1
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Segev A, Heady L, Crewe M, Madabhushi R. Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome. Cell Rep 2024; 43:113809. [PMID: 38377005 PMCID: PMC11064056 DOI: 10.1016/j.celrep.2024.113809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
We trapped catalytically engaged topoisomerase IIβ (TOP2B) in covalent DNA cleavage complexes (TOP2Bccs) and mapped their positions genome-wide in cultured mouse cortical neurons. We report that TOP2Bcc distribution varies with both nucleosome and compartmental chromosome organization. While TOP2Bccs in gene bodies correlate with their level of transcription, highly expressed genes that lack the usually associated chromatin marks, such as H3K36me3, show reduced TOP2Bccs, suggesting that histone posttranslational modifications regulate TOP2B activity. Promoters with high RNA polymerase II occupancy show elevated TOP2B chromatin immunoprecipitation sequencing signals but low TOP2Bccs, indicating that TOP2B catalytic engagement is curtailed at active promoters. Surprisingly, either poisoning or inhibiting TOP2B increases nascent transcription at most genes and enhancers but reduces transcription within long genes. These effects are independent of transcript length and instead correlate with the presence of intragenic enhancers. Together, these results clarify how cells modulate the catalytic engagement of topoisomerases to affect transcription.
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Affiliation(s)
- Amir Segev
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lance Heady
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Morgan Crewe
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ram Madabhushi
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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2
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Nettles SA, Ikeuchi Y, Lefton KB, Abbasi L, Erickson A, Agwu C, Papouin T, Bonni A, Gabel HW. MeCP2 represses the activity of topoisomerase IIβ in long neuronal genes. Cell Rep 2023; 42:113538. [PMID: 38096051 PMCID: PMC10844882 DOI: 10.1016/j.celrep.2023.113538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
A unique signature of neurons is the high expression of the longest genes in the genome. These genes have essential neuronal functions, and disruption of their expression has been implicated in neurological disorders. DNA topoisomerases resolve DNA topological constraints and facilitate neuronal long gene expression. Conversely, the Rett syndrome protein, methyl-CpG-binding protein 2 (MeCP2), can transcriptionally repress long genes. How these factors regulate long genes is not well understood, and whether they interact is not known. Here, we identify and map a functional interaction between MeCP2 and topoisomerase IIβ (TOP2β) in mouse neurons. We profile neuronal TOP2β activity genome wide, detecting enrichment at regulatory regions and gene bodies of long genes, including MeCP2-regulated genes. We show that loss and overexpression of MeCP2 alter TOP2β activity at MeCP2-regulated genes. These findings uncover a mechanism of TOP2β inhibition by MeCP2 in neurons and implicate TOP2β dysregulation in disorders caused by MeCP2 disruption.
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Affiliation(s)
- Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yoshiho Ikeuchi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katheryn B Lefton
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ladan Abbasi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alyssa Erickson
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chibueze Agwu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA.
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3
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Cowell IG, Casement JW, Austin CA. To Break or Not to Break: The Role of TOP2B in Transcription. Int J Mol Sci 2023; 24:14806. [PMID: 37834253 PMCID: PMC10573011 DOI: 10.3390/ijms241914806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Transcription and its regulation pose challenges related to DNA torsion and supercoiling of the DNA template. RNA polymerase tracking the helical groove of the DNA introduces positive helical torsion and supercoiling upstream and negative torsion and supercoiling behind its direction of travel. This can inhibit transcriptional elongation and other processes essential to transcription. In addition, chromatin remodeling associated with gene activation can generate or be hindered by excess DNA torsional stress in gene regulatory regions. These topological challenges are solved by DNA topoisomerases via a strand-passage reaction which involves transiently breaking and re-joining of one (type I topoisomerases) or both (type II topoisomerases) strands of the phosphodiester backbone. This review will focus on one of the two mammalian type II DNA topoisomerase enzymes, DNA topoisomerase II beta (TOP2B), that have been implicated in correct execution of developmental transcriptional programs and in signal-induced transcription, including transcriptional activation by nuclear hormone ligands. Surprisingly, several lines of evidence indicate that TOP2B-mediated protein-free DNA double-strand breaks are involved in signal-induced transcription. We discuss the possible significance and origins of these DSBs along with a network of protein interaction data supporting a variety of roles for TOP2B in transcriptional regulation.
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Affiliation(s)
- Ian G. Cowell
- Biosciences Institute, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - John W. Casement
- Bioinformatics Support Unit, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Caroline A. Austin
- Biosciences Institute, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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4
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Miyaji M, Kawano S, Furuta R, Murakami E, Ikeda S, Tsutsui KM, Tsutsui K. Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA. PLoS One 2023; 18:e0289599. [PMID: 37540655 PMCID: PMC10403129 DOI: 10.1371/journal.pone.0289599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/20/2023] [Indexed: 08/06/2023] Open
Abstract
A human protein heterogeneous ribonucleoprotein U (hnRNP U) also known as Scaffold attachment factor A (SAF-A) and its orthologous rat protein SP120 are abundant and multifunctional nuclear protein that directly binds to both DNA and RNA. The C-terminal region of hnRNP U enriched with arginine and glycine is essential for the interaction with RNA and the N-terminal region of SAF-A termed SAP domain has been ascribed to the DNA binding. We have reported that rat hnRNP U specifically and cooperatively binds to AT-rich DNA called nuclear scaffold/matrix-associated region (S/MAR) although its detailed mechanism remained unclear. In the present study analysis of hnRNP U deletion mutants revealed for the first time that a C-terminal domain enriched with Arg-Gly (defined here as 'RG domain') is predominantly important for the S/MAR-selective DNA binding activities. RG domain alone directly bound to S/MAR and coexistence with the SAP domain exerted a synergistic effect. The binding was inhibited by netropsin, a minor groove binder with preference to AT pairs that are enriched in S/MAR, suggesting that RG domain interacts with minor groove of S/MAR DNA. Interestingly, excess amounts of RNA attenuated the RG domain-dependent S/MAR-binding of hnRNP U. Taken together, hnRNP U may be the key element for the RNA-regulated recognition of S/MAR DNA and thus contributing to the dynamic structural changes of chromatin compartments.
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Affiliation(s)
- Mary Miyaji
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shinji Kawano
- Faculty of Science, Department of Biochemistry, Okayama University of Science, Okayama, Japan
| | - Ryohei Furuta
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Emi Murakami
- Faculty of Science, Department of Biochemistry, Okayama University of Science, Okayama, Japan
| | - Shogo Ikeda
- Faculty of Science, Department of Biochemistry, Okayama University of Science, Okayama, Japan
| | - Kimiko M Tsutsui
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Ken Tsutsui
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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5
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Akter S, Shimba A, Ikuta K, Mahmud MRA, Yamada S, Sasanuma H, Tsuda M, Sone M, Ago Y, Murai K, Tanaka H, Takeda S. Physiological concentrations of glucocorticoids induce pathological DNA double-strand breaks. Genes Cells 2023; 28:53-67. [PMID: 36415926 DOI: 10.1111/gtc.12993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022]
Abstract
Steroid hormones induce the transcription of target genes by activating nuclear receptors. Early transcriptional response to various stimuli, including hormones, involves the active catalysis of topoisomerase II (TOP2) at transcription regulatory sequences. TOP2 untangles DNAs by transiently generating double-strand breaks (DSBs), where TOP2 covalently binds to DSB ends. When TOP2 fails to rejoin, called "abortive" catalysis, the resulting DSBs are repaired by tyrosyl-DNA phosphodiesterase 2 (TDP2) and non-homologous end-joining (NHEJ). A steroid, cortisol, is the most important glucocorticoid, and dexamethasone (Dex), a synthetic glucocorticoid, is widely used for suppressing inflammation in clinics. We here revealed that clinically relevant concentrations of Dex and physiological concentrations of cortisol efficiently induce DSBs in G1 phase cells deficient in TDP2 and NHEJ. The DSB induction depends on glucocorticoid receptor (GR) and TOP2. Considering the specific role of TDP2 in removing TOP2 adducts from DSB ends, induced DSBs most likely represent stalled TOP2-DSB complexes. Inhibition of RNA polymerase II suppressed the DSBs formation only modestly in the G1 phase. We propose that cortisol and Dex frequently generate DSBs through the abortive catalysis of TOP2 at transcriptional regulatory sequences, including promoters or enhancers, where active TOP2 catalysis occurs during early transcriptional response.
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Affiliation(s)
- Salma Akter
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihiro Shimba
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Md Rasel Al Mahmud
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shintaro Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masakatsu Sone
- Department of Metabolic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Metabolism and Endocrinology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Yukio Ago
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenichi Murai
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Shenzhen University School of Medicine, Shenzhen University, Shenzhen, Guangdong, China
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6
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Morotomi-Yano K, Hiromoto Y, Higaki T, Yano KI. Disease-associated H58Y mutation affects the nuclear dynamics of human DNA topoisomerase IIβ. Sci Rep 2022; 12:20627. [PMID: 36450898 PMCID: PMC9712534 DOI: 10.1038/s41598-022-24883-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
DNA topoisomerase II (TOP2) is an enzyme that resolves DNA topological problems and plays critical roles in various nuclear processes. Recently, a heterozygous H58Y substitution in the ATPase domain of human TOP2B was identified from patients with autism spectrum disorder, but its biological significance remains unclear. In this study, we analyzed the nuclear dynamics of TOP2B with H58Y (TOP2B H58Y). Although wild-type TOP2B was highly mobile in the nucleus of a living cell, the nuclear mobility of TOP2B H58Y was markedly reduced, suggesting that the impact of H58Y manifests as low protein mobility. We found that TOP2B H58Y is insensitive to ICRF-187, a TOP2 inhibitor that halts TOP2 as a closed clamp on DNA. When the ATPase activity of TOP2B was compromised, the nuclear mobility of TOP2B H58Y was restored to wild-type levels, indicating the contribution of the ATPase activity to the low nuclear mobility. Analysis of genome-edited cells harboring TOP2B H58Y showed that TOP2B H58Y retains sensitivity to the TOP2 poison etoposide, implying that TOP2B H58Y can undergo at least a part of its catalytic reactions. Collectively, TOP2 H58Y represents a unique example of the relationship between a disease-associated mutation and perturbed protein dynamics.
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Affiliation(s)
- Keiko Morotomi-Yano
- grid.274841.c0000 0001 0660 6749Institute of Industrial Nanomaterials, Kumamoto University, Kumamoto, Japan
| | - Yukiko Hiromoto
- grid.274841.c0000 0001 0660 6749Faculty of Science, Kumamoto University, Kumamoto, Japan
| | - Takumi Higaki
- grid.274841.c0000 0001 0660 6749Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Ken-ichi Yano
- grid.274841.c0000 0001 0660 6749Institute of Industrial Nanomaterials, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
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7
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Neha S, Dholaniya PS. The Prevailing Role of Topoisomerase 2 Beta and its Associated Genes in Neurons. Mol Neurobiol 2021; 58:6443-6459. [PMID: 34546528 DOI: 10.1007/s12035-021-02561-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/11/2021] [Indexed: 12/01/2022]
Abstract
Topoisomerase 2 beta (TOP2β) is an enzyme that alters the topological states of DNA by making a transient double-strand break during the transcription process. The direct interaction of TOP2β with DNA strand results in transcriptional regulation of certain genes and some studies have suggested that a particular set of genes are regulated by TOP2β, which have a prominent role in various stages of neuron from development to degeneration. In this review, we discuss the role of TOP2β in various phases of the neuron's life. Based on the existing reports, we have compiled the list of genes, which are directly regulated by the enzyme, from different studies and performed their functional classification. We discuss the role of these genes in neurogenesis, neuron migration, fate determination, differentiation and maturation, generation of neural circuits, and senescence.
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Affiliation(s)
- Neha S
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500 046, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500 046, India.
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8
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TOP2B's contributions to transcription. Biochem Soc Trans 2021; 49:2483-2493. [PMID: 34747992 DOI: 10.1042/bst20200454] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022]
Abstract
Transcription is regulated and mediated by multiprotein complexes in a chromatin context. Transcription causes changes in DNA topology which is modulated by DNA topoisomerases, enzymes that catalyse changes in DNA topology via transient breaking and re-joining of one or both strands of the phosphodiester backbone. Mammals have six DNA topoisomerases, this review focuses on one, DNA topoisomerase II beta (TOP2B). In the absence of TOP2B transcription of many developmentally regulated genes is altered. Long genes seem particularly susceptible to the lack of TOP2B. Biochemical studies of the role of TOP2B in transcription regulated by ligands such as nuclear hormones, growth factors and insulin has revealed PARP1 associated with TOP2B and also PRKDC, XRCC5 and XRCC6. Analysis of publicly available databases of protein interactions confirms these interactions and illustrates interactions with other key transcriptional regulators including TRIM28. TOP2B has been shown to interact with proteins involved in chromosome organisation including CTCF and RAD21. Comparison of publicly available Chip-seq datasets reveals the location at which these proteins interact with genes. The availability of resources such as large datasets of protein-protein interactions, e.g. BioGrid and IntAct and protein-DNA interactions such as Chip-seq in GEO enables scientists to extend models and propose new hypotheses.
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9
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Nucleolar translocation of human DNA topoisomerase II by ATP depletion and its disruption by the RNA polymerase I inhibitor BMH-21. Sci Rep 2021; 11:21533. [PMID: 34728715 PMCID: PMC8563764 DOI: 10.1038/s41598-021-00958-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
DNA topoisomerase II (TOP2) is a nuclear protein that resolves DNA topological problems and plays critical roles in multiple nuclear processes. Human cells have two TOP2 proteins, TOP2A and TOP2B, that are localized in both the nucleoplasm and nucleolus. Previously, ATP depletion was shown to augment the nucleolar localization of TOP2B, but the molecular details of subnuclear distributions, particularly of TOP2A, remained to be fully elucidated in relation to the status of cellular ATP. Here, we analyzed the nuclear dynamics of human TOP2A and TOP2B in ATP-depleted cells. Both proteins rapidly translocated from the nucleoplasm to the nucleolus in response to ATP depletion. FRAP analysis demonstrated that they were highly mobile in the nucleoplasm and nucleolus. The nucleolar retention of both proteins was sensitive to the RNA polymerase I inhibitor BMH-21, and the TOP2 proteins in the nucleolus were immediately dispersed into the nucleoplasm by BMH-21. Under ATP-depleted conditions, the TOP2 poison etoposide was less effective, indicating the therapeutic relevance of TOP2 subnuclear distributions. These results give novel insights into the subnuclear dynamics of TOP2 in relation to cellular ATP levels and also provide discussions about its possible mechanisms and biological significance.
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10
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Gonzalez-Buendia E, Zhao J, Wang L, Mukherjee S, Zhang D, Arrieta VA, Feldstein E, Kane JR, Kang SJ, Lee-Chang C, Mahajan A, Chen L, Realubit R, Karan C, Magnuson L, Horbinski C, Marshall SA, Sarkaria JN, Mohyeldin A, Nakano I, Bansal M, James CD, Brat DJ, Ahmed A, Canoll P, Rabadan R, Shilatifard A, Sonabend AM. TOP2B Enzymatic Activity on Promoters and Introns Modulates Multiple Oncogenes in Human Gliomas. Clin Cancer Res 2021; 27:5669-5680. [PMID: 34433651 PMCID: PMC8818263 DOI: 10.1158/1078-0432.ccr-21-0312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/07/2021] [Accepted: 07/28/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE The epigenetic mechanisms involved in transcriptional regulation leading to malignant phenotype in gliomas remains poorly understood. Topoisomerase IIB (TOP2B), an enzyme that decoils and releases torsional forces in DNA, is overexpressed in a subset of gliomas. Therefore, we investigated its role in epigenetic regulation in these tumors. EXPERIMENTAL DESIGN To investigate the role of TOP2B in epigenetic regulation in gliomas, we performed paired chromatin immunoprecipitation sequencing for TOP2B and RNA-sequencing analysis of glioma cell lines with and without TOP2B inhibition and in human glioma specimens. These experiments were complemented with assay for transposase-accessible chromatin using sequencing, gene silencing, and mouse xenograft experiments to investigate the function of TOP2B and its role in glioma phenotypes. RESULTS We discovered that TOP2B modulates transcription of multiple oncogenes in human gliomas. TOP2B regulated transcription only at sites where it was enzymatically active, but not at all native binding sites. In particular, TOP2B activity localized in enhancers, promoters, and introns of PDGFRA and MYC, facilitating their expression. TOP2B levels and genomic localization was associated with PDGFRA and MYC expression across glioma specimens, which was not seen in nontumoral human brain tissue. In vivo, TOP2B knockdown of human glioma intracranial implants prolonged survival and downregulated PDGFRA. CONCLUSIONS Our results indicate that TOP2B activity exerts a pleiotropic role in transcriptional regulation of oncogenes in a subset of gliomas promoting a proliferative phenotype.
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Affiliation(s)
- Edgar Gonzalez-Buendia
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Junfei Zhao
- Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Subhas Mukherjee
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Daniel Zhang
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Víctor A Arrieta
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- PECEM, Facultad de Medicina, Universidad Nacional Autónoma de México, México
| | - Eric Feldstein
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - J Robert Kane
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Seong Jae Kang
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Catalina Lee-Chang
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Aayushi Mahajan
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Li Chen
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ronald Realubit
- High-Throughput Screening Genome Center, Columbia University, New York, New York
| | - Charles Karan
- High-Throughput Screening Genome Center, Columbia University, New York, New York
| | - Lisa Magnuson
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Craig Horbinski
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Ahmed Mohyeldin
- Department of Neurosurgery, Ohio State University, Columbus, Ohio
| | - Ichiro Nakano
- Department of Neurosurgery, University of Alabama, Birmingham, Alabama
| | - Mukesh Bansal
- Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Charles D James
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Daniel J Brat
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Atique Ahmed
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Raul Rabadan
- Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Adam M Sonabend
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
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11
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Yasuda K, Kato Y, Ikeda S, Kawano S. Regulation of catalytic activity and nucleolar localization of rat DNA topoisomerase IIα through its C-terminal domain. Genes Genet Syst 2021; 95:291-302. [PMID: 33551432 DOI: 10.1266/ggs.20-00038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Type II DNA topoisomerase (topo II) catalyzes double-stranded DNA cleavage and re-ligation, thus solving problems in DNA topology. Vertebrates have two isozymes (α and β). Recently, the C-terminal regulatory domain (CRD), which regulates catalytic activity and subnuclear localization by associating with RNA, was identified within the C-terminal domain (CTD) of rat topo IIβ. In contrast, it is unclear whether a β CRD-like domain is present in the CTD of topo IIα. In this study, we aimed to identify an RNA-mediated regulatory domain in the rat topo IIα CTD. First, we exchanged the CTDs of rat topo IIα (amino acids 1,192-1,528) and β (1,201-1,614) and examined the two chimeras' in vitro catalytic activities. Interestingly, the relaxation activities of topo IIα WT enzyme and both of the CTD-swapped mutants were inhibited in the presence of isolated cellular RNA, suggesting that the α CTD is involved in the RNA-mediated regulation of catalytic activity in topo IIα. The results of on-bead assays using a CTD-deleted mutant of rat topo IIα indicated that the RNA-mediated inhibition of the relaxation activity was caused by an interaction between the α CTD and RNA. Further, to identify the domain within the CTD that is associated with subnuclear localization of rat topo IIα, we transiently expressed EGFP-tagged CTD deletion mutants in human cells. The data indicated that the 1,192-1,289 region of rat topo IIα was required for targeting the enzyme to nucleoli. Finally, a relaxation assay using 1-1,289 and Δ1,192-1,289 truncated mutants indicated that the 1,192-1,289 region is involved in RNA-mediated inhibition. These results indicated that the CTD of rat topo IIα, containing the 1,192-1,289 region, is involved in the regulation of catalytic activity by associating with RNA, as well as in the localization to nucleoli in interphase cells.
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Affiliation(s)
- Kazushi Yasuda
- Department of Biochemistry, Faculty of Science, Okayama University of Science
| | - Yuri Kato
- Department of Biochemistry, Faculty of Science, Okayama University of Science
| | - Shogo Ikeda
- Department of Biochemistry, Faculty of Science, Okayama University of Science
| | - Shinji Kawano
- Department of Biochemistry, Faculty of Science, Okayama University of Science
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12
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Liu J, Yi S, Shi W, Zhang G, Wang S, Qi Q, Cong B, Li Y. The Pathology of Morphine-Inhibited Nerve Repair and Morphine-Induced Nerve Damage Is Mediated via Endoplasmic Reticulum Stress. Front Neurosci 2021; 15:618190. [PMID: 33679302 PMCID: PMC7935558 DOI: 10.3389/fnins.2021.618190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/25/2021] [Indexed: 01/01/2023] Open
Abstract
Objective The aim of the present study was to observe the pathological damage in the cerebral cortex of rats under acute morphine exposure (AME) and different durations of morphine dependence (MD), explore whether endoplasmic reticulum stress (ERS) is involved in the damage process, and assess the effect of morphine exposure on the proliferation and differentiation of newborn neurons. Methods Rat models of AME and different durations of MD were established. Pathological changes in cortical neurons were assessed by hematoxylin and eosin (H&E) and thionine staining. The expression of nuclear receptor-related factor 1 (NURR1) and that of the ERS-related proteins glucose-regulated protein 78 (GRP78), p-eIF2α, activating transcription factor 6 (ATF6), and CHOP in cortical neurons was assessed by immunohistochemistry. Double immunofluorescence labeling was used to observe the expression of Ki-67. Results H&E and thionine staining revealed that AME resulted in pyknotic changes in cortical neurons. With prolonged morphine exposure, the number of pyknotic neurons was significantly increased, the protein expression of Ki-67 and NURR1 was significantly decreased, and the protein levels of GRP78, p-eIF2α, ATF6, and CHOP showed marked dynamic changes. Conclusion AME and different durations of MD caused varying degrees of pathological changes in the cortex. Furthermore, the dynamic changes observed in ERS-related protein expression suggested that ERS may be associated with cortical injury. Different durations of MD inhibited the proliferation, differentiation, and migration of newborn neurons, which may affect the nerve repair process after injury.
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Affiliation(s)
- Jie Liu
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China.,Research Center of Basic Medical Sciences, Department of Pathology, School of Basic Medical Sciences, Hubei University of Science and Technology, Xianning, China
| | - Shanyong Yi
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China.,School of Forensic Medicine, Xinxiang Medical University, Xinxiang, China
| | - Weibo Shi
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Guozhong Zhang
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Songjun Wang
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Qian Qi
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Bin Cong
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Yingmin Li
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China
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13
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Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to induce chromatin opening. Sci Rep 2020; 10:18550. [PMID: 33122676 PMCID: PMC7596052 DOI: 10.1038/s41598-020-75004-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/09/2020] [Indexed: 11/08/2022] Open
Abstract
Type II DNA topoisomerases (topo II) flip the spatial positions of two DNA duplexes, called G- and T- segments, by a cleavage-passage-resealing mechanism. In living cells, these DNA segments can be derived from distant sites on the same chromosome. Due to lack of proper methodology, however, no direct evidence has been described so far. The beta isoform of topo II (topo IIβ) is essential for transcriptional regulation of genes expressed in the final stage of neuronal differentiation. Here we devise a genome-wide mapping technique (eTIP-seq) for topo IIβ target sites that can measure the genomic distance between G- and T-segments. It revealed that the enzyme operates in two distinctive modes, termed proximal strand passage (PSP) and distal strand passage (DSP). PSP sites are concentrated around transcription start sites, whereas DSP sites are heavily clustered in small number of hotspots. While PSP represent the conventional topo II targets that remove local torsional stresses, DSP sites have not been described previously. Most remarkably, DSP is driven by the pairing between homologous sequences or repeats located in a large distance. A model-building approach suggested that topo IIβ acts on crossovers to unknot the intertwined DSP sites, leading to chromatin decondensation.
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14
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Type II DNA Topoisomerases Cause Spontaneous Double-Strand Breaks in Genomic DNA. Genes (Basel) 2019; 10:genes10110868. [PMID: 31671674 PMCID: PMC6895833 DOI: 10.3390/genes10110868] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/31/2022] Open
Abstract
Type II DNA topoisomerase enzymes (TOP2) catalyze topological changes by strand passage reactions. They involve passing one intact double stranded DNA duplex through a transient enzyme-bridged break in another (gated helix) followed by ligation of the break by TOP2. A TOP2 poison, etoposide blocks TOP2 catalysis at the ligation step of the enzyme-bridged break, increasing the number of stable TOP2 cleavage complexes (TOP2ccs). Remarkably, such pathological TOP2ccs are formed during the normal cell cycle as well as in postmitotic cells. Thus, this ‘abortive catalysis’ can be a major source of spontaneously arising DNA double-strand breaks (DSBs). TOP2-mediated DSBs are also formed upon stimulation with physiological concentrations of androgens and estrogens. The frequent occurrence of TOP2-mediated DSBs was previously not appreciated because they are efficiently repaired. This repair is performed in collaboration with BRCA1, BRCA2, MRE11 nuclease, and tyrosyl-DNA phosphodiesterase 2 (TDP2) with nonhomologous end joining (NHEJ) factors. This review first discusses spontaneously arising DSBs caused by the abortive catalysis of TOP2 and then summarizes proteins involved in repairing stalled TOP2ccs and discusses the genotoxicity of the sex hormones.
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15
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Atkin ND, Raimer HM, Wang YH. Broken by the Cut: A Journey into the Role of Topoisomerase II in DNA Fragility. Genes (Basel) 2019; 10:E791. [PMID: 31614754 PMCID: PMC6826763 DOI: 10.3390/genes10100791] [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: 09/14/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023] Open
Abstract
DNA topoisomerase II (TOP2) plays a critical role in many processes such as replication and transcription, where it resolves DNA structures and relieves torsional stress. Recent evidence demonstrated the association of TOP2 with topologically associated domains (TAD) boundaries and CCCTC-binding factor (CTCF) binding sites. At these sites, TOP2 promotes interactions between enhancers and gene promoters, and relieves torsional stress that accumulates at these physical barriers. Interestingly, in executing its enzymatic function, TOP2 contributes to DNA fragility through re-ligation failure, which results in persistent DNA breaks when unrepaired or illegitimately repaired. Here, we discuss the biological processes for which TOP2 is required and the steps at which it can introduce DNA breaks. We describe the repair processes that follow removal of TOP2 adducts and the resultant broken DNA ends, and present how these processes can contribute to disease-associated mutations. Furthermore, we examine the involvement of TOP2-induced breaks in the formation of oncogenic translocations of leukemia and papillary thyroid cancer, as well as the role of TOP2 and proteins which repair TOP2 adducts in other diseases. The participation of TOP2 in generating persistent DNA breaks and leading to diseases such as cancer, could have an impact on disease treatment and prevention.
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Affiliation(s)
- Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
| | - Heather M Raimer
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
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16
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Okamoto Y, Abe M, Itaya A, Tomida J, Ishiai M, Takaori-Kondo A, Taoka M, Isobe T, Takata M. FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress. FEBS J 2018; 286:139-150. [PMID: 30431240 DOI: 10.1111/febs.14700] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/02/2018] [Accepted: 11/12/2018] [Indexed: 01/19/2023]
Abstract
R-loops, which consist of DNA : RNA hybrids and displaced single-strand DNA, are a major threat to genome stability. We have previously reported that a key Fanconi anemia protein, FANCD2, accumulates on large fragile genes during mild replication stress in a manner depending on R-loops. In this study, we found that FANCD2 suppresses R-loop levels. Furthermore, we identified FANCD2 interactions with RNA processing factors, including hnRNP U and DDX47. Our data suggest that FANCD2, which accumulates with R-loops in chromatin, recruits these factors and thereby promotes efficient processing of long RNA transcripts. This may lead to a reduction in transcription-replication collisions, as detected by PLA between PCNA and RNA Polymerase II, and hence, lowered R-loop levels. We propose that this mechanism might contribute to maintenance of genome stability during mild replication stress.
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Affiliation(s)
- Yusuke Okamoto
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Masako Abe
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
| | - Akiko Itaya
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
| | - Junya Tomida
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
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17
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Marinello J, Delcuratolo M, Capranico G. Anthracyclines as Topoisomerase II Poisons: From Early Studies to New Perspectives. Int J Mol Sci 2018; 19:ijms19113480. [PMID: 30404148 PMCID: PMC6275052 DOI: 10.3390/ijms19113480] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 12/22/2022] Open
Abstract
Mammalian DNA topoisomerases II are targets of anticancer anthracyclines that act by stabilizing enzyme-DNA complexes wherein DNA strands are cut and covalently linked to the protein. This molecular mechanism is the molecular basis of anthracycline anticancer activity as well as the toxic effects such as cardiomyopathy and induction of secondary cancers. Even though anthracyclines have been used in the clinic for more than 50 years for solid and blood cancers, the search of breakthrough analogs has substantially failed. The recent developments of personalized medicine, availability of individual genomic information, and immune therapy are expected to change significantly human cancer therapy. Here, we discuss the knowledge of anthracyclines as Topoisomerase II poisons, their molecular and cellular effects and toxicity along with current efforts to improve the therapeutic index. Then, we discuss the contribution of the immune system in the anticancer activity of anthracyclines, and the need to increase our knowledge of molecular mechanisms connecting the drug targets to the immune stimulatory pathways in cancer cells. We propose that the complete definition of the molecular interaction of anthracyclines with the immune system may open up more effective and safer ways to treat patients with these drugs.
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Affiliation(s)
- Jessica Marinello
- Department of Pharmacy and Biotechnology, University of Bologna, via Selmi 3, 40126 Bologna, Italy.
| | - Maria Delcuratolo
- Department of Pharmacy and Biotechnology, University of Bologna, via Selmi 3, 40126 Bologna, Italy.
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna, via Selmi 3, 40126 Bologna, Italy.
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18
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BRCA1 ensures genome integrity by eliminating estrogen-induced pathological topoisomerase II-DNA complexes. Proc Natl Acad Sci U S A 2018; 115:E10642-E10651. [PMID: 30352856 DOI: 10.1073/pnas.1803177115] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Women having BRCA1 germ-line mutations develop cancer in breast and ovary, estrogen-regulated tissues, with high penetrance. Binding of estrogens to the estrogen receptor (ER) transiently induces DNA double-strand breaks (DSBs) by topoisomerase II (TOP2) and controls gene transcription. TOP2 resolves catenated DNA by transiently generating DSBs, TOP2-cleavage complexes (TOP2ccs), where TOP2 covalently binds to 5' ends of DSBs. TOP2 frequently fails to complete its catalysis, leading to formation of pathological TOP2ccs. We have previously shown that the endonucleolytic activity of MRE11 plays a key role in removing 5' TOP2 adducts in G1 phase. We show here that BRCA1 promotes MRE11-mediated removal of TOP2 adducts in G1 phase. We disrupted the BRCA1 gene in 53BP1-deficient ER-positive breast cancer and B cells. The loss of BRCA1 caused marked increases of pathological TOP2ccs in G1 phase following exposure to etoposide, which generates pathological TOP2ccs. We conclude that BRCA1 promotes the removal of TOP2 adducts from DSB ends for subsequent nonhomologous end joining. BRCA1-deficient cells showed a decrease in etoposide-induced MRE11 foci in G1 phase, suggesting that BRCA1 repairs pathological TOP2ccs by promoting the recruitment of MRE11 to TOP2cc sites. BRCA1 depletion also leads to the increase of unrepaired DSBs upon estrogen treatment both in vitro in G1-arrested breast cancer cells and in vivo in epithelial cells of mouse mammary glands. BRCA1 thus plays a critical role in removing pathological TOP2ccs induced by estrogens as well as etoposide. We propose that BRCA1 suppresses tumorigenesis by removing estrogen-induced pathological TOP2ccs throughout the cell cycle.
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19
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Bhanothu V, Kondapi AK. Status of topoisomerase-2β protein in all-trans retinoic acid-treated human neuroblastoma (SK-N-SH) cells. J Cell Biochem 2018; 120:5169-5182. [PMID: 30318608 DOI: 10.1002/jcb.27793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 09/10/2018] [Indexed: 01/23/2023]
Abstract
Of the mammalian topoisomerase (Topo)-2 isozymes (α and β), Topo-2β protein has been reported to regulate neuronal development and differentiation. However, the status of Topo-2β in all-trans retinoic acid (ATRA)-treated human neuroblastoma (SK-N-SH) cells is not understood. More information about the effects of ATRA on SK-N-SH cells is needed to reveal the role of ATRA in the regulation of Topo-2β levels and spontaneous regression of SK-N-SH cells to predict the clinical activity. This study was proposed to investigate the status and role of Topo-2β protein in ATRA-induced survival and neuronal differentiation of SK-N-SH cells. Microscopic, sodium dodecyl sulfate polyacrylamide gel electrophoresis after immunoprecipitations and Western blot analysis were used to study and compare Topo-2β protein among 10 µM ATRA-treated SK-N-SH cells and controls at different time points. The level of Topo-2β protein increased in the initial days of treatment but markedly decreased upon induction of differentiation by ATRA in later stages. Upon ATRA treatment, SK-N-SH cells stretched, exhibited neurite extensions, and acquired a neuronal phenotype. Both treated and untreated SK-N-SH cells were able to migrate, occupy the scratched area, and completely recolonized 24 hours later. These results suggest an indirect role of Topo-2β protein in regulation of genes involved in cell migration and differentiation of ATRA-treated SK-N-SH cells. This study suggests that Topo-2β may be part of activation/repression of protein complexes activated by epigenetic modifying agents, differentiating signals, and inducible locus. However, detailed studies are needed to explore the ATRA-downstream genes leading to Topo-2β regulation and regulatory proteins of neuronal differentiation.
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Affiliation(s)
- Venkanna Bhanothu
- Department of Biotechnology and Bioinformatics, SLS, University of Hyderabad, Hyderabad, India
| | - Anand Kumar Kondapi
- Department of Biotechnology and Bioinformatics, SLS, University of Hyderabad, Hyderabad, India
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20
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Austin CA, Lee KC, Swan RL, Khazeem MM, Manville CM, Cridland P, Treumann A, Porter A, Morris NJ, Cowell IG. TOP2B: The First Thirty Years. Int J Mol Sci 2018; 19:ijms19092765. [PMID: 30223465 PMCID: PMC6163646 DOI: 10.3390/ijms19092765] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022] Open
Abstract
Type II DNA topoisomerases (EC 5.99.1.3) are enzymes that catalyse topological changes in DNA in an ATP dependent manner. Strand passage reactions involve passing one double stranded DNA duplex (transported helix) through a transient enzyme-bridged break in another (gated helix). This activity is required for a range of cellular processes including transcription. Vertebrates have two isoforms: topoisomerase IIα and β. Topoisomerase IIβ was first reported in 1987. Here we review the research on DNA topoisomerase IIβ over the 30 years since its discovery.
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Affiliation(s)
- Caroline A Austin
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Ka C Lee
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Rebecca L Swan
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Mushtaq M Khazeem
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Catriona M Manville
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Peter Cridland
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Achim Treumann
- NUPPA, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Andrew Porter
- NUPPA, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Nick J Morris
- School of Biomedical Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Ian G Cowell
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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21
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The Roles of DNA Topoisomerase IIβ in Transcription. Int J Mol Sci 2018; 19:ijms19071917. [PMID: 29966298 PMCID: PMC6073266 DOI: 10.3390/ijms19071917] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 12/22/2022] Open
Abstract
Type IIA topoisomerases allow DNA double helical strands to pass through each other by generating transient DNA double strand breaks βDSBs), and in so doing, resolve torsional strain that accumulates during transcription, DNA replication, chromosome condensation, chromosome segregation and recombination. Whereas most eukaryotes possess a single type IIA enzyme, vertebrates possess two distinct type IIA topoisomerases, Topo IIα and Topo IIβ. Although the roles of Topo IIα, especially in the context of chromosome condensation and segregation, have been well-studied, the roles of Topo IIβ are only beginning to be illuminated. This review begins with a summary of the initial studies surrounding the discovery and characterization of Topo IIβ and then focuses on the insights gained from more recent studies that have elaborated important functions for Topo IIβ in transcriptional regulation.
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22
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Bollimpelli VS, Dholaniya PS, Kondapi AK. Topoisomerase IIβ and its role in different biological contexts. Arch Biochem Biophys 2017; 633:78-84. [PMID: 28669856 DOI: 10.1016/j.abb.2017.06.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 06/24/2017] [Accepted: 06/27/2017] [Indexed: 12/27/2022]
Abstract
Topoisomerase IIβ is a type II DNA topoisomerase that was reported to be expressed in all mammalian cells but abundantly expressed in cells that have undergone terminal differentiation to attain a post mitotic state. Enzymatically it catalyzes ATP-dependent topological changes of double stranded DNA, while as a protein it was reported to be associated with several factors in promoting cell growth, migration, DNA repair and transcription regulation. The cellular roles of topoisomerase IIβ are very less understood compared to its counterpart topoisomerase IIα. This review discusses origin of Topoisomerase II beta, its structure, activities reported in vitro and in vivo along with implications in cellular processes namely transcription, DNA repair, neuronal development, aging, HIV-infection and cancer.
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Affiliation(s)
- V Satish Bollimpelli
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Pankaj S Dholaniya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Anand K Kondapi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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23
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Yu X, Davenport JW, Urtishak KA, Carillo ML, Gosai SJ, Kolaris CP, Byl JAW, Rappaport EF, Osheroff N, Gregory BD, Felix CA. Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci. Genome Res 2017; 27:1238-1249. [PMID: 28385713 PMCID: PMC5495075 DOI: 10.1101/gr.211615.116] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 04/05/2017] [Indexed: 01/22/2023]
Abstract
Type II topoisomerases orchestrate proper DNA topology, and they are the targets of anti-cancer drugs that cause treatment-related leukemias with balanced translocations. Here, we develop a high-throughput sequencing technology to define TOP2 cleavage sites at single-base precision, and use the technology to characterize TOP2A cleavage genome-wide in the human K562 leukemia cell line. We find that TOP2A cleavage has functionally conserved local sequence preferences, occurs in cleavage cluster regions (CCRs), and is enriched in introns and lincRNA loci. TOP2A CCRs are biased toward the distal regions of gene bodies, and TOP2 poisons cause a proximal shift in their distribution. We find high TOP2A cleavage levels in genes involved in translocations in TOP2 poison–related leukemia. In addition, we find that a large proportion of genes involved in oncogenic translocations overall contain TOP2A CCRs. The TOP2A cleavage of coding and lincRNA genes is independently associated with both length and transcript abundance. Comparisons to ENCODE data reveal distinct TOP2A CCR clusters that overlap with marks of transcription, open chromatin, and enhancers. Our findings implicate TOP2A cleavage as a broad DNA damage mechanism in oncogenic translocations as well as a functional role of TOP2A cleavage in regulating transcription elongation and gene activation.
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Affiliation(s)
- Xiang Yu
- Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - James W Davenport
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Karen A Urtishak
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Marie L Carillo
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sager J Gosai
- Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Christos P Kolaris
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Eric F Rappaport
- NAPCore, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, USA.,Department of Medicine (Hematology/Oncology), Vanderbilt University, Nashville, Tennessee 37232, USA.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, USA
| | - Brian D Gregory
- Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Carolyn A Felix
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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24
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Miller EL, Hargreaves DC, Kadoch C, Chang CY, Calarco JP, Hodges C, Buenrostro JD, Cui K, Greenleaf WJ, Zhao K, Crabtree GR. TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nat Struct Mol Biol 2017; 24:344-352. [PMID: 28250416 PMCID: PMC5395302 DOI: 10.1038/nsmb.3384] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/01/2017] [Indexed: 12/19/2022]
Abstract
Resolution and formation of facultative heterochromatin is essential to development, reprogramming, and oncogenesis. The mechanisms underlying these changes are poorly understood due to the inability to study heterochromatin dynamics and structure in vivo. We devised an in vivo approach to investigate these mechanisms and found that topoisomerase II (TOP2), but not TOP1, synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin independent of transcription, indicating that changes in DNA topology through (de-)catenation rather than release of torsional stress through swiveling is necessary for heterochromatin resolution. In turn, TOP2 and BAF cooperate to recruit pluripotency factors, explaining some of the instructive roles of BAF complexes. Unexpectedly, we found that TOP2, also plays a role in the reformation of facultative heterochromatin, suggesting that facultative heterochromatin and accessible chromatin exist at different states of catenation or other topologies, which may be critical to their structures.
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Affiliation(s)
- Erik L Miller
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Diana C Hargreaves
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chiung-Ying Chang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Joseph P Calarco
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Courtney Hodges
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Society of Fellows, Harvard University, Cambridge, Massachusetts, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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25
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Abstract
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo.
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26
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Kenig S, Faoro V, Bourkoula E, Podergajs N, Ius T, Vindigni M, Skrap M, Lah T, Cesselli D, Storici P, Vindigni A. Topoisomerase IIβ mediates the resistance of glioblastoma stem cells to replication stress-inducing drugs. Cancer Cell Int 2016; 16:58. [PMID: 27462186 PMCID: PMC4960855 DOI: 10.1186/s12935-016-0339-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 07/18/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Glioblastoma stem cells (GSC) have been extensively recognized as a plausible cause of glioblastoma resistance to therapy and recurrence resulting in high glioblastoma mortality. Abnormalities in the DNA repair pathways might be responsible for the inability of the currently used chemotherapeutics to eliminate the (GSC) subpopulation. METHODS In this work, we compared the expression of sixty DNA repair related genes between primary glioblastoma cell cultures and the glioblastoma enriched stem cell primary cultures. MTT test was used to analyze the effect of selected drugs and immunofluorescence to evaluate the load of DNA damage. RESULTS We found several differentially expressed genes and we identified topoisomerase IIβ (Top2β) as the gene with highest up-regulation in GSC. Also among the tested cell lines the expression of Top2β was the highest in NCH421k cells, a well-characterized glioblastoma cell line with all the stemness characteristics. On the other hand, Top2β expression markedly decreased upon the induction of differentiation by all trans-retinoic acid. Depletion of Top2β increased the sensitivity of NCH421k cells to replication stress inducing drugs, such as cisplatin, methyl-methanesulfonate, hydrogen peroxide, and temozolomide. Consistently, we found an increased load of DNA damage and increased Chk1 activation upon Top2β depletion in NCH421k cells. CONCLUSION We suggest that Top2β may represent a new target for gene therapy in glioblastoma. In addition, the other genes that we found to be up-regulated in GSC versus glioblastoma primary cells should be further investigated as glioblastoma theranostics.
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Affiliation(s)
- Saša Kenig
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Strada Statale 14-km 163, 5, Basovizza, 34149 Trieste, Italy
| | - Valentina Faoro
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Strada Statale 14-km 163, 5, Basovizza, 34149 Trieste, Italy
| | - Evgenia Bourkoula
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Neža Podergajs
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Tamara Ius
- Neurosurgery Unit, Department of Neurosciences, Santa Maria della Misericordia University Hospital, Piazzale Santa Maria della Misericordia, 15, Udine, Italy
| | - Marco Vindigni
- Neurosurgery Unit, Department of Neurosciences, Santa Maria della Misericordia University Hospital, Piazzale Santa Maria della Misericordia, 15, Udine, Italy
| | - Miran Skrap
- Neurosurgery Unit, Department of Neurosciences, Santa Maria della Misericordia University Hospital, Piazzale Santa Maria della Misericordia, 15, Udine, Italy
| | - Tamara Lah
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia ; Faculty of Chemistry and Chemical Engineering, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Daniela Cesselli
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Paola Storici
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Strada Statale 14-km 163, 5, Basovizza, 34149 Trieste, Italy
| | - Alessandro Vindigni
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Strada Statale 14-km 163, 5, Basovizza, 34149 Trieste, Italy ; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO USA
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27
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Corless S, Gilbert N. Effects of DNA supercoiling on chromatin architecture. Biophys Rev 2016; 8:245-258. [PMID: 27738453 PMCID: PMC5039215 DOI: 10.1007/s12551-016-0210-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022] Open
Abstract
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo.
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Affiliation(s)
- Samuel Corless
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH42XU UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH42XU UK
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28
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Miyaji M, Furuta R, Sano K, Tsutsui KM, Tsutsui K. Genomic regions targeted by DNA topoisomerase IIβ frequently interact with a nuclear scaffold/matrix protein hnRNP U/SAF-A/SP120. J Cell Biochem 2016; 116:677-85. [PMID: 25418483 PMCID: PMC5024068 DOI: 10.1002/jcb.25024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/18/2014] [Indexed: 11/16/2022]
Abstract
Type II DNA topoisomerases (topo II) play critical roles in some cellular events through repeated cleavage/rejoining of nuclear DNA. The β isoform (topo IIβ) is essential for the transcriptional induction of neuronal genes in terminal differentiation. Genomic sites targeted by the enzyme are nonrandom. Although previous studies have claimed that topo II cleavage sites are close to the nuclear scaffold/matrix attachment region (S/MAR), it is still unclear whether this view can be generalized. We report here that a library of cloned genomic DNA fragments targeted by topo IIβ in vivo frequently contains S/MAR and binding sites for hnRNP U/SAF‐A/SP120. Binding assays in vitro showed that a large proportion of the target DNAs bound to SP120 but their affinity to the nuclear scaffold/matrix varied significantly. Topo IIβ targets were extremely AT‐rich and often located in gene‐poor long intergenic regions (so‐called gene desert) that are juxtaposed to long genes expressed in neurons under differentiation. Sequence analysis revealed that topo IIβ targets are not just AT‐rich but are enriched with short tracts of A's and T's (termed A/T‐patches). Their affinity to the nuclear scaffold/matrix showed a moderate positive correlation with the coverage rate of A/T‐patches. The results suggest that the interaction of topo IIβ/SP120 with target regions modulates their proximity to the nuclear scaffold/matrix in a dynamic fashion and that A/T‐patch is a sequence motif assisting this process. J. Cell. Biochem. 116: 677–685, 2015. © 2014 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Mary Miyaji
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
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29
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Jabbari K, Nürnberg P. A genomic view on epilepsy and autism candidate genes. Genomics 2016; 108:31-6. [PMID: 26772991 DOI: 10.1016/j.ygeno.2016.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/15/2015] [Accepted: 01/01/2016] [Indexed: 01/25/2023]
Abstract
Epilepsy is a common complex disorder most frequently associated with psychiatric and neurological diseases. Massive parallel sequencing of individual or cohort genomes and exomes led the identification of several disease associated genes. We review here the candidate genes in epilepsy genetics with focus on exome and gene panel data. Together with the examination of brain expressed genes and post synaptic proteome the results show that: (1) Non-metabolic epilepsies and autism candidate genes tend to be AT-rich and (2) large transcript size and local AT-richness are characteristic features of genes involved in developmental brain disorders and synaptic functions. These results point to the preferential location of core epilepsy and autism candidate genes in late replicating, GC-poor chromosomal regions (isochores). These results indicate that the genomic alterations leading to some brain disorders are confined to responsive chromatin areas harboring brain critical genes.
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Affiliation(s)
- Kamel Jabbari
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
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30
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Manville CM, Smith K, Sondka Z, Rance H, Cockell S, Cowell IG, Lee KC, Morris NJ, Padget K, Jackson GH, Austin CA. Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells. Biol Open 2015; 4:1436-47. [PMID: 26459242 PMCID: PMC4728365 DOI: 10.1242/bio.014308] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We report the whole genome ChIP seq for human TOP2B from MCF7 cells. Using three different peak calling methods, regions of binding were identified in the presence or absence of the nuclear hormone estradiol, as TOP2B has been reported to play a role in ligand-induced transcription. TOP2B peaks were found across the whole genome, 50% of the peaks fell either within a gene or within 5 kb of a transcription start site. TOP2B peaks coincident with gene promoters were less frequently associated with epigenetic features marking active promoters in estradiol treated than in untreated cells. Significantly enriched transcription factor motifs within the DNA sequences underlying the peaks were identified. These included SP1, KLF4, TFAP2A, MYF, REST, CTCF, ESR1 and ESR2. Gene ontology analysis of genes associated with TOP2B peaks found neuronal development terms including axonogenesis and axon guidance were significantly enriched. In the absence of functional TOP2B there are errors in axon guidance in the zebrafish eye. Specific heparin sulphate structures are involved in retinal axon targeting. The glycosaminoglycan biosynthesis–heparin sulphate/heparin pathway is significantly enriched in the TOP2B gene ontology analysis, suggesting changes in this pathway in the absence of TOP2B may cause the axon guidance faults. Summary: Gene ontology enrichment analysis of genes associated with human TOP2B peaks, identified by whole genome ChIP seq used to identify regions of binding, highlighted a number of processes in neuronal development including axonogenesis and axon guidance.
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Affiliation(s)
- Catriona M Manville
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kayleigh Smith
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Zbyslaw Sondka
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Holly Rance
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Simon Cockell
- The Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ian G Cowell
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ka Cheong Lee
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Nicholas J Morris
- School of Biomedical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kay Padget
- Department of Applied Biology, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Graham H Jackson
- Institute for Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Caroline A Austin
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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31
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DNA topoisomerase IIβ as a molecular switch in neural differentiation of mesenchymal stem cells. Ann Hematol 2014; 94:307-18. [DOI: 10.1007/s00277-014-2209-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 08/28/2014] [Indexed: 12/27/2022]
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32
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Onoda A, Hosoya O, Sano K, Kiyama K, Kimura H, Kawano S, Furuta R, Miyaji M, Tsutsui K, Tsutsui KM. Nuclear dynamics of topoisomerase IIβ reflects its catalytic activity that is regulated by binding of RNA to the C-terminal domain. Nucleic Acids Res 2014; 42:9005-20. [PMID: 25034690 PMCID: PMC4132749 DOI: 10.1093/nar/gku640] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
DNA topoisomerase II (topo II) changes DNA topology by cleavage/re-ligation cycle(s) and thus contributes to various nuclear DNA transactions. It is largely unknown how the enzyme is controlled in a nuclear context. Several studies have suggested that its C-terminal domain (CTD), which is dispensable for basal relaxation activity, has some regulatory influence. In this work, we examined the impact of nuclear localization on regulation of activity in nuclei. Specifically, human cells were transfected with wild-type and mutant topo IIβ tagged with EGFP. Activity attenuation experiments and nuclear localization data reveal that the endogenous activity of topo IIβ is correlated with its subnuclear distribution. The enzyme shuttles between an active form in the nucleoplasm and a quiescent form in the nucleolus in a dynamic equilibrium. Mechanistically, the process involves a tethering event with RNA. Isolated RNA inhibits the catalytic activity of topo IIβ in vitro through the interaction with a specific 50-residue region of the CTD (termed the CRD). Taken together, these results suggest that both the subnuclear distribution and activity regulation of topo IIβ are mediated by the interplay between cellular RNA and the CRD.
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Affiliation(s)
- Akihisa Onoda
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Osamu Hosoya
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Kuniaki Sano
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Kazuko Kiyama
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Hiroshi Kimura
- Laboratory of Biological Science, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shinji Kawano
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Ryohei Furuta
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Mary Miyaji
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Ken Tsutsui
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Kimiko M Tsutsui
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
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33
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Li Y, Hao H, Tzatzalos E, Lin RK, Doh S, Liu LF, Lyu YL, Cai L. Topoisomerase IIbeta is required for proper retinal development and survival of postmitotic cells. Biol Open 2014; 3:172-84. [PMID: 24463367 PMCID: PMC3925320 DOI: 10.1242/bio.20146767] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Topoisomerase IIbeta (Top2b) is an enzyme that modulates DNA supercoiling by catalyzing the passage of DNA duplexes through one another. It is ubiquitously expressed in postmitotic cells and known to function during the development of neuromuscular junctions in the diaphragm and the proper formation of laminar structure in the cerebral cortex. However, due to the perinatal death phenotype of the traditional constitutive and brain-specific Top2b knockout mice, the precise in vivo function of Top2b, especially during postnatal neural development, remains to be determined. Using both the constitutive and retina-specific knockout mouse models, we showed that Top2b deficiency resulted in delayed neuronal differentiation, degeneration of the plexiform layers and outer segment of photoreceptors, as well as dramatic reduction in cell number in the retina. Genome-wide transcriptome analysis by RNA sequencing revealed that genes involved in neuronal survival and neural system development were preferentially affected in Top2b-deficient retinas. Collectively, our findings have indicated an important function of Top2b in proper development and the maintenance/survival of postmitotic neurons in the retina.
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Affiliation(s)
- Ying Li
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
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34
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King IF, Yandava CN, Mabb AM, Hsiao JS, Huang HS, Pearson BL, Calabrese JM, Starmer J, Parker JS, Magnuson T, Chamberlain SJ, Philpot BD, Zylka MJ. Topoisomerases facilitate transcription of long genes linked to autism. Nature 2013; 501:58-62. [PMID: 23995680 PMCID: PMC3767287 DOI: 10.1038/nature12504] [Citation(s) in RCA: 304] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 07/24/2013] [Indexed: 12/12/2022]
Abstract
Topoisomerases are expressed throughout the developing and adult brain and are mutated in some individuals with autism spectrum disorder (ASD). However, how topoisomerases are mechanistically connected to ASD is unknown. Here we found that topotecan, a Topoisomerase 1 (TOP1) inhibitor, dose-dependently reduced the expression of extremely long genes in mouse and human neurons, including nearly all genes >200 kb. Expression of long genes was also reduced following knockdown of Top1 or Top2b in neurons, highlighting that each enzyme was required for full expression of long genes. By mapping RNA polymerase II density genome-wide in neurons, we found that this length-dependent effect on gene expression was due to impaired transcription elongation. Interestingly, many high confidence ASD candidate genes are exceptionally long and were reduced in expression following TOP1 inhibition. Our findings suggest that chemicals and genetic mutations that impair topoisomerases could commonly contribute to ASD and other neurodevelopmental disorders.
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Affiliation(s)
- Ian F King
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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35
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Nikolaou C, Bermúdez I, Manichanh C, García-Martinez J, Guigó R, Pérez-Ortín JE, Roca J. Topoisomerase II regulates yeast genes with singular chromatin architectures. Nucleic Acids Res 2013; 41:9243-56. [PMID: 23935120 PMCID: PMC3814376 DOI: 10.1093/nar/gkt707] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic topoisomerase II (topo II) is the essential decatenase of newly replicated chromosomes and the main relaxase of nucleosomal DNA. Apart from these general tasks, topo II participates in more specialized functions. In mammals, topo IIα interacts with specific RNA polymerases and chromatin-remodeling complexes, whereas topo IIβ regulates developmental genes in conjunction with chromatin remodeling and heterochromatin transitions. Here we show that in budding yeast, topo II regulates the expression of specific gene subsets. To uncover this, we carried out a genomic transcription run-on shortly after the thermal inactivation of topo II. We identified a modest number of genes not involved in the general stress response but strictly dependent on topo II. These genes present distinctive functional and structural traits in comparison with the genome average. Yeast topo II is a positive regulator of genes with well-defined promoter architecture that associates to chromatin remodeling complexes; it is a negative regulator of genes extremely hypo-acetylated with complex promoters and undefined nucleosome positioning, many of which are involved in polyamine transport. These findings indicate that yeast topo II operates on singular chromatin architectures to activate or repress DNA transcription and that this activity produces functional responses to ensure chromatin stability.
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Affiliation(s)
- Christoforos Nikolaou
- Molecular Biology Institute of Barcelona, CSIC, 08028 Barcelona, Spain, Department of Biology, University of Crete, 71409 Heraklion, Greece, Department of Genetics and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain and Department of Biochemistry and Molecular Biology and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain
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36
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Dykhuizen EC, Hargreaves DC, Miller EL, Cui K, Korshunov A, Kool M, Pfister S, Cho YJ, Zhao K, Crabtree GR. BAF complexes facilitate decatenation of DNA by topoisomerase IIα. Nature 2013; 497:624-7. [PMID: 23698369 PMCID: PMC3668793 DOI: 10.1038/nature12146] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 04/03/2013] [Indexed: 12/19/2022]
Abstract
Recent exon-sequencing studies of human tumours have revealed that subunits of BAF (mammalian SWI/SNF) complexes are mutated in more than 20% of all human malignancies, but the mechanisms involved in tumour suppression are unclear. BAF chromatin-remodelling complexes are polymorphic assemblies that use energy provided by ATP hydrolysis to regulate transcription through the control of chromatin structure and the placement of Polycomb repressive complex 2 (PRC2) across the genome. Several proteins dedicated to this multisubunit complex, including BRG1 (also known as SMARCA4) and BAF250a (also known as ARID1A), are mutated at frequencies similar to those of recognized tumour suppressors. In particular, the core ATPase BRG1 is mutated in 5-10% of childhood medulloblastomas and more than 15% of Burkitt's lymphomas. Here we show a previously unknown function of BAF complexes in decatenating newly replicated sister chromatids, a requirement for proper chromosome segregation during mitosis. We find that deletion of Brg1 in mouse cells, as well as the expression of BRG1 point mutants identified in human tumours, leads to anaphase bridge formation (in which sister chromatids are linked by catenated strands of DNA) and a G2/M-phase block characteristic of the decatenation checkpoint. Endogenous BAF complexes interact directly with endogenous topoisomerase IIα (TOP2A) through BAF250a and are required for the binding of TOP2A to approximately 12,000 sites across the genome. Our results demonstrate that TOP2A chromatin binding is dependent on the ATPase activity of BRG1, which is compromised in oncogenic BRG1 mutants. These studies indicate that the ability of TOP2A to prevent DNA entanglement at mitosis requires BAF complexes and suggest that this activity contributes to the role of BAF subunits as tumour suppressors.
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Affiliation(s)
- Emily C Dykhuizen
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
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DNA topoisomerase II is involved in regulation of cyst wall protein genes and differentiation in Giardia lamblia. PLoS Negl Trop Dis 2013; 7:e2218. [PMID: 23696909 PMCID: PMC3656124 DOI: 10.1371/journal.pntd.0002218] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 04/04/2013] [Indexed: 12/16/2022] Open
Abstract
The protozoan Giardia lamblia differentiates into infectious cysts within the human intestinal tract for disease transmission. Expression of the cyst wall protein (cwp) genes increases with similar kinetics during encystation. However, little is known how their gene regulation shares common mechanisms. DNA topoisomerases maintain normal topology of genomic DNA. They are necessary for cell proliferation and tissue development as they are involved in transcription, DNA replication, and chromosome condensation. A putative topoisomerase II (topo II) gene has been identified in the G. lamblia genome. We asked whether Topo II could regulate Giardia encystation. We found that Topo II was present in cell nuclei and its gene was up-regulated during encystation. Topo II has typical ATPase and DNA cleavage activity of type II topoisomerases. Mutation analysis revealed that the catalytic important Tyr residue and cleavage domain are important for Topo II function. We used etoposide-mediated topoisomerase immunoprecipitation assays to confirm the binding of Topo II to the cwp promoters in vivo. Interestingly, Topo II overexpression increased the levels of cwp gene expression and cyst formation. Microarray analysis identified up-regulation of cwp and specific vsp genes by Topo II. We also found that the type II topoisomerase inhibitor etoposide has growth inhibition effect on Giardia. Addition of etoposide significantly decreased the levels of cwp gene expression and cyst formation. Our results suggest that Topo II has been functionally conserved during evolution and that Topo II plays important roles in induction of the cwp genes, which is key to Giardia differentiation into cysts. Giardia lamblia becomes infective by differentiation into water-resistant cysts. During encystation, cyst wall proteins (CWPs) are highly synthesized and are targeted to the cyst wall. However, little is known about the regulation mechanisms of these genes. DNA topoisomerases can resolve the topological problems and are needed for a variety of key cellular functions, including cell proliferation, cell differentiation and organ development in higher eukaryotes. We found that giardial Topo II was highly expressed during encystation. Topo II is present in Giardia nuclei and is associated with the encystation-induced cwp gene promoters. Topo II has typical DNA cleavage activity of type II topoisomerases. Interestingly, overexpression of Topo II can induce cwp gene expression and cyst formation. Addition of a type II topoisomerase inhibitor, etoposide, significantly decreased the levels of cwp gene expression and cyst formation. Etoposide also has growth inhibition effect on Giardia. Our results suggest that Topo II plays an important role in induction of encystation by up-regulation of the cwp gene expression. Our results provide insights into the function of Topo II in parasite differentiation into cysts and help develop ways to interrupt the parasite life cycle.
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Rouzeau S, Cordelières FP, Buhagiar-Labarchède G, Hurbain I, Onclercq-Delic R, Gemble S, Magnaghi-Jaulin L, Jaulin C, Amor-Guéret M. Bloom's syndrome and PICH helicases cooperate with topoisomerase IIα in centromere disjunction before anaphase. PLoS One 2012; 7:e33905. [PMID: 22563370 PMCID: PMC3338505 DOI: 10.1371/journal.pone.0033905] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/19/2012] [Indexed: 11/19/2022] Open
Abstract
Centromeres are specialized chromosome domains that control chromosome segregation during mitosis, but little is known about the mechanisms underlying the maintenance of their integrity. Centromeric ultrafine anaphase bridges are physiological DNA structures thought to contain unresolved DNA catenations between the centromeres separating during anaphase. BLM and PICH helicases colocalize at these ultrafine anaphase bridges and promote their resolution. As PICH is detectable at centromeres from prometaphase onwards, we hypothesized that BLM might also be located at centromeres and that the two proteins might cooperate to resolve DNA catenations before the onset of anaphase. Using immunofluorescence analyses, we demonstrated the recruitment of BLM to centromeres from G2 phase to mitosis. With a combination of fluorescence in situ hybridization, electron microscopy, RNA interference, chromosome spreads and chromatin immunoprecipitation, we showed that both BLM-deficient and PICH-deficient prometaphase cells displayed changes in centromere structure. These cells also had a higher frequency of centromeric non disjunction in the absence of cohesin, suggesting the persistence of catenations. Both proteins were required for the correct recruitment to the centromere of active topoisomerase IIα, an enzyme specialized in the catenation/decatenation process. These observations reveal the existence of a functional relationship between BLM, PICH and topoisomerase IIα in the centromere decatenation process. They indicate that the higher frequency of centromeric ultrafine anaphase bridges in BLM-deficient cells and in cells treated with topoisomerase IIα inhibitors is probably due not only to unresolved physiological ultrafine anaphase bridges, but also to newly formed ultrafine anaphase bridges. We suggest that BLM and PICH cooperate in rendering centromeric catenates accessible to topoisomerase IIα, thereby facilitating correct centromere disjunction and preventing the formation of supernumerary centromeric ultrafine anaphase bridges.
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Affiliation(s)
- Sébastien Rouzeau
- Institut Curie, Centre de Recherche, Centre Universitaire, Bât, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
| | - Fabrice P. Cordelières
- Institut Curie, Centre de Recherche, Centre Universitaire, Bât, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Institut Curie, Centre de Recherche, Plateforme d’Imagerie Cellulaire et Tissulaire IBiSA, Centre Universitaire, Bât, Orsay, France
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, Centre de Recherche, Centre Universitaire, Bât, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
| | - Ilse Hurbain
- Institut Curie, Centre de Recherche, Paris, France
- Structure et Compartimentation membranaire, CNRS UMR144, Paris, France
- Plateforme d’Imagerie Cellulaire et Tissulaire IBiSA, CNRS UMR 144, Paris, France
| | - Rosine Onclercq-Delic
- Institut Curie, Centre de Recherche, Centre Universitaire, Bât, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
| | - Simon Gemble
- Institut Curie, Centre de Recherche, Centre Universitaire, Bât, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
| | - Laura Magnaghi-Jaulin
- Institut de Génétique et Développement, CNRS UMR 6290, Université de Rennes 1, Rennes, France
| | - Christian Jaulin
- Institut de Génétique et Développement, CNRS UMR 6290, Université de Rennes 1, Rennes, France
| | - Mounira Amor-Guéret
- Institut Curie, Centre de Recherche, Centre Universitaire, Bât, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
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Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state. Proc Natl Acad Sci U S A 2012; 109:E934-43. [PMID: 22474351 DOI: 10.1073/pnas.1119798109] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Topoisomerases are essential for DNA replication in dividing cells, but their genomic targets and function in postmitotic cells remain poorly understood. Here we show that a switch in the expression from Topoisomerases IIα (Top2α) to IIβ (Top2β) occurs during neuronal differentiation in vitro and in vivo. Genome-scale location analysis in stem cell-derived postmitotic neurons reveals Top2β binding to chromosomal sites that are methylated at lysine 4 of histone H3, a feature of regulatory regions. Indeed Top2β-bound sites are preferentially promoters and become targets during the transition from neuronal progenitors to neurons, at a time when cells exit the cell cycle. Absence of Top2β protein or its activity leads to changes in transcription and chromatin accessibility at many target genes. Top2β deficiency does not impair stem cell properties and early steps of neuronal differentiation but causes premature death of postmitotic neurons. This neuronal degeneration is caused by up-regulation of Ngfr p75, a gene bound and repressed by Top2β. These findings suggest a chromatin-based targeting of Top2β to regulatory regions in the genome to govern the transcriptional program associated with neuronal differentiation and longevity.
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Vávrová A, Šimůnek T. DNA topoisomerase IIβ: a player in regulation of gene expression and cell differentiation. Int J Biochem Cell Biol 2012; 44:834-7. [PMID: 22465709 DOI: 10.1016/j.biocel.2012.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/02/2012] [Accepted: 03/06/2012] [Indexed: 01/06/2023]
Abstract
DNA topoisomerases II regulate conformational changes in DNA topology. They act on double-stranded DNA, catalyzing its relaxation, decatenation and unknotting. Vertebrate cells express two isoforms of topoisomerase II, which are similar in structure, but different in function and regulation. Whereas the alpha isoform is indispensable for proper cell replication, the functions of the beta isoform as well as reasons for its evolution in vertebrates were long unclear. Unlike topoisomerase II alpha, the beta isoform is predominantly expressed in quiescent cells and has been implicated mainly in the process of gene transcription. Recently, new discoveries point on the role of the topoisomerase II beta in regulation of cellular differentiation and tissue development. Furthermore, contemporary discoveries are raising possibilities for novel therapeutic approaches involving selective targeting of either topoisomerase II isoform in potentiating antitumor and/or reducing adverse effects of topoisomerase II poisons.
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Affiliation(s)
- Anna Vávrová
- Charles University in Prague, Faculty of Pharmacy in Hradec Králové, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
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Nurr1 regulates Top IIβ and functions in axon genesis of mesencephalic dopaminergic neurons. Mol Neurodegener 2012; 7:4. [PMID: 22296971 PMCID: PMC3359158 DOI: 10.1186/1750-1326-7-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 02/02/2012] [Indexed: 01/28/2023] Open
Abstract
Background NURR1 (also named as NR4A2) is a member of the steroid/thyroid hormone receptor family, which can bind to DNA and modulate expression of target genes. Previous studies have shown that NURR1 is essential for the nigral dopaminergic neuron phenotype and function maintenance, and the defects of the gene are possibly associated with Parkinson's disease (PD). Results In this study, we used new born Nurr1 knock-out mice combined with Affymetrix genechip technology and real time polymerase chain reaction (PCR) to identify Nurr1 regulated genes, which led to the discovery of several transcripts differentially expressed in the nigro-striatal pathway of Nurr1 knock-out mice. We found that an axon genesis gene called Topoisomerase IIβ (Top IIβ) was down-regulated in Nurr1 knock-out mice and we identified two functional NURR1 binding sites in the proximal Top IIβ promoter. While in Top IIβ null mice, we saw a significant loss of dopaminergic neurons in the substantial nigra and lack of neurites along the nigro-striatal pathway. Using specific TOP II antagonist ICRF-193 or Top IIβ siRNA in the primary cultures of ventral mesencephalic (VM) neurons, we documented that suppression of TOP IIβ expression resulted in VM neurites shortening and growth cones collapsing. Furthermore, microinjection of ICRF-193 into the mouse medial forebrain bundle (MFB) led to the loss of nigro-striatal projection. Conclusion Taken together, our findings suggest that Top IIβ might be a down-stream target of Nurr1, which might influence the processes of axon genesis in dopaminergic neurons via the regulation of TOP IIβ expression. The Nurr1-Top IIβ interaction may shed light on the pathologic role of Nurr1 defect in the nigro-striatal pathway deficiency associated with PD.
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Nevin LM, Xiao T, Staub W, Baier H. Topoisomerase IIbeta is required for lamina-specific targeting of retinal ganglion cell axons and dendrites. Development 2011; 138:2457-65. [PMID: 21610027 DOI: 10.1242/dev.060335] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The specific partnering of synaptically connected neurons is central to nervous system function. Proper wiring requires the interchange of signals between a postmitotic neuron and its environment, a distinct pattern of transcription in the nucleus, and deployment of guidance and adhesion cues to the cell surface. To identify genes involved in neurite targeting by retinal ganglion cells (GCs), their presynaptic partners in the retina, and their postsynaptic targets in the optic tectum, we undertook a forward genetic screen for mutations disrupting visual responses in zebrafish. This rapid primary screen was subsequently refined by immunohistochemical labeling of retinal and tectal neurites to detect patterning errors. From this unbiased screen, the notorious (noto) mutant exhibited the most specific phenotypes: intact retinal and tectal differentiation but multiple neurite targeting defects in the retinal inner plexiform layer (IPL) and tectal neuropil. Positional cloning and morpholino phenocopy revealed that the mutation disrupts Topoisomerase IIβ (Top2b), a broadly distributed nuclear protein involved in chromatin modifications during postmitotic differentiation. Top2b-DNA interactions are known to regulate transcription of developmentally important genes, including axon guidance factors and cell adhesion molecules, but a specific role in local synaptic targeting has not been previously described. The neurite targeting defects among GC axons are largely restricted to crossovers between sublaminae of a specific layer, SFGS, and were shown by mosaic analysis to be autonomous to the GC axons. The noto mutant provides the first example of the importance of an epigenetic regulator, Top2b, in the intricate series of events that lead to a properly wired visual system.
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Affiliation(s)
- Linda M Nevin
- Department of Physiology, University of California, San Francisco, 1550 4th Street, San Francisco, CA 94158-2722, USA
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Abstract
Type II DNA topoisomerases (Tops) are ATP-dependent enzymes that catalyze topological transformations of genomic DNA by the transport of one DNA double helix through another. In mammals, there are 2 isoforms of DNA Top II, termed Top IIα and Top IIβ. The IIβ isoform is abundantly expressed in cells that have undergone the final cell division and are committed to differentiation into neuronal cells. In recent years, there have been accumulating studies showing the significant role of Top IIβ in neuronal development through regulating expression of certain genes in cells committed to the neuronal fate after the final division. These genes are involved in the processes of neuronal differentiation, migration, axon guidance and so on. The present review mainly focused on the research progress on the role of Top IIβ in neuronal development over the recent decades.
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Affiliation(s)
- Xin Heng
- Institute of Health Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai 200025, China
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Pietrzak M, Smith SC, Geralds JT, Hagg T, Gomes C, Hetman M. Nucleolar disruption and apoptosis are distinct neuronal responses to etoposide-induced DNA damage. J Neurochem 2011; 117:1033-46. [PMID: 21517844 DOI: 10.1111/j.1471-4159.2011.07279.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although DNA damaging topoisomerase inhibitors induce apoptosis in developing neurons, their effects on adult neurons have not yet been characterized. We report a blockage of RNA-Polymerase-1-driven transcription and nucleolar stress in neocortical neurons of adult rats after intracarotid injection of the DNA-topoisomerase-2 inhibitor, etoposide. Intracerebroventricular injection of etoposide induced a similar response in neonatal rats. In contrast, etoposide triggered neuronal apoptosis in the neonates, but not the adults. Nucleolar disruption and apoptosis were also observed in etoposide-challenged cultured cortical neurons from newborn rats. In that system, activation of the DNA double strand break signaling kinase ataxia telangiectasia-mutated protein kinase, p53 and p53-dependent apoptosis required lower etoposide concentrations than did the p53-independent induction of nucleolar stress. These distinct responses may be coupled to different forms of etoposide-induced DNA damage. Indeed, double strand breaks by the over-expressed endonuclease I-Ppo1 were sufficient to induce p53-dependent apoptosis. Moreover, nucleolar transcription was insensitive to such damage implying single strand breaks and/or topoisomerase-2-DNA adducts as triggers of nucleolar stress. Because nucleolar stress is not age-restricted, it may underlie non-apoptotic neurotoxicity of chemotherapy- or neurodegeneration-associated DNA damage by reducing ribosomal biogenesis in adult brain. Conversely, nucleolar insensitivity to double strand breaks likely contributes to mature neuron tolerance of such lesions.
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Affiliation(s)
- Maciej Pietrzak
- Kentucky Spinal Cord Injury Research Center and the Departments of Neurological Surgery, University of Louisville, Louisville, Kentucky 40292, USA
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Selective silencing of DNA topoisomerase IIβ in human mesenchymal stem cells by siRNAs (small interfering RNAs). CELL BIOLOGY INTERNATIONAL REPORTS 2011; 18:e00010. [PMID: 23119146 PMCID: PMC3475440 DOI: 10.1042/cbr20110003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 03/22/2011] [Indexed: 01/16/2023]
Abstract
hMSCs (human mesenchymal stem cells) express two isoforms of DNA topo II (topoisomerase II). Although both isoforms have the same catalytic activity, they are specialized for different functions in the cell: while topo IIα is essential for chromosome segregation in mitotic cells, topo IIβ is involved in more specific cellular functions. A number of inhibitors are available that inhibit the catalytic activity of both topo II isoforms. However, in order to investigate the isoform-specific inhibition of these two enzymes, it is necessary to use other techniques such as siRNA (small interfering RNA) interference to selectively silence either one of the isoforms individually. Depending on the lipid charge densities and protein varieties of the cell membrane, previous studies have demonstrated that transfection efficiencies of siRNAs to hMSCs are very low. In the study reported here, we demonstrate the use of Lipofectamine RNAiMAX as an efficient transfection reagent to introduce siRNAs into human mesenchymal stem cells with significantly great efficiency to silence topo IIβ selectively. A high level of transfection efficiency (80%) was achieved by using unlabelled topo IIβ-specific siRNA oligos. Specifically, it was confirmed repeatedly that green labelled siRNAs interfere with the transfection of siRNAs. The reagent induced minimal cytotoxicity (3.5–4.5%), and cell viability of the transfected hMSCs decreased 20–30% compared with untreated cells, depending on the concentration of the reagent.
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Key Words
- DMEM, Dulbecco's modified Eagle's medium
- DNA topoisomerase IIβ
- GFP, green fluorescent protein
- HEK, human embryonic kidney
- LDH, lactate dehydrogenase
- MSC, mesenchymal stem cell
- MSC-FBS, MSC-qualified fetal bovine serum
- PE, phycoerythrin
- RNAi, RNA interference
- RNAiMAX
- hMSC, human mesenchymal stem cell
- human mesenchymal stem cell
- siRNA transfection
- siRNA, small interfering RNA
- topo II, topoisomerase II
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Gilroy KL, Austin CA. The impact of the C-terminal domain on the interaction of human DNA topoisomerase II α and β with DNA. PLoS One 2011; 6:e14693. [PMID: 21358820 PMCID: PMC3040172 DOI: 10.1371/journal.pone.0014693] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 01/19/2011] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND Type II DNA topoisomerases are essential, ubiquitous enzymes that act to relieve topological problems arising in DNA from normal cellular activity. Their mechanism of action involves the ATP-dependent transport of one DNA duplex through a transient break in a second DNA duplex; metal ions are essential for strand passage. Humans have two isoforms, topoisomerase IIα and topoisomerase IIβ, that have distinct roles in the cell. The C-terminal domain has been linked to isoform specific differences in activity and DNA interaction. METHODOLOGY/PRINCIPAL FINDINGS We have investigated the role of the C-terminal domain in the binding of human topoisomerase IIα and topoisomerase IIβ to DNA in fluorescence anisotropy assays using full length and C-terminally truncated enzymes. We find that the C-terminal domain of topoisomerase IIβ but not topoisomerase IIα affects the binding of the enzyme to the DNA. The presence of metal ions has no effect on DNA binding. Additionally, we have examined strand passage of the full length and truncated enzymes in the presence of a number of supporting metal ions and find that there is no difference in relative decatenation between isoforms. We find that calcium and manganese, in addition to magnesium, can support strand passage by the human topoisomerase II enzymes. CONCLUSIONS/SIGNIFICANCE The C-terminal domain of topoisomerase IIβ, but not that of topoisomerase IIα, alters the enzyme's K(D) for DNA binding. This is consistent with previous data and may be related to the differential modes of action of the two isoforms in vivo. We also show strand passage with different supporting metal ions for human topoisomerase IIα or topoisomerase IIβ, either full length or C-terminally truncated. They all show the same preferences, whereby Mg > Ca > Mn.
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Affiliation(s)
- Kathryn L. Gilroy
- Institute for Cell and Molecular Biosciences, University of Newcastle Upon Tyne, Newcastle upon Tyne, United Kingdom
| | - Caroline A. Austin
- Institute for Cell and Molecular Biosciences, University of Newcastle Upon Tyne, Newcastle upon Tyne, United Kingdom
- * E-mail:
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Azarova AM, Lin RK, Tsai YC, Liu LF, Lin CP, Lyu YL. Genistein induces topoisomerase IIbeta- and proteasome-mediated DNA sequence rearrangements: Implications in infant leukemia. Biochem Biophys Res Commun 2010; 399:66-71. [PMID: 20638367 DOI: 10.1016/j.bbrc.2010.07.043] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 07/13/2010] [Indexed: 10/19/2022]
Abstract
Genistein is a bioflavonoid enriched in soy products. However, high levels of maternal soy consumption have been linked to the development of infant leukemia ALL and AML. The majority of infant leukemia is linked to mixed lineage leukemia gene (MLL) translocations. Previous studies have implicated topoisomerase II (Top2) in genistein-induced infant leukemia. In order to understand the roles of the two Top2 isozymes in and the molecular mechanism for genistein-induced infant leukemia, we carried out studies in vitro using purified recombinant human Top2 isozymes, as well as studies in cultured mouse myeloid progenitor cells (32Dc13) and Top2beta knockout mouse embryonic fibroblasts (MEFs). First, we showed that genistein efficiently induced both Top2alpha and Top2beta cleavage complexes in the purified system as well as in cultured mouse cells. Second, genistein induced proteasomal degradation of Top2beta in 32Dc13 cells. Third, the genistein-induced DNA double-strand break (DSB) signal, gamma-H2AX, was dependent on the Top2beta isozyme and proteasome activity. Fourth, the requirement for Top2beta and proteasome activity was mirrored in genistein-induced DNA sequence rearrangements, as monitored by a DNA integration assay. Together, our results suggest a model in which genistein-induced Top2beta cleavage complexes are processed by proteasome, leading to the exposure of otherwise Top2beta-concealed DSBs and subsequent chromosome rearrangements, and implicate a major role of Top2beta and proteasome in genistein-induced infant leukemia.
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Affiliation(s)
- Anna M Azarova
- Department of Pharmacology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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Kawano S, Miyaji M, Ichiyasu S, Tsutsui KM, Tsutsui K. Regulation of DNA Topoisomerase IIbeta through RNA-dependent association with heterogeneous nuclear ribonucleoprotein U (hnRNP U). J Biol Chem 2010; 285:26451-60. [PMID: 20554522 DOI: 10.1074/jbc.m110.112979] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent studies suggest that DNA topoisomerase IIbeta (topo IIbeta) is involved in transcriptional activation of certain genes, which assumes accurate targeting of the enzyme to its action site. The target selection may be achieved by cooperation with unknown regulatory factors. To seek out such factors, we looked for proteins associated with the enzyme in differentiating cerebellar neurons. Antibody against topo IIbeta co-precipitated RNA-binding proteins including PSF, NonO/p54nrb, as well as hnRNP U/SAF-A/SP120. Reconstitution experiments with tag-purified proteins showed that topo IIbeta associates stoichiometrically with SP120 in the presence of RNA that was co-purified with SP120. The most effective RNA species for the complex formation was a subset of cellular polyadenylated RNAs. The C-terminal 187-residue domain of SP120 was necessary and sufficient for the association with both topo IIbeta and the endogenous RNA. The RNA isolated from the tag-purified SP120 inhibited the relaxation of supercoiled DNA by topo IIbeta. When the enzyme associates with SP120, however, the inhibition was abolished and the catalytic property was modulated to more processive mode, which may prolong its residence time at the genomic target site. Furthermore, the presence of SP120 was required for the stable expression of topo IIbeta in vivo. Thus, SP120 regulates the enzyme in dual ways.
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Affiliation(s)
- Shinji Kawano
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
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