oncogenes or inhibition of DNA replication is sufficient to trigger sister chromatid cohesion loss. Importantly, cell growth under conditions of replication stress requires the cohesin remover WAPL. WAPL promotes rapid RAD51-dependent repair and restart of broken replication forks. We propose that active removal of cohesin allows cancer cells to overcome DNA replication stress. This leads to oncogene-induced cohesion loss from newly synthesized sister chromatids that may contribute to genomic instability and likely represents a targetable cancer cell vulnerability.
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Affiliation(s)
- Bente Benedict
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, the Netherlands
| | - Janne J M van Schie
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Anneke B Oostra
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jesper A Balk
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Rob M F Wolthuis
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
| | - Hein Te Riele
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, the Netherlands.
| | - Job de Lange
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
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62
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Lafta IJ, Kudhair BK, Alabid NN. Characterization of the major human STAG3 variants using some proteomics and bioinformatics assays. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-0051-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract
Background
STAG3 is the meiotic component of cohesin and a member of the Cancer Testis Antigen (CTA) family. This gene has been found to be overexpressed in many types of cancer, and recently, its variants have been implicated in other disorders and many human diseases. Therefore, this study aimed to analyze the major variants of STAG3. Western blot (WB) and immunoprecipitation (IP) assays were performed using two different anti-STAG3 antibodies that targeted the relevant protein in MCF-7, T-47D, MDA-MB-468, and MDA-MB-231 breast cancer cells with Jurkat and MCF-10A cells as positive and negative controls, respectively. In silico analyses were searched to study the major isoforms.
Results
WB and IP assays revealed two abundant polypeptides < 191 kDa and ~ 75 kDa in size. Specific bioinformatics tools successfully determined the three-dimensional (3-D) structure, the subcellular localization, and the secondary structures of the isoforms. Furthermore, some of the physicochemical properties of the STAG3 proteins were also determined.
Conclusions
The results of this study revealed the power of applying the biological techniques (WB and IP) with the bioinformatics assays and the possibility of their exploitation in understanding diseased genes. Exploring the major variants of STAG3 at the protein level could help decipher some disorders associated with their occurrence, along with designing drugs effective at least for some relevant diseases.
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Abstract
Effective maintenance and stability of our genomes is essential for normal cell division, tissue homeostasis, and cellular and organismal fitness. The processes of chromosome replication and segregation require continual surveillance to insure fidelity. Accurate and efficient repair of DNA damage preserves genome integrity, which if lost can lead to multiple diseases, including cancer. Poly(ADP-ribose) a dynamic and reversible posttranslational modification and the enzymes that catalyze it (PARP1, PARP2, tankyrase 1, and tankyrase 2) function to maintain genome stability through diverse mechanisms. Here we review the role of these enzymes and the modification in genome repair, replication, and resolution in human cells.
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Affiliation(s)
- Kameron Azarm
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
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64
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Eisemann T, Pascal JM. Poly(ADP-ribose) polymerase enzymes and the maintenance of genome integrity. Cell Mol Life Sci 2020; 77:19-33. [PMID: 31754726 PMCID: PMC11104942 DOI: 10.1007/s00018-019-03366-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 01/15/2023]
Abstract
DNA damage response (DDR) relies on swift and accurate signaling to rapidly identify DNA lesions and initiate repair. A critical DDR signaling and regulatory molecule is the posttranslational modification poly(ADP-ribose) (PAR). PAR is synthesized by a family of structurally and functionally diverse proteins called poly(ADP-ribose) polymerases (PARPs). Although PARPs share a conserved catalytic domain, unique regulatory domains of individual family members endow PARPs with unique properties and cellular functions. Family members PARP-1, PARP-2, and PARP-3 (DDR-PARPs) are catalytically activated in the presence of damaged DNA and act as damage sensors. Family members tankyrase-1 and closely related tankyrase-2 possess SAM and ankyrin repeat domains that regulate their diverse cellular functions. Recent studies have shown that the tankyrases share some overlapping functions with the DDR-PARPs, and even perform novel functions that help preserve genomic integrity. In this review, we briefly touch on DDR-PARP functions, and focus on the emerging roles of tankyrases in genome maintenance. Preservation of genomic integrity thus appears to be a common function of several PARP family members, depicting PAR as a multifaceted guardian of the genome.
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Affiliation(s)
- Travis Eisemann
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada.
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65
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Lee J. Is age-related increase of chromosome segregation errors in mammalian oocytes caused by cohesin deterioration? Reprod Med Biol 2020; 19:32-41. [PMID: 31956283 PMCID: PMC6955592 DOI: 10.1002/rmb2.12299] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mammalian oocytes initiate meiosis in fetal ovary and are arrested at dictyate stage in prophase I for a long period. It is known that incidence of chromosome segregation errors in oocytes increases with advancing age, but the molecular mechanism underlying this phenomenon has not been clarified. METHODS Cohesin, a multi-subunit protein complex, mediates sister chromatid cohesion in both mitosis and meiosis. In this review, molecular basis of meiotic chromosome cohesion and segregation is summarized. Further, the relationship between chromosome segregation errors and cohesin deterioration in aged oocytes is discussed. RESULTS Recent studies show that chromosome-associated cohesin decreases in an age-dependent manner in mouse oocytes. Furthermore, conditional knockout or activation of cohesin in oocytes indicates that only the cohesin expressed before premeiotic S phase can establish and maintain sister chromatic cohesion and that cohesin does not turnover during the dictyate arrest. CONCLUSION In mice, the accumulating evidence suggests that deterioration of cohesin due to the lack of turnover during dictyate arrest is one of the major causes of chromosome segregation errors in aged oocytes. However, whether the same is true in human remains elusive since even the deterioration of cohesin during dictyate arrest has not been demonstrated in human oocytes.
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Affiliation(s)
- Jibak Lee
- Laboratory of Developmental BiotechnologyGraduate School of Agricultural ScienceKobe UniversityKobeJapan
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66
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Keyamura K, Hishida T. Topological DNA-binding of structural maintenance of chromosomes-like RecN promotes DNA double-strand break repair in Escherichia coli. Commun Biol 2019; 2:413. [PMID: 31754643 PMCID: PMC6856136 DOI: 10.1038/s42003-019-0655-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/16/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial RecN, closely related to the structural maintenance of chromosomes (SMC) family of proteins, functions in the repair of DNA double-strand breaks (DSBs) by homologous recombination. Here we show that the purified Escherichia coli RecN protein topologically loads onto both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) that has a preference for ssDNA. RecN topologically bound to dsDNA slides off the end of linear dsDNA, but this is prevented by RecA nucleoprotein filaments on ssDNA, thereby allowing RecN to translocate to DSBs. Furthermore, we found that, once RecN is recruited onto ssDNA, it can topologically capture a second dsDNA substrate in an ATP-dependent manner, suggesting a role in synapsis. Indeed, RecN stimulates RecA-mediated D-loop formation and subsequent strand exchange activities. Our findings provide mechanistic insights into the recruitment of RecN to DSBs and sister chromatid interactions by RecN, both of which function in RecA-mediated DSB repair.
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Affiliation(s)
- Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
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67
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Zhurinsky J, Salas-Pino S, Iglesias-Romero AB, Torres-Mendez A, Knapp B, Flor-Parra I, Wang J, Bao K, Jia S, Chang F, Daga RR. Effects of the microtubule nucleator Mto1 on chromosomal movement, DNA repair, and sister chromatid cohesion in fission yeast. Mol Biol Cell 2019; 30:2695-2708. [PMID: 31483748 PMCID: PMC6761766 DOI: 10.1091/mbc.e19-05-0301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/27/2019] [Accepted: 08/30/2019] [Indexed: 11/11/2022] Open
Abstract
Although the function of microtubules (MTs) in chromosomal segregation during mitosis is well characterized, much less is known about the role of MTs in chromosomal functions during interphase. In the fission yeast Schizosaccharomyces pombe, dynamic cytoplasmic MT bundles move chromosomes in an oscillatory manner during interphase via linkages through the nuclear envelope (NE) at the spindle pole body (SPB) and other sites. Mto1 is a cytoplasmic factor that mediates the nucleation and attachment of cytoplasmic MTs to the nucleus. Here, we test the function of these cytoplasmic MTs and Mto1 on DNA repair and recombination during interphase. We find that mto1Δ cells exhibit defects in DNA repair and homologous recombination (HR) and abnormal DNA repair factory dynamics. In these cells, sister chromatids are not properly paired, and binding of Rad21 cohesin subunit along chromosomal arms is reduced. Our findings suggest a model in which cytoplasmic MTs and Mto1 facilitate efficient DNA repair and HR by promoting dynamic chromosomal organization and cohesion in the nucleus.
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Affiliation(s)
- Jacob Zhurinsky
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Silvia Salas-Pino
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Ana B. Iglesias-Romero
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Antonio Torres-Mendez
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Benjamin Knapp
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | - Ignacio Flor-Parra
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Jiyong Wang
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Kehan Bao
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Songtao Jia
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Fred Chang
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | - Rafael R. Daga
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
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68
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Taheri F, Goudarzi H, Faghihloo E. Aneuploidy and oncoviruses. Rev Med Virol 2019; 29:e2076. [PMID: 31407416 DOI: 10.1002/rmv.2076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/01/2023]
Abstract
Seven oncogenic viruses are known for tumorigenesis and contribute to 12% of all human cancers. The oncogenic factors, the target tissue, and pathology of cancer vary among these viruses with several mechanisms proposed for the initiation and development of cancer. Aneuploidy in cells is associated with anomalies in chromosome number that can be a hallmark of cancer, a disease defined by expanded proliferative potential. In this review, we summarize the different mechanisms of aneuploidy and furthermore discuss recent findings of the role of viral oncoproteins in inducing cellular aneuploidy that might facilitate tumorigenesis. Improved understanding of viral oncogenesis may help to find new strategies for controlling virus-associated cancers.
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Affiliation(s)
- Fateme Taheri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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69
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Tarnopol RL, Bowden S, Hinkle K, Balakrishnan K, Nishii A, Kaczmarek CJ, Pawloski T, Vecchiarelli AG. Lessons from a Minimal Genome: What Are the Essential Organizing Principles of a Cell Built from Scratch? Chembiochem 2019; 20:2535-2545. [DOI: 10.1002/cbic.201900249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Rebecca L. Tarnopol
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI 48109 USA
| | - Sierra Bowden
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI 48109 USA
| | - Kevin Hinkle
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI 48109 USA
| | - Krithika Balakrishnan
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI 48109 USA
| | - Akira Nishii
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI 48109 USA
| | - Caleb J. Kaczmarek
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI 48109 USA
| | - Tara Pawloski
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI 48109 USA
| | - Anthony G. Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI 48109 USA
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70
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Nishiyama T. Cohesion and cohesin-dependent chromatin organization. Curr Opin Cell Biol 2019; 58:8-14. [PMID: 30544080 DOI: 10.1016/j.ceb.2018.11.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 11/29/2018] [Indexed: 02/08/2023]
Abstract
Cohesin, one of structural maintenance of chromosomes (SMC) complexes, forms a ring-shaped protein complex, and mediates sister chromatid cohesion for accurate chromosome segregation and precise genome inheritance. The cohesin ring entraps one or two DNA molecules to achieve cohesion, which is further regulated by cohesin-binding proteins and modification enzymes in a cell cycle-dependent manner. Recent significant advancements in Hi-C technologies have revealed numerous cohesin-dependent higher-order chromatin structures. Simultaneously, single-molecule imaging has also unveiled the detailed dynamics of cohesin on DNA and/or chromatin. Thus, those studies are providing novel visions for the authentic chromatin structure regulated by cohesin.
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Affiliation(s)
- Tomoko Nishiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan.
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71
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Johnston KJA, Adams MJ, Nicholl BI, Ward J, Strawbridge RJ, Ferguson A, McIntosh AM, Bailey MES, Smith DJ. Genome-wide association study of multisite chronic pain in UK Biobank. PLoS Genet 2019; 15:e1008164. [PMID: 31194737 PMCID: PMC6592570 DOI: 10.1371/journal.pgen.1008164] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/25/2019] [Accepted: 04/27/2019] [Indexed: 12/20/2022] Open
Abstract
Chronic pain is highly prevalent worldwide and represents a significant socioeconomic and public health burden. Several aspects of chronic pain, for example back pain and a severity-related phenotype 'chronic pain grade', have been shown previously to be complex heritable traits with a polygenic component. Additional pain-related phenotypes capturing aspects of an individual's overall sensitivity to experiencing and reporting chronic pain have also been suggested as a focus for investigation. We made use of a measure of the number of sites of chronic pain in individuals within the UK general population. This measure, termed Multisite Chronic Pain (MCP), is a complex trait and its genetic architecture has not previously been investigated. To address this, we carried out a large-scale genome-wide association study (GWAS) of MCP in ~380,000 UK Biobank participants. Our findings were consistent with MCP having a significant polygenic component, with a Single Nucleotide Polymorphism (SNP) heritability of 10.2%. In total 76 independent lead SNPs at 39 risk loci were associated with MCP. Additional gene-level association analyses identified neurogenesis, synaptic plasticity, nervous system development, cell-cycle progression and apoptosis genes as enriched for genetic association with MCP. Genetic correlations were observed between MCP and a range of psychiatric, autoimmune and anthropometric traits, including major depressive disorder (MDD), asthma and Body Mass Index (BMI). Furthermore, in Mendelian randomisation (MR) analyses a causal effect of MCP on MDD was observed. Additionally, a polygenic risk score (PRS) for MCP was found to significantly predict chronic widespread pain (pain all over the body), indicating the existence of genetic variants contributing to both of these pain phenotypes. Overall, our findings support the proposition that chronic pain involves a strong nervous system component with implications for our understanding of the physiology of chronic pain. These discoveries may also inform the future development of novel treatment approaches.
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Affiliation(s)
- Keira J. A. Johnston
- Institute of Health and Wellbeing, University of Glasgow, Scotland, United Kingdom
- Deanery of Molecular, Genetic and Population Health Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Scotland, United Kingdom
- School of Life Sciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Mark J. Adams
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Scotland, United Kingdom
| | - Barbara I. Nicholl
- Institute of Health and Wellbeing, University of Glasgow, Scotland, United Kingdom
| | - Joey Ward
- Institute of Health and Wellbeing, University of Glasgow, Scotland, United Kingdom
| | - Rona J. Strawbridge
- Institute of Health and Wellbeing, University of Glasgow, Scotland, United Kingdom
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Amy Ferguson
- Institute of Health and Wellbeing, University of Glasgow, Scotland, United Kingdom
| | - Andrew M. McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Scotland, United Kingdom
| | - Mark E. S. Bailey
- School of Life Sciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Daniel J. Smith
- Institute of Health and Wellbeing, University of Glasgow, Scotland, United Kingdom
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Mintzas K, Heuser M. Emerging strategies to target the dysfunctional cohesin complex in cancer. Expert Opin Ther Targets 2019; 23:525-537. [PMID: 31020869 DOI: 10.1080/14728222.2019.1609943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Mutations in cohesin genes have been described in numerous solid cancers and hematologic malignancies; subsequent experimental evidence has linked these mutations with carcinogenesis. Areas covered: In this review, we present current information about the physiological role of the cohesin complex in normal and malignant cells and describe current therapeutic strategies that are being explored in cohesin-mutated cancers. We discuss a range of targets and strategies that should be explored to develop targeted therapies for patients with aberrant cohesin. Expert opinion: Targeting of the cohesin complex is an underexplored area of drug development. There is a high frequency of cohesin mutations in multiple cancers, hence specific targeting strategies should be explored. Cohesins play a crucial role in cellular organization; therefore, we expect a narrow therapeutic window of direct inhibitors of cohesin components. Exploiting experimental approaches that correct dysfunctional cohesins and coupling them with current therapeutic strategies can provide novel, innovative and more effective treatment regimens.
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Affiliation(s)
- Konstantinos Mintzas
- a Department of Hematology , Oncology, Hemostasis and Stem Cell Transplantation, Hannover Medical School , Hannover , Germany
| | - Michael Heuser
- a Department of Hematology , Oncology, Hemostasis and Stem Cell Transplantation, Hannover Medical School , Hannover , Germany
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73
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Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T. Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. J Biol Chem 2019; 294:8760-8772. [PMID: 31010829 PMCID: PMC6552432 DOI: 10.1074/jbc.ra119.007832] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/18/2019] [Indexed: 12/23/2022] Open
Abstract
The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.
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Affiliation(s)
- Jung-Sik Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Xiaoyuan He
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Jie Liu
- the Department of Genome Sciences
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, and
- Division of Hematology, University of Washington, Seattle, Washington 98195
| | - Taeyeon Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Julia Gerard
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Brian Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Manoj M Pillai
- the Section of Hematology, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, and
| | - William S Lane
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | | | - Bogdan Budnik
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | - Todd Waldman
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057,
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74
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Tong P, Pidoux AL, Toda NRT, Ard R, Berger H, Shukla M, Torres-Garcia J, Müller CA, Nieduszynski CA, Allshire RC. Interspecies conservation of organisation and function between nonhomologous regional centromeres. Nat Commun 2019; 10:2343. [PMID: 31138803 PMCID: PMC6538654 DOI: 10.1038/s41467-019-09824-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 03/27/2019] [Indexed: 01/31/2023] Open
Abstract
Despite the conserved essential function of centromeres, centromeric DNA itself is not conserved. The histone-H3 variant, CENP-A, is the epigenetic mark that specifies centromere identity. Paradoxically, CENP-A normally assembles on particular sequences at specific genomic locations. To gain insight into the specification of complex centromeres, here we take an evolutionary approach, fully assembling genomes and centromeres of related fission yeasts. Centromere domain organization, but not sequence, is conserved between Schizosaccharomyces pombe, S. octosporus and S. cryophilus with a central CENP-ACnp1 domain flanked by heterochromatic outer-repeat regions. Conserved syntenic clusters of tRNA genes and 5S rRNA genes occur across the centromeres of S. octosporus and S. cryophilus, suggesting conserved function. Interestingly, nonhomologous centromere central-core sequences from S. octosporus and S. cryophilus are recognized in S. pombe, resulting in cross-species establishment of CENP-ACnp1 chromatin and functional kinetochores. Therefore, despite the lack of sequence conservation, Schizosaccharomyces centromere DNA possesses intrinsic conserved properties that promote assembly of CENP-A chromatin.
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Affiliation(s)
- Pin Tong
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
| | - Alison L. Pidoux
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
| | - Nicholas R. T. Toda
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK ,0000 0001 2203 0006grid.464101.6Present Address: UPMC CNRS, Roscoff Marine Station, Place Georges Teissier, 29680 Roscoff, France
| | - Ryan Ard
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK ,0000 0001 0674 042Xgrid.5254.6Present Address: Copenhagen Plant Science Centre, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Harald Berger
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK ,0000 0001 2298 5320grid.5173.0Present Address: Symbiocyte, Universität für Bodenkultur Wien, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Manu Shukla
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
| | - Jesus Torres-Garcia
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
| | - Carolin A. Müller
- 0000 0004 1936 8948grid.4991.5Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE UK
| | - Conrad A. Nieduszynski
- 0000 0004 1936 8948grid.4991.5Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE UK
| | - Robin C. Allshire
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
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75
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Muñoz S, Minamino M, Casas-Delucchi CS, Patel H, Uhlmann F. A Role for Chromatin Remodeling in Cohesin Loading onto Chromosomes. Mol Cell 2019; 74:664-673.e5. [PMID: 30922844 PMCID: PMC6527865 DOI: 10.1016/j.molcel.2019.02.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/14/2019] [Accepted: 02/15/2019] [Indexed: 12/18/2022]
Abstract
Cohesin is a conserved, ring-shaped protein complex that topologically embraces DNA. Its central role in genome organization includes functions in sister chromatid cohesion, DNA repair, and transcriptional regulation. Cohesin loading onto chromosomes requires the Scc2-Scc4 cohesin loader, whose presence on chromatin in budding yeast depends on the RSC chromatin remodeling complex. Here we reveal a dual role of RSC in cohesin loading. RSC acts as a chromatin receptor that recruits Scc2-Scc4 by a direct protein interaction independent of chromatin remodeling. In addition, chromatin remodeling is required to generate a nucleosome-free region that is the substrate for cohesin loading. An engineered cohesin loading module can be created by fusing the Scc2 C terminus to RSC or to other chromatin remodelers, but not to unrelated DNA binding proteins. These observations demonstrate the importance of nucleosome-free DNA for cohesin loading and provide insight into how cohesin accesses DNA during its varied chromosomal activities.
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Affiliation(s)
- Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Masashi Minamino
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Corella S Casas-Delucchi
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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76
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Perkins AT, Greig MM, Sontakke AA, Peloquin AS, McPeek MA, Bickel SE. Increased levels of superoxide dismutase suppress meiotic segregation errors in aging oocytes. Chromosoma 2019; 128:215-222. [PMID: 31037468 PMCID: PMC6823651 DOI: 10.1007/s00412-019-00702-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/04/2019] [Accepted: 03/25/2019] [Indexed: 12/19/2022]
Abstract
The risk of meiotic segregation errors increases dramatically during a woman’s thirties, a phenomenon known as the maternal age effect. In addition, several lines of evidence indicate that meiotic cohesion deteriorates as oocytes age. One mechanism that may contribute to age-induced loss of cohesion is oxidative damage. In support of this model, we recently reported (Perkins et al. in Proc Natl Acad Sci U S A 113(44):E6823–E6830, 2016) that the knockdown of the reactive oxygen species (ROS)–scavenging enzyme, superoxide dismutase (SOD), during meiotic prophase causes premature loss of arm cohesion and segregation errors in Drosophila oocytes. If age-dependent oxidative damage causes meiotic segregation errors, then the expression of extra SOD1 (cytosolic/nuclear) or SOD2 (mitochondrial) in oocytes may attenuate this effect. To test this hypothesis, we generated flies that contain a UAS-controlled EMPTY, SOD1, or SOD2 cassette and induced expression using a Gal4 driver that turns on during meiotic prophase. We then compared the fidelity of chromosome segregation in aged and non-aged Drosophila oocytes for all three genotypes. As expected, p{EMPTY} oocytes subjected to aging exhibited a significant increase in nondisjunction (NDJ) compared with non-aged oocytes. In contrast, the magnitude of age-dependent NDJ was significantly reduced when expression of extra SOD1 or SOD2 was induced during prophase. Our findings support the hypothesis that a major factor underlying the maternal age effect in humans is age-induced oxidative damage that results in premature loss of meiotic cohesion. Moreover, our work raises the exciting possibility that antioxidant supplementation may provide a preventative strategy to reduce the risk of meiotic segregation errors in older women.
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Affiliation(s)
- Adrienne T Perkins
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA.,Intermountain Healthcare Precision Genomics, 600 S. Medical Center Drive, St. George, UT, 84770, USA
| | - Miranda M Greig
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Amrita A Sontakke
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Andrew S Peloquin
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Mark A McPeek
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Sharon E Bickel
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA.
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77
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Braccioli L, de Wit E. CTCF: a Swiss-army knife for genome organization and transcription regulation. Essays Biochem 2019; 63:157-165. [PMID: 30940740 DOI: 10.1042/ebc20180069] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
Abstract
Orchestrating vertebrate genomes require a complex interplay between the linear composition of the genome and its 3D organization inside the nucleus. This requires the function of specialized proteins, able to tune various aspects of genome organization and gene regulation. The CCCTC-binding factor (CTCF) is a DNA binding factor capable of regulating not only the 3D genome organization, but also key aspects of gene expression, including transcription activation and repression, RNA splicing, and enhancer/promoter insulation. A growing body of evidence proposes that CTCF, together with cohesin contributes to DNA loop formation and 3D genome organization. CTCF binding sites are mutation hotspots in cancer, while mutations in CTCF itself lead to intellectual disabilities, emphasizing its importance in disease etiology. In this review we cover various aspects of CTCF function, revealing the polyvalence of this factor as a highly diversified tool for vertebrate genome organization and transcription regulation.
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Affiliation(s)
- Luca Braccioli
- Oncode Institute and Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Elzo de Wit
- Oncode Institute and Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
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78
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Liang C, Zhang Z, Chen Q, Yan H, Zhang M, Xiang X, Yi Q, Pan X, Cheng H, Wang F. A positive feedback mechanism ensures proper assembly of the functional inner centromere during mitosis in human cells. J Biol Chem 2019; 294:1437-1450. [PMID: 30498087 PMCID: PMC6364785 DOI: 10.1074/jbc.ra118.006046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/27/2018] [Indexed: 01/25/2023] Open
Abstract
The inner centromere region of a mitotic chromosome critically regulates sister chromatid cohesion and kinetochore-microtubule attachments. However, the molecular mechanism underlying inner centromere assembly remains elusive. Here, using CRISPR/Cas9-based gene editing in HeLa cells, we disrupted the interaction of Shugoshin 1 (Sgo1) with histone H2A phosphorylated on Thr-120 (H2ApT120) to selectively release Sgo1 from mitotic centromeres. Interestingly, cells expressing the H2ApT120-binding defective mutant of Sgo1 have an elevated rate of chromosome missegregation accompanied by weakened centromeric cohesion and decreased centromere accumulation of the chromosomal passenger complex (CPC), an integral part of the inner centromere and a key player in the correction of erroneous kinetochore-microtubule attachments. When artificially tethered to centromeres, a Sgo1 mutant defective in binding protein phosphatase 2A (PP2A) is not able to support proper centromeric cohesion and CPC accumulation, indicating that the Sgo1-PP2A interaction is essential for the integrity of mitotic centromeres. We further provide evidence indicating that Sgo1 protects centromeric cohesin to create a binding site for the histone H3-associated protein kinase Haspin, which not only inhibits the cohesin release factor Wapl and thereby strengthens centromeric cohesion but also phosphorylates histone H3 at Thr-3 to position CPC at inner centromeres. Taken together, our findings reveal a positive feedback-based mechanism that ensures proper assembly of the functional inner centromere during mitosis. They further suggest a causal link between centromeric cohesion defects and chromosomal instability in cancer cells.
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Affiliation(s)
- Cai Liang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhenlei Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qinfu Chen
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Haiyan Yan
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Miao Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xingfeng Xiang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qi Yi
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuan Pan
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Hankun Cheng
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Fangwei Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
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79
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Warmerdam DO, Wolthuis RMF. Keeping ribosomal DNA intact: a repeating challenge. Chromosome Res 2018; 27:57-72. [PMID: 30556094 PMCID: PMC6394564 DOI: 10.1007/s10577-018-9594-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/20/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
More than half of the human genome consists of repetitive sequences, with the ribosomal DNA (rDNA) representing two of the largest repeats. Repetitive rDNA sequences may form a threat to genomic integrity and cellular homeostasis due to the challenging aspects of their transcription, replication, and repair. Predisposition to cancer, premature aging, and neurological impairment in ataxia-telangiectasia and Bloom syndrome, for instance, coincide with increased cellular rDNA repeat instability. However, the mechanisms by which rDNA instability contributes to these hereditary syndromes and tumorigenesis remain unknown. Here, we review how cells govern rDNA stability and how rDNA break repair influences expansion and contraction of repeat length, a process likely associated with human disease. Recent advancements in CRISPR-based genome engineering may help to explain how cells keep their rDNA intact in the near future.
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Affiliation(s)
- Daniël O Warmerdam
- CRISPR Platform, University of Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands.
| | - Rob M F Wolthuis
- Section of Oncogenetics, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, de Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
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80
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Minamino M, Higashi TL, Bouchoux C, Uhlmann F. Topological in vitro loading of the budding yeast cohesin ring onto DNA. Life Sci Alliance 2018; 1. [PMID: 30381802 PMCID: PMC6205631 DOI: 10.26508/lsa.201800143] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The biochemical reconstitution of topological DNA binding by budding yeast cohesin yields surprises and opens opportunities to exploit experimental approaches developed in this model organism. The ring-shaped chromosomal cohesin complex holds sister chromatids together by topological embrace, a prerequisite for accurate chromosome segregation. Cohesin plays additional roles in genome organization, transcriptional regulation, and DNA repair. The cohesin ring includes an ABC family ATPase, but the molecular mechanism by which the ATPase contributes to cohesin function is not yet understood. In this study, we have purified budding yeast cohesin, as well as its Scc2–Scc4 cohesin loader complex, and biochemically reconstituted ATP-dependent topological cohesin loading onto DNA. Our results reproduce previous observations obtained using fission yeast cohesin, thereby establishing conserved aspects of cohesin behavior. Unexpectedly, we find that nonhydrolyzable ATP ground state mimetics ADP·BeF2, ADP·BeF3−, and ADP·AlFx, but not a hydrolysis transition state analog ADP·VO43−, support cohesin loading. The energy from nucleotide binding is sufficient to drive the DNA entry reaction into the cohesin ring. ATP hydrolysis, believed to be essential for in vivo cohesin loading, must serve a subsequent reaction step. These results provide molecular insights into cohesin function and open new experimental opportunities that the budding yeast model affords.
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Affiliation(s)
- Masashi Minamino
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
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81
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Cortone G, Zheng G, Pensieri P, Chiappetta V, Tatè R, Malacaria E, Pichierri P, Yu H, Pisani FM. Interaction of the Warsaw breakage syndrome DNA helicase DDX11 with the replication fork-protection factor Timeless promotes sister chromatid cohesion. PLoS Genet 2018; 14:e1007622. [PMID: 30303954 PMCID: PMC6179184 DOI: 10.1371/journal.pgen.1007622] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022] Open
Abstract
Establishment of sister chromatid cohesion is coupled to DNA replication, but the underlying molecular mechanisms are incompletely understood. DDX11 (also named ChlR1) is a super-family 2 Fe-S cluster-containing DNA helicase implicated in Warsaw breakage syndrome (WABS). Herein, we examined the role of DDX11 in cohesion establishment in human cells. We demonstrated that DDX11 interacts with Timeless, a component of the replication fork-protection complex, through a conserved peptide motif. The DDX11-Timeless interaction is critical for sister chromatid cohesion in interphase and mitosis. Immunofluorescence studies further revealed that cohesin association with chromatin requires DDX11. Finally, we demonstrated that DDX11 localises at nascent DNA by SIRF analysis. Moreover, we found that DDX11 promotes cohesin binding to the DNA replication forks in concert with Timeless and that recombinant purified cohesin interacts with DDX11 in vitro. Collectively, our results establish a critical role for the DDX11-Timeless interaction in coordinating DNA replication with sister chromatid cohesion, and have important implications for understanding the molecular basis of WABS.
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Affiliation(s)
- Giuseppe Cortone
- Istituto di Biochimica delle Proteine, Consiglio Nazionale Ricerche, Naples, Italy
| | - Ge Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Pasquale Pensieri
- Istituto di Biochimica delle Proteine, Consiglio Nazionale Ricerche, Naples, Italy
| | - Viviana Chiappetta
- Istituto di Biochimica delle Proteine, Consiglio Nazionale Ricerche, Naples, Italy
| | - Rosarita Tatè
- Istituto di Genetica e Biofisica "Adriano Buzzati Traverso", Consiglio Nazionale Ricerche, Naples, Italy
| | - Eva Malacaria
- Istituto Superiore di Sanità, Dipartimento Ambiente e Salute, Rome, Italy
| | - Pietro Pichierri
- Istituto Superiore di Sanità, Dipartimento Ambiente e Salute, Rome, Italy
| | - Hongtao Yu
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- * E-mail: (HY); (FMP)
| | - Francesca M. Pisani
- Istituto di Biochimica delle Proteine, Consiglio Nazionale Ricerche, Naples, Italy
- * E-mail: (HY); (FMP)
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82
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Kim MK. Novel insight into the function of tankyrase. Oncol Lett 2018; 16:6895-6902. [PMID: 30546421 PMCID: PMC6256358 DOI: 10.3892/ol.2018.9551] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/31/2018] [Indexed: 01/14/2023] Open
Abstract
Tankyrases are multifunctional poly(ADP-ribose) polymerases that regulate a variety of cellular processes, including Wnt signaling, telomere maintenance and mitosis regulation. Tankyrases interact with target proteins and regulate their interactions and stability through poly(ADP-ribosyl) ation. In addition to their roles in telomere maintenance and regulation of mitosis, tankyrase proteins regulate tumor suppressors, including AXIN, phosphatase and tensin homolog and angiomotin. Therefore, tankyrases may be effective targets for cancer treatment. Tankyrase inhibitors could affect a variety of carcinogenic pathways that promote uncontrolled proliferation, including Wnt, AKT, yes-associated protein, telomere maintenance and mitosis regulation. Recently, novel aspects of the function and mechanism of tankyrases have been reported, and a number of tankyrase inhibitors have been identified. A combination of conventional chemotherapy agents with tankyrase inhibitors may have synergistic anticancer effects. Therefore, it is expected that more advanced and improved tankyrase inhibitors will be developed, enabling novel therapeutic strategies against cancer and other tankyrase-associated diseases. The present review discusses tankyrase function and the role of tankyrase inhibitors in the treatment of cancer.
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Affiliation(s)
- Mi Kyung Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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83
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Villa-Hernández S, Bermejo R. Replisome-Cohesin Interfacing: A Molecular Perspective. Bioessays 2018; 40:e1800109. [PMID: 30106480 DOI: 10.1002/bies.201800109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/23/2018] [Indexed: 12/27/2022]
Abstract
Cohesion is established in S-phase through the action of key replisome factors as replication forks engage cohesin molecules. By holding sister chromatids together, cohesion critically assists both an equal segregation of the duplicated genetic material and an efficient repair of DNA breaks. Nonetheless, the molecular events leading the entrapment of nascent chromatids by cohesin during replication are only beginning to be understood. The authors describe here the essential structural features of the cohesin complex in connection to its ability to associate DNA molecules and review the current knowledge on the architectural-functional organization of the eukaryotic replisome, significantly advanced by recent biochemical and structural studies. In light of this novel insight, the authors discuss the mechanisms proposed to assist interfacing of replisomes with chromatin-bound cohesin complexes and elaborate on models for nascent chromatids entrapment by cohesin in the environment of the replication fork.
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Affiliation(s)
- Sara Villa-Hernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain
| | - Rodrigo Bermejo
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain
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84
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Lelo A, Prip F, Harris BT, Solomon D, Berry DL, Chaldekas K, Kumar A, Simko J, Jensen JB, Bhattacharyya P, Mannion C, Kim JS, Philips G, Dyrskjøt L, Waldman T. STAG2 Is a Biomarker for Prediction of Recurrence and Progression in Papillary Non-Muscle-Invasive Bladder Cancer. Clin Cancer Res 2018; 24:4145-4153. [PMID: 29954776 PMCID: PMC6125225 DOI: 10.1158/1078-0432.ccr-17-3244] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/27/2018] [Accepted: 05/23/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Most bladder cancers are early-stage tumors known as papillary non-muscle-invasive bladder cancer (NMIBC). After resection, up to 70% of NMIBCs recur locally, and up to 20% of these recurrences progress to muscle invasion. There is an unmet need for additional biomarkers for stratifying tumors based on their risk of recurrence and progression. We previously identified STAG2 as among the most commonly mutated genes in NMIBC and provided initial evidence in a pilot cohort that STAG2-mutant tumors recurred less frequently than STAG2 wild-type tumors. Here, we report a STAG2 biomarker validation study using two independent cohorts of clinically annotated papillary NMIBC tumors from the United States and Europe.Experimental Design: The value of STAG2 immunostaining for prediction of recurrence was initially evaluated in a cohort of 82 patients with papillary NMIBC ("Georgetown cohort"). Next, the value of STAG2 immunostaining for prediction of progression to muscle invasion was evaluated in a progressor-enriched cohort of 253 patients with papillary NMIBC ("Aarhus cohort").Results: In the Georgetown cohort, 52% of NMIBC tumors with intact STAG2 expression recurred, whereas 25% of STAG2-deficient tumors recurred (P = 0.02). Multivariable analysis identified intact STAG2 expression as an independent predictor of recurrence (HR = 2.4; P = 0.05). In the progressor-enriched Aarhus cohort, 38% of tumors with intact STAG2 expression progressed within 5 years, versus 16% of STAG2-deficient tumors (P < 0.01). Multivariable analysis identified intact STAG2 expression as an independent predictor of progression (HR = 1.86; P = 0.05).Conclusions: STAG2 IHC is a simple, binary, new assay for risk stratification in papillary NMIBC. Clin Cancer Res; 24(17); 4145-53. ©2018 AACR.
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Affiliation(s)
- Alana Lelo
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
- Tumor Biology Training Program, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Brent T Harris
- Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
- Histopathology and Tissue Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - David Solomon
- Department of Pathology, University of California San Francisco School of Medicine, San Francisco, California
| | - Deborah L Berry
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
- Histopathology and Tissue Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - Krysta Chaldekas
- Histopathology and Tissue Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - Anagha Kumar
- Department of Biostatistics, MedStar Health Research Institute, Washington, District of Columbia
| | - Jeffry Simko
- Department of Pathology, University of California San Francisco School of Medicine, San Francisco, California
| | | | - Pritish Bhattacharyya
- Department of Pathology, Hackensack University Medical Center, Hackensack, New Jersey
| | - Ciaran Mannion
- Department of Pathology, Hackensack University Medical Center, Hackensack, New Jersey
| | - Jung-Sik Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - George Philips
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
- MedStar Washington Hospital Center, Washington, District of Columbia
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia.
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85
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Gao D, Zhu B, Cao X, Zhang M, Wang X. Roles of NIPBL in maintenance of genome stability. Semin Cell Dev Biol 2018; 90:181-186. [PMID: 30096364 DOI: 10.1016/j.semcdb.2018.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/06/2018] [Indexed: 12/24/2022]
Abstract
A cohesin-loading factor (NIPBL) is one of important regulatory factors in the maintenance of 3D genome organization and function, by interacting with a large number of factors, e.g. cohesion, CCCTC-binding factor (CTCF) or cohesin complex component. The present article overviews the critical and regulatory roles of NIBPL in cohesion loading on chromotin and in gene expression and transcriptional signaling. We explore molecular mechanisms by which NIPBL recruits endogenous histone deacetylase (HDAC) to induce histone deacetylation and influence multi-dimensions of genome, through which NIPBL "hop" movement in chromatin regulates gene expression and alters genome folding. NIPBL regulates the process of CTCF and cohesion into chromatin loops and topologically associated domains, binding of cohesion and H3K4mes3 through interaction among promoters and enhancers. HP1 recruits NIPBL to DNA damage site through RNF8/RNF168 ubiquitylation pathway. NIPBL contributes to regulation of genome-controlled gene expression through the influence of cohesin in chromosome structure. NIPBL interacts with cohesin and then increases transcriptional activities of REC8 promoter, leading to up-regulation of gene expression. NIPBL movement among chromosomal loops regulates gene expression through dynamic alterations of genome organization. Thus, we expect a new and deep insight to understand dynamics of chromosome and explore potential strategies of therapiesc on basis of NIPBL.
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Affiliation(s)
- Danyan Gao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Bijun Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xin Cao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Miaomiao Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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86
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Li Y, Muir KW, Bowler MW, Metz J, Haering CH, Panne D. Structural basis for Scc3-dependent cohesin recruitment to chromatin. eLife 2018; 7:e38356. [PMID: 30109982 PMCID: PMC6120753 DOI: 10.7554/elife.38356] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
The cohesin ring complex is required for numerous chromosomal transactions including sister chromatid cohesion, DNA damage repair and transcriptional regulation. How cohesin engages its chromatin substrate has remained an unresolved question. We show here, by determining a crystal structure of the budding yeast cohesin HEAT-repeat subunit Scc3 bound to a fragment of the Scc1 kleisin subunit and DNA, that Scc3 and Scc1 form a composite DNA interaction module. The Scc3-Scc1 subcomplex engages double-stranded DNA through a conserved, positively charged surface. We demonstrate that this conserved domain is required for DNA binding by Scc3-Scc1 in vitro, as well as for the enrichment of cohesin on chromosomes and for cell viability. These findings suggest that the Scc3-Scc1 DNA-binding interface plays a central role in the recruitment of cohesin complexes to chromosomes and therefore for cohesin to faithfully execute its functions during cell division.
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Affiliation(s)
- Yan Li
- European Molecular Biology LaboratoryGrenobleFrance
| | - Kyle W Muir
- European Molecular Biology LaboratoryGrenobleFrance
| | | | - Jutta Metz
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Christian H Haering
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Daniel Panne
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUnited Kingdom
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87
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Ivanov MP, Ladurner R, Poser I, Beveridge R, Rampler E, Hudecz O, Novatchkova M, Hériché JK, Wutz G, van der Lelij P, Kreidl E, Hutchins JR, Axelsson-Ekker H, Ellenberg J, Hyman AA, Mechtler K, Peters JM. The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion. EMBO J 2018; 37:e97150. [PMID: 29930102 PMCID: PMC6068434 DOI: 10.15252/embj.201797150] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 02/27/2018] [Accepted: 04/09/2018] [Indexed: 11/09/2022] Open
Abstract
Chromosome segregation depends on sister chromatid cohesion which is established by cohesin during DNA replication. Cohesive cohesin complexes become acetylated to prevent their precocious release by WAPL before cells have reached mitosis. To obtain insight into how DNA replication, cohesion establishment and cohesin acetylation are coordinated, we analysed the interaction partners of 55 human proteins implicated in these processes by mass spectrometry. This proteomic screen revealed that on chromatin the cohesin acetyltransferase ESCO2 associates with the MCM2-7 subcomplex of the replicative Cdc45-MCM-GINS helicase. The analysis of ESCO2 mutants defective in MCM binding indicates that these interactions are required for proper recruitment of ESCO2 to chromatin, cohesin acetylation during DNA replication, and centromeric cohesion. We propose that MCM binding enables ESCO2 to travel with replisomes to acetylate cohesive cohesin complexes in the vicinity of replication forks so that these complexes can be protected from precocious release by WAPL Our results also indicate that ESCO1 and ESCO2 have distinct functions in maintaining cohesion between chromosome arms and centromeres, respectively.
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Affiliation(s)
| | - Rene Ladurner
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Evelyn Rampler
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Otto Hudecz
- Institute of Molecular Biotechnology, Vienna, Austria
| | | | | | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna, Austria
| | | | - Emanuel Kreidl
- Research Institute of Molecular Pathology, Vienna, Austria
| | | | | | - Jan Ellenberg
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Karl Mechtler
- Research Institute of Molecular Pathology, Vienna, Austria
- Institute of Molecular Biotechnology, Vienna, Austria
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88
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Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA. Emerging Evidence of Chromosome Folding by Loop Extrusion. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 82:45-55. [PMID: 29728444 PMCID: PMC6512960 DOI: 10.1101/sqb.2017.82.034710] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chromosome organization poses a remarkable physical problem with many biological consequences: How can molecular interactions between proteins at the nanometer scale organize micron-long chromatinized DNA molecules, insulating or facilitating interactions between specific genomic elements? The mechanism of active loop extrusion holds great promise for explaining interphase and mitotic chromosome folding, yet remains difficult to assay directly. We discuss predictions from our polymer models of loop extrusion with barrier elements and review recent experimental studies that provide strong support for loop extrusion, focusing on perturbations to CTCF and cohesin assayed via Hi-C in interphase. Finally, we discuss a likely molecular mechanism of loop extrusion by structural maintenance of chromosomes complexes.
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Affiliation(s)
- Geoffrey Fudenberg
- Gladstone Institute of Data Science and Technology, University of California, San Francisco, California 94158
| | - Nezar Abdennur
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Maxim Imakaev
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Anton Goloborodko
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Leonid A Mirny
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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89
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Kakui Y, Uhlmann F. SMC complexes orchestrate the mitotic chromatin interaction landscape. Curr Genet 2018; 64:335-339. [PMID: 28936767 PMCID: PMC5851691 DOI: 10.1007/s00294-017-0755-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 09/14/2017] [Accepted: 09/16/2017] [Indexed: 12/24/2022]
Abstract
Chromatin is a very long DNA-protein complex that controls the expression and inheritance of the genetic information. Chromatin is stored within the nucleus in interphase and further compacted into chromosomes during mitosis. This process, known as chromosome condensation, is essential for faithful segregation of genomic DNA into daughter cells. Condensin and cohesin, members of the structural maintenance of chromosomes (SMC) family, are fundamental for chromosome architecture, both for establishment of chromatin structure in the interphase nucleus and for the formation of condensed chromosomes in mitosis. These ring-shaped SMC complexes are thought to regulate the interactions between DNA strands by topologically entrapping DNA. How this activity shapes chromosomes is not yet understood. Recent high throughput chromosome conformation capture studies revealed how chromatin is reorganized during the cell cycle and have started to explore the role of SMC complexes in mitotic chromatin architecture. Here, we summarize these findings and discuss the conserved nature of chromosome condensation in eukaryotes. We highlight the unexpected finding that condensin-dependent intra-chromosomal interactions in mitosis increase within a distinctive distance range that is characteristic for an organism, while longer and shorter-range interactions are suppressed. This reveals important molecular insight into chromosome architecture.
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Affiliation(s)
- Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
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90
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Yi Q, Chen Q, Liang C, Yan H, Zhang Z, Xiang X, Zhang M, Qi F, Zhou L, Wang F. HP1 links centromeric heterochromatin to centromere cohesion in mammals. EMBO Rep 2018; 19:embr.201745484. [PMID: 29491004 DOI: 10.15252/embr.201745484] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/28/2018] [Accepted: 02/05/2018] [Indexed: 01/09/2023] Open
Abstract
Heterochromatin protein-1 (HP1) is a key component of heterochromatin. Reminiscent of the cohesin complex which mediates sister-chromatid cohesion, most HP1 proteins in mammalian cells are displaced from chromosome arms during mitotic entry, whereas a pool remains at the heterochromatic centromere region. The function of HP1 at mitotic centromeres remains largely elusive. Here, we show that double knockout (DKO) of HP1α and HP1γ causes defective mitosis progression and weakened centromeric cohesion. While mutating the chromoshadow domain (CSD) prevents HP1α from protecting sister-chromatid cohesion, centromeric targeting of HP1α CSD alone is sufficient to rescue the cohesion defects in HP1 DKO cells. Interestingly, HP1-dependent cohesion protection requires Haspin, an antagonist of the cohesin-releasing factor Wapl. Moreover, HP1α CSD directly binds the N-terminal region of Haspin and facilitates its centromeric localization. The need for HP1 in cohesion protection can be bypassed by centromeric targeting of Haspin or inhibiting Wapl activity. Taken together, these results reveal a redundant role for HP1α and HP1γ in the protection of centromeric cohesion through promoting Haspin localization at mitotic centromeres in mammalian cells.
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Affiliation(s)
- Qi Yi
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Qinfu Chen
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Cai Liang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Haiyan Yan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Zhenlei Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Xingfeng Xiang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Miao Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Feifei Qi
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Linli Zhou
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Fangwei Wang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
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91
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Abe T, Kawasumi R, Arakawa H, Hori T, Shirahige K, Losada A, Fukagawa T, Branzei D. Chromatin determinants of the inner-centromere rely on replication factors with functions that impart cohesion. Oncotarget 2018; 7:67934-67947. [PMID: 27636994 PMCID: PMC5356530 DOI: 10.18632/oncotarget.11982] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/06/2016] [Indexed: 01/08/2023] Open
Abstract
Replication fork-associated factors promote genome integrity and protect against cancer. Mutations in the DDX11 helicase and the ESCO2 acetyltransferase also cause related developmental disorders classified as cohesinopathies. Here we generated vertebrate model cell lines of these disorders and cohesinopathies-related genes. We found that vertebrate DDX11 and Tim-Tipin are individually needed to compensate for ESCO2 loss in chromosome segregation, with DDX11 also playing complementary roles with ESCO2 in centromeric cohesion. Our study reveals that overt centromeric cohesion loss does not necessarily precede chromosome missegregation, while both these problems correlate with, and possibly originate from, inner-centromere defects involving reduced phosphorylation of histone H3T3 (pH3T3) in the region. Interestingly, the mitotic pH3T3 mark was defective in all analyzed replication-related mutants with functions in cohesion. The results pinpoint mitotic pH3T3 as a postreplicative chromatin mark that is sensitive to replication stress and conducts with different kinetics to robust centromeric cohesion and correct chromosome segregation.
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Affiliation(s)
- Takuya Abe
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Ryotaro Kawasumi
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy.,Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa, Hachioji-shi, Tokyo, Japan
| | - Hiroshi Arakawa
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Tetsuya Hori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi Bunkyo-Ku, Tokyo, Japan
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Dana Branzei
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy
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92
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Hou H, Cooper JP. Stretching, scrambling, piercing and entangling: Challenges for telomeres in mitotic and meiotic chromosome segregation. Differentiation 2018; 100:12-20. [PMID: 29413748 DOI: 10.1016/j.diff.2018.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/21/2018] [Accepted: 01/23/2018] [Indexed: 12/24/2022]
Abstract
The consequences of telomere loss or dysfunction become most prominent when cells enter the nuclear division stage of the cell cycle. At this climactic stage when chromosome segregation occurs, telomere fusions or entanglements can lead to chromosome breakage, wreaking havoc on genome stability. Here we review recent progress in understanding the mechanisms of detangling and breaking telomere associations at mitosis, as well as the unique ways in which telomeres are processed to allow regulated sister telomere separation. Moreover, we discuss unexpected roles for telomeres in orchestrating nuclear envelope breakdown and spindle formation, crucial processes for nuclear division. Finally, we discuss the discovery that telomeres create microdomains in the nucleus that are conducive to centromere assembly, cementing the unexpectedly influential role of telomeres in mitosis.
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Affiliation(s)
- Haitong Hou
- Telomere Biology Section, LBMB, NCI, NIH, Building 37, Room 6050, Bethesda MD 20892, USA
| | - Julia Promisel Cooper
- Telomere Biology Section, LBMB, NCI, NIH, Building 37, Room 6050, Bethesda MD 20892, USA.
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93
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Murayama Y, Samora CP, Kurokawa Y, Iwasaki H, Uhlmann F. Establishment of DNA-DNA Interactions by the Cohesin Ring. Cell 2018; 172:465-477.e15. [PMID: 29358048 PMCID: PMC5786502 DOI: 10.1016/j.cell.2017.12.021] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/12/2017] [Accepted: 12/16/2017] [Indexed: 01/14/2023]
Abstract
The ring-shaped structural maintenance of chromosome (SMC) complexes are multi-subunit ATPases that topologically encircle DNA. SMC rings make vital contributions to numerous chromosomal functions, including mitotic chromosome condensation, sister chromatid cohesion, DNA repair, and transcriptional regulation. They are thought to do so by establishing interactions between more than one DNA. Here, we demonstrate DNA-DNA tethering by the purified fission yeast cohesin complex. DNA-bound cohesin efficiently and topologically captures a second DNA, but only if that is single-stranded DNA (ssDNA). Like initial double-stranded DNA (dsDNA) embrace, second ssDNA capture is ATP-dependent, and it strictly requires the cohesin loader complex. Second-ssDNA capture is relatively labile but is converted into stable dsDNA-dsDNA cohesion through DNA synthesis. Our study illustrates second-DNA capture by an SMC complex and provides a molecular model for the establishment of sister chromatid cohesion.
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Affiliation(s)
- Yasuto Murayama
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Catarina P Samora
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yumiko Kurokawa
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Frank Uhlmann
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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94
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Murayama Y. DNA entry, exit and second DNA capture by cohesin: insights from biochemical experiments. Nucleus 2018; 9:492-502. [PMID: 30205748 PMCID: PMC6244732 DOI: 10.1080/19491034.2018.1516486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/28/2018] [Accepted: 08/16/2018] [Indexed: 12/23/2022] Open
Abstract
Cohesin is a ring-shaped, multi-subunit ATPase assembly that is fundamental to the spatiotemporal organization of chromosomes. The ring establishes a variety of chromosomal structures including sister chromatid cohesion and chromatin loops. At the core of the ring is a pair of highly conserved SMC (Structural Maintenance of Chromosomes) proteins, which are closed by the flexible kleisin subunit. In common with other essential SMC complexes including condensin and the SMC5-6 complex, cohesin encircles DNA inside its cavity, with the aid of HEAT (Huntingtin, elongation factor 3, protein phosphatase 2A and TOR) repeat auxiliary proteins. Through this topological embrace, cohesin is thought to establish a series of intra- and interchromosomal interactions by tethering more than one DNA molecule. Recent progress in biochemical reconstitution of cohesin provides molecular insights into how this ring complex topologically binds and mediates DNA-DNA interactions. Here, I review these studies and discuss how cohesin mediates such chromosome interactions.
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Affiliation(s)
- Yasuto Murayama
- Chromosome Biochemistry Laboratory, Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
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95
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Liang C, Chen Q, Yi Q, Zhang M, Yan H, Zhang B, Zhou L, Zhang Z, Qi F, Ye S, Wang F. A kinase-dependent role for Haspin in antagonizing Wapl and protecting mitotic centromere cohesion. EMBO Rep 2018; 19:43-56. [PMID: 29138236 PMCID: PMC5757254 DOI: 10.15252/embr.201744737] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 11/09/2022] Open
Abstract
Sister-chromatid cohesion mediated by the cohesin complex is fundamental for precise chromosome segregation in mitosis. Through binding the cohesin subunit Pds5, Wapl releases the bulk of cohesin from chromosome arms in prophase, whereas centromeric cohesin is protected from Wapl until anaphase onset. Strong centromere cohesion requires centromeric localization of the mitotic histone kinase Haspin, which is dependent on the interaction of its non-catalytic N-terminus with Pds5B. It remains unclear how Haspin fully blocks the Wapl-Pds5B interaction at centromeres. Here, we show that the C-terminal kinase domain of Haspin (Haspin-KD) binds and phosphorylates the YSR motif of Wapl (Wapl-YSR), thereby directly inhibiting the YSR motif-dependent interaction of Wapl with Pds5B. Cells expressing a Wapl-binding-deficient mutant of Haspin or treated with Haspin inhibitors show centromeric cohesion defects. Phospho-mimetic mutation in Wapl-YSR prevents Wapl from binding Pds5B and releasing cohesin. Forced targeting Haspin-KD to centromeres partly bypasses the need for Haspin-Pds5B interaction in cohesion protection. Taken together, these results indicate a kinase-dependent role for Haspin in antagonizing Wapl and protecting centromeric cohesion in mitosis.
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Affiliation(s)
- Cai Liang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Qinfu Chen
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Qi Yi
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Miao Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Haiyan Yan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Bo Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Linli Zhou
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Zhenlei Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Feifei Qi
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Sheng Ye
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Fangwei Wang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
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96
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Perkins AT, Bickel SE. Using Fluorescence In Situ Hybridization (FISH) to Monitor the State of Arm Cohesion in Prometaphase and Metaphase I Drosophila Oocytes. J Vis Exp 2017. [PMID: 29286418 DOI: 10.3791/56802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In humans, chromosome segregation errors in oocytes are responsible for the majority of miscarriages and birth defects. Moreover, as women age, their risk of conceiving an aneuploid fetus increases dramatically and this phenomenon is known as the maternal age effect. One requirement for accurate chromosome segregation during the meiotic divisions is maintenance of sister chromatid cohesion during the extended prophase period that oocytes experience. Cytological evidence in both humans and model organisms suggests that meiotic cohesion deteriorates during the aging process. In addition, segregation errors in human oocytes are most prevalent during meiosis I, consistent with premature loss of arm cohesion. The use of model organisms is critical for unraveling the mechanisms that underlie age-dependent loss of cohesion. Drosophila melanogaster offers several advantages for studying the regulation of meiotic cohesion in oocytes. However, until recently, only genetic tests were available to assay for loss of arm cohesion in oocytes of different genotypes or under different experimental conditions. Here, a detailed protocol is provided for using fluorescence in situ hybridization (FISH) to directly visualize defects in arm cohesion in prometaphase I and metaphase I arrested Drosophila oocytes. By generating a FISH probe that hybridizes to the distal arm of the X chromosome and collecting confocal Z stacks, a researcher can visualize the number of individual FISH signals in three dimensions and determine whether sister chromatid arms are separated. The procedure outlined makes it possible to quantify arm cohesion defects in hundreds of Drosophila oocytes. As such, this method provides an important tool for investigating the mechanisms that contribute to cohesion maintenance as well as the factors that lead to its demise during the aging process.
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97
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Kawasumi R, Abe T, Arakawa H, Garre M, Hirota K, Branzei D. ESCO1/2's roles in chromosome structure and interphase chromatin organization. Genes Dev 2017; 31:2136-2150. [PMID: 29196537 PMCID: PMC5749162 DOI: 10.1101/gad.306084.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/09/2017] [Indexed: 11/24/2022]
Abstract
In this study, Kawasumi et al. researched how ESCO1/2 acetyltransferases mediating SMC3 acetylation and sister chromatid cohesion (SCC) interact and contribute to chromosome structure and proliferation. Using chicken DT40 cell lines with mutations in ESCO1/2, SMC3 acetylation, and the cohesin remover WAPL, they show that cohesion establishment by vertebrate ESCO1/2 is linked to interphase chromatin architecture formation. ESCO1/2 acetyltransferases mediating SMC3 acetylation and sister chromatid cohesion (SCC) are differentially required for genome integrity and development. Here we established chicken DT40 cell lines with mutations in ESCO1/2, SMC3 acetylation, and the cohesin remover WAPL. Both ESCO1 and ESCO2 promoted SCC, while ESCO2 was additionally and specifically required for proliferation and centromere integrity. ESCO1 overexpression fully suppressed the slow proliferation and centromeric separation phenotypes of esco2 cells but only partly suppressed its chromosome arm SCC defects. Concomitant inactivation of ESCO1 and ESCO2 caused lethality owing to compromised mitotic chromosome segregation. Neither wapl nor acetyl-mimicking smc3-QQ mutations rescued esco1 esco2 lethality. Notably, esco1 esco2 wapl conditional mutants showed very severe proliferation defects associated with catastrophic mitoses and also abnormal interphase chromatin organization patterns. The results indicate that cohesion establishment by vertebrate ESCO1/2 is linked to interphase chromatin architecture formation, a newly identified function of cohesin acetyltransferases that is both fundamentally and medically relevant.
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Affiliation(s)
- Ryotaro Kawasumi
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Takuya Abe
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy.,Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hiroshi Arakawa
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Massimiliano Garre
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Dana Branzei
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100 Pavia, Italy
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98
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van der Lelij P, Lieb S, Jude J, Wutz G, Santos CP, Falkenberg K, Schlattl A, Ban J, Schwentner R, Hoffmann T, Kovar H, Real FX, Waldman T, Pearson MA, Kraut N, Peters JM, Zuber J, Petronczki M. Synthetic lethality between the cohesin subunits STAG1 and STAG2 in diverse cancer contexts. eLife 2017; 6:e26980. [PMID: 28691904 PMCID: PMC5531830 DOI: 10.7554/elife.26980] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/03/2017] [Indexed: 11/13/2022] Open
Abstract
Recent genome analyses have identified recurrent mutations in the cohesin complex in a wide range of human cancers. Here we demonstrate that the most frequently mutated subunit of the cohesin complex, STAG2, displays a strong synthetic lethal interaction with its paralog STAG1. Mechanistically, STAG1 loss abrogates sister chromatid cohesion in STAG2 mutated but not in wild-type cells leading to mitotic catastrophe, defective cell division and apoptosis. STAG1 inactivation inhibits the proliferation of STAG2 mutated but not wild-type bladder cancer and Ewing sarcoma cell lines. Restoration of STAG2 expression in a mutated bladder cancer model alleviates the dependency on STAG1. Thus, STAG1 and STAG2 support sister chromatid cohesion to redundantly ensure cell survival. STAG1 represents a vulnerability of cancer cells carrying mutations in the major emerging tumor suppressor STAG2 across different cancer contexts. Exploiting synthetic lethal interactions to target recurrent cohesin mutations in cancer, e.g. by inhibiting STAG1, holds the promise for the development of selective therapeutics.
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Affiliation(s)
- Petra van der Lelij
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Catarina P Santos
- Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Katrina Falkenberg
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | | | - Jozef Ban
- Children’s Cancer Research Institute, Vienna, Austria
| | | | - Thomas Hoffmann
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Heinrich Kovar
- Children’s Cancer Research Institute, Vienna, Austria
- Department for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Francisco X Real
- Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Department de Ciències Experimentals I de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Todd Waldman
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington DC, United States
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
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Diebold-Durand ML, Lee H, Ruiz Avila LB, Noh H, Shin HC, Im H, Bock FP, Bürmann F, Durand A, Basfeld A, Ham S, Basquin J, Oh BH, Gruber S. Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization. Mol Cell 2017; 67:334-347.e5. [PMID: 28689660 PMCID: PMC5526789 DOI: 10.1016/j.molcel.2017.06.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/03/2017] [Accepted: 06/09/2017] [Indexed: 01/09/2023]
Abstract
Multi-subunit SMC complexes control chromosome superstructure and promote chromosome disjunction, conceivably by actively translocating along DNA double helices. SMC subunits comprise an ABC ATPase "head" and a "hinge" dimerization domain connected by a 49 nm coiled-coil "arm." The heads undergo ATP-dependent engagement and disengagement to drive SMC action on the chromosome. Here, we elucidate the architecture of prokaryotic Smc dimers by high-throughput cysteine cross-linking and crystallography. Co-alignment of the Smc arms tightly closes the interarm space and misaligns the Smc head domains at the end of the rod by close apposition of their ABC signature motifs. Sandwiching of ATP molecules between Smc heads requires them to substantially tilt and translate relative to each other, thereby opening up the Smc arms. We show that this mechanochemical gating reaction regulates chromosome targeting and propose a mechanism for DNA translocation based on the merging of DNA loops upon closure of Smc arms.
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Affiliation(s)
- Marie-Laure Diebold-Durand
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland
| | - Hansol Lee
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Laura B Ruiz Avila
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Haemin Noh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Ho-Chul Shin
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Haeri Im
- Department of Chemistry, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul 04310, Korea
| | - Florian P Bock
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland
| | - Frank Bürmann
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexandre Durand
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland
| | - Alrun Basfeld
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Sihyun Ham
- Department of Chemistry, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul 04310, Korea
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
| | - Stephan Gruber
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland.
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100
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Gruber S. Shaping chromosomes by DNA capture and release: gating the SMC rings. Curr Opin Cell Biol 2017; 46:87-93. [PMID: 28460277 DOI: 10.1016/j.ceb.2017.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/22/2022]
Abstract
SMC proteins organize chromosomes to coordinate essential nuclear processes such as gene expression and DNA recombination as well as to segregate chromosomes during cell division. SMC mediated DNA bridging keeps sister chromatids aligned for much of the cell cycle, while the active extrusion of DNA loops by SMC presumably compacts chromosomes. Chromosome superstructure is thus given by the number of DNA linkages and the size of chromosomal DNA loops, which in turn depend on the dynamics of SMC loading and unloading. The latter is regulated by the intrinsic SMC ATPase activity, multiple external factors and post-translational modification. Here, I highlight recent advances in our understanding of DNA capture and release by SMC-with a focus on cohesin.
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Affiliation(s)
- Stephan Gruber
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland.
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