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Das R, Sakaue T, Shivashankar GV, Prost J, Hiraiwa T. Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics. PHYSICAL REVIEW LETTERS 2024; 132:058401. [PMID: 38364140 DOI: 10.1103/physrevlett.132.058401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus-some of those transiently link and pass two chromatin segments. Here, we study how such an active perturbation affects fluctuating dynamics of an inclusion in the chromatic medium. Using numerical simulations and a versatile effective model, we categorize inclusion dynamics into three distinct modes. The transient-link-and-pass activity speeds up inclusion dynamics by affecting a slow mode related to chromatin remodeling, viz., size and shape of the chromatin meshes.
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Affiliation(s)
- Rakesh Das
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, Kanagawa 252-5258, Japan
| | - G V Shivashankar
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Villigen 8092, Switzerland
- Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Jacques Prost
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Laboratoire Physico Chimie Curie, Institut Curie, Paris Science et Lettres Research University, 75005 Paris, France
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Institute of Physics, Academia Sinica, Taipei City 115201, Taiwan
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2
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Milano L, Gautam A, Caldecott KW. DNA damage and transcription stress. Mol Cell 2024; 84:70-79. [PMID: 38103560 DOI: 10.1016/j.molcel.2023.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023]
Abstract
Genome damage and transcription are intimately linked. Tens to hundreds of thousands of DNA lesions arise in each cell each day, many of which can directly or indirectly impede transcription. Conversely, the process of gene expression is itself a source of endogenous DNA lesions as a result of the susceptibility of single-stranded DNA to damage, conflicts with the DNA replication machinery, and engagement by cells of topoisomerases and base excision repair enzymes to regulate the initiation and progression of gene transcription. Although such processes are tightly regulated and normally accurate, on occasion, they can become abortive and leave behind DNA breaks that can drive genome rearrangements, instability, or cell death.
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Affiliation(s)
- Larissa Milano
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Amit Gautam
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Keith W Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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3
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Lau MS, Hu Z, Zhao X, Tan YS, Liu J, Huang H, Yeo CJ, Leong HF, Grinchuk OV, Chan JK, Yan J, Tee WW. Transcriptional repression by a secondary DNA binding surface of DNA topoisomerase I safeguards against hypertranscription. Nat Commun 2023; 14:6464. [PMID: 37833256 PMCID: PMC10576097 DOI: 10.1038/s41467-023-42078-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Regulation of global transcription output is important for normal development and disease, but little is known about the mechanisms involved. DNA topoisomerase I (TOP1) is an enzyme well-known for its role in relieving DNA supercoils for enabling transcription. Here, we report a non-enzymatic function of TOP1 that downregulates RNA synthesis. This function is dependent on specific DNA-interacting residues located on a conserved protein surface. A loss-of-function knock-in mutation on this surface, R548Q, is sufficient to cause hypertranscription and alter differentiation outcomes in mouse embryonic stem cells (mESCs). Hypertranscription in mESCs is accompanied by reduced TOP1 chromatin binding and change in genomic supercoiling. Notably, the mutation does not impact TOP1 enzymatic activity; rather, it diminishes TOP1-DNA binding and formation of compact protein-DNA structures. Thus, TOP1 exhibits opposing influences on transcription through distinct activities which are likely to be coordinated. This highlights TOP1 as a safeguard of appropriate total transcription levels in cells.
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Affiliation(s)
- Mei Sheng Lau
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Zhenhua Hu
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaodan Zhao
- Department of Physics, National University of Singapore, Singapore, 117551, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
| | - Jinyue Liu
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Hua Huang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Electrophysiology Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Clarisse Jingyi Yeo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwei Fen Leong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Oleg V Grinchuk
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Justin Kaixuan Chan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, 117551, Singapore.
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117557, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
| | - Wee-Wei Tee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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4
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Das SK, Lewis BA, Levens D. MYC: a complex problem. Trends Cell Biol 2023; 33:235-246. [PMID: 35963793 PMCID: PMC9911561 DOI: 10.1016/j.tcb.2022.07.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/22/2022]
Abstract
The MYC protooncogene functions as a universal amplifier of transcription through interaction with numerous factors and complexes that regulate almost every cellular process. However, a comprehensive model that explains MYC's actions and the interplay governing the complicated dynamics of components of the transcription and replication machinery is still lacking. Here, we review the potency of MYC as an oncogenic driver and how it regulates the broad spectrum of complexes (effectors and regulators). We propose a 'hand-over model' for differential partitioning and trafficking of unstructured MYC via a loose interaction network between various gene-regulatory complexes and factors. Additionally, the article discusses how unstructured-MYC energetically favors efficient modulation of the energy landscape of the transcription cycle.
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Affiliation(s)
- Subhendu K Das
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA
| | - Brian A Lewis
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA.
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5
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Morao AK, Kim J, Obaji D, Sun S, Ercan S. Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans. Mol Cell 2022; 82:4202-4217.e5. [PMID: 36302374 PMCID: PMC9837612 DOI: 10.1016/j.molcel.2022.10.002] [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: 11/29/2021] [Revised: 05/24/2022] [Accepted: 10/03/2022] [Indexed: 11/18/2022]
Abstract
Condensins are evolutionarily conserved molecular motors that translocate along DNA and form loops. To address how DNA topology affects condensin translocation, we applied auxin-inducible degradation of topoisomerases I and II and analyzed the binding and function of an interphase condensin that mediates X chromosome dosage compensation in C. elegans. TOP-2 depletion reduced long-range spreading of condensin-DC (dosage compensation) from its recruitment sites and shortened 3D DNA contacts measured by Hi-C. TOP-1 depletion did not affect long-range spreading but resulted in condensin-DC accumulation within expressed gene bodies. Both TOP-1 and TOP-2 depletion resulted in X chromosome derepression, indicating that condensin-DC translocation at both scales is required for its function. Together, the distinct effects of TOP-1 and TOP-2 suggest two distinct modes of condensin-DC association with chromatin: long-range DNA loop extrusion that requires decatenation/unknotting of DNA and short-range translocation across genes that requires resolution of transcription-induced supercoiling.
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Affiliation(s)
- Ana Karina Morao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Daniel Obaji
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Siyu Sun
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
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6
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Qin S, Yuan Y, Huang X, Tan Z, Hu X, Liu H, Pu Y, Ding YQ, Su Z, He C. Topoisomerase IIA in adult NSCs regulates SVZ neurogenesis by transcriptional activation of Usp37. Nucleic Acids Res 2022; 50:9319-9338. [PMID: 36029179 PMCID: PMC9458435 DOI: 10.1093/nar/gkac731] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 07/31/2022] [Accepted: 08/14/2022] [Indexed: 01/27/2023] Open
Abstract
Topoisomerase IIA (TOP2a) has traditionally been known as an important nuclear enzyme that resolves entanglements and relieves torsional stress of DNA double strands. However, its function in genomic transcriptional regulation remains largely unknown, especially during adult neurogenesis. Here, we show that TOP2a is preferentially expressed in neurogenic niches in the brain of adult mice, such as the subventricular zone (SVZ). Conditional knockout of Top2a in adult neural stem cells (NSCs) of the SVZ significantly inhibits their self-renewal and proliferation, and ultimately reduces neurogenesis. To gain insight into the molecular mechanisms by which TOP2a regulates adult NSCs, we perform RNA-sequencing (RNA-Seq) plus chromatin immunoprecipitation sequencing (ChIP-Seq) and identify ubiquitin-specific protease 37 (Usp37) as a direct TOP2a target gene. Importantly, overexpression of Usp37 is sufficient to rescue the impaired self-renewal ability of adult NSCs caused by Top2a knockdown. Taken together, this proof-of-principle study illustrates a TOP2a/Usp37-mediated novel molecular mechanism in adult neurogenesis, which will significantly expand our understanding of the function of topoisomerase in the adult brain.
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Affiliation(s)
- Shangyao Qin
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yimin Yuan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Xiao Huang
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Zijian Tan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Xin Hu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Hong Liu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yingyan Pu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yu-qiang Ding
- Department of Laboratory Animal Science, and State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhida Su
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Cheng He
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
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7
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Das R, Sakaue T, Shivashankar GV, Prost J, Hiraiwa T. How enzymatic activity is involved in chromatin organization. eLife 2022; 11:79901. [PMID: 36472500 PMCID: PMC9810329 DOI: 10.7554/elife.79901] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
Spatial organization of chromatin plays a critical role in genome regulation. Previously, various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at the mechanistic level, enzymes act in their unique ways and perturb the chromatin. Here, we construct a polymer physics model following the mechanistic scheme of Topoisomerase-II, an enzyme resolving topological constraints of chromatin, and investigate how it affects interphase chromatin organization. Our computer simulations demonstrate Topoisomerase-II's ability to phase separate chromatin into eu- and heterochromatic regions with a characteristic wall-like organization of the euchromatic regions. We realized that the ability of the euchromatic regions to cross each other due to enzymatic activity of Topoisomerase-II induces this phase separation. This realization is based on the physical fact that partial absence of self-avoiding interaction can induce phase separation of a system into its self-avoiding and non-self-avoiding parts, which we reveal using a mean-field argument. Furthermore, motivated from recent experimental observations, we extend our model to a bidisperse setting and show that the characteristic features of the enzymatic activity-driven phase separation survive there. The existence of these robust characteristic features, even under the non-localized action of the enzyme, highlights the critical role of enzymatic activity in chromatin organization.
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Affiliation(s)
- Rakesh Das
- Mechanobiology Institute, National University of SingaporeSingaporeSingapore
| | - Takahiro Sakaue
- Department of Physics and Mathematics, Aoyama Gakuin UniversityKanagawaJapan
| | - GV Shivashankar
- ETH ZurichZurichSwitzerland,Paul Scherrer InstituteVilligenSwitzerland
| | - Jacques Prost
- Mechanobiology Institute, National University of SingaporeSingaporeSingapore,Laboratoire Physico Chimie Curie, Institut Curie, Paris Science et Lettres Research UniversityParisFrance
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, National University of SingaporeSingaporeSingapore
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8
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Bhattacharjee S, Rehman I, Nandy S, Das BB. Post-translational regulation of Tyrosyl-DNA phosphodiesterase (TDP1 and TDP2) for the repair of the trapped topoisomerase-DNA covalent complex. DNA Repair (Amst) 2022; 111:103277. [DOI: 10.1016/j.dnarep.2022.103277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/24/2021] [Accepted: 01/20/2022] [Indexed: 12/23/2022]
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9
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Das SK, Kuzin V, Cameron DP, Sanford S, Jha RK, Nie Z, Rosello MT, Holewinski R, Andresson T, Wisniewski J, Natsume T, Price DH, Lewis BA, Kouzine F, Levens D, Baranello L. MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome". Mol Cell 2021; 82:140-158.e12. [PMID: 34890565 DOI: 10.1016/j.molcel.2021.11.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 08/11/2021] [Accepted: 11/13/2021] [Indexed: 12/25/2022]
Abstract
High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must manage this interfering torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with topoisomerase 1 (TOP1) and TOP2 that was confirmed in vitro and in cells. Beyond recruiting topoisomerases, MYC directly stimulates their activities. We identify a MYC-nucleated "topoisome" complex that unites TOP1 and TOP2 and increases their levels and activities at promoters, gene bodies, and enhancers. Whether TOP2A or TOP2B is included in the topoisome is dictated by the presence of MYC versus MYCN, respectively. Thus, in vitro and in cells, MYC assembles tools that simplify DNA topology and promote genome function under high output conditions.
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Affiliation(s)
- Subhendu K Das
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Donald P Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Suzanne Sanford
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Rajiv Kumar Jha
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Zuqin Nie
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Marta Trullols Rosello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Ronald Holewinski
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 21701, USA
| | - Thorkell Andresson
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 21701, USA
| | - Jan Wisniewski
- Confocal Microscopy and Digital Imaging Facility, National Cancer Institute, Bethesda, MD 20892, USA
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Shizuoka 411-8540, Japan; Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - David H Price
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Brian A Lewis
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Fedor Kouzine
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - David Levens
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA.
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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10
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Topoisomerase poisoning by the flavonoid nevadensin triggers DNA damage and apoptosis in human colon carcinoma HT29 cells. Arch Toxicol 2021; 95:3787-3802. [PMID: 34635930 PMCID: PMC8536574 DOI: 10.1007/s00204-021-03162-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022]
Abstract
Nevadensin, an abundant polyphenol of basil, is reported to reduce alkenylbenzene DNA adduct formation. Furthermore, it has a wide spectrum of further pharmacological properties. The presented study focuses the impact of nevadensin on topoisomerases (TOPO) in vitro. Considering the DNA-intercalating properties of flavonoids, first, minor groove binding properties (IC50 = 31.63 µM), as well as DNA intercalation (IC50 = 296.91 µM) of nevadensin, was found. To determine potential in vitro effects on TOPO I and TOPO IIα, the relaxation and decatenation assay was performed in a concentration range of 1–500 µM nevadensin. A partial inhibition was detected for TOPO I at concentrations ≥ 100 µM, whereas TOPO IIα activity is only inhibited at concentrations ≥ 250 µM. To clarify the mode of action, the isolating in vivo complex of enzyme assay was carried out using human colon carcinoma HT29 cells. After 1 h of incubation, the amount of TOPO I linked to DNA was significantly increased by nevadensin (500 µM), why nevadensin was characterized as TOPO I poison. However, no effects on TOPO IIα were detected in the cellular test system. As a subsequent cellular response to TOPO I poisoning, a highly significant increase of DNA damage after 2 h and a decrease of cell viability after 48 h at the same concentration range were found. Furthermore, after 24 h of incubation a G2/M arrest was observed at concentrations ≥ 100 µM by flow cytometry. The analysis of cell death revealed that nevadensin induces the intrinsic apoptotic pathway via activation of caspase-9 and caspase-3. The results suggest that cell cycle disruption and apoptotic events play key roles in the cellular response to TOPO I poisoning caused by nevadensin in HT29 cells.
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11
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Olmedo-Pelayo J, Rubio-Contreras D, Gómez-Herreros F. Canonical non-homologous end-joining promotes genome mutagenesis and translocations induced by transcription-associated DNA topoisomerase 2 activity. Nucleic Acids Res 2020; 48:9147-9160. [PMID: 32749454 PMCID: PMC7498328 DOI: 10.1093/nar/gkaa640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023] Open
Abstract
DNA topoisomerase II (TOP2) is a major DNA metabolic enzyme, with important roles in replication, transcription, chromosome segregation and spatial organisation of the genome. TOP2 is the target of a class of anticancer drugs that poison the DNA-TOP2 transient complex to generate TOP2-linked DNA double-strand breaks (DSBs). The accumulation of DSBs kills tumour cells but can also result in genome instability. The way in which topoisomerase activity contributes to transcription remains unclear. In this work we have investigated how transcription contributes to TOP2-dependent DSB formation, genome instability and cell death. Our results demonstrate that gene transcription is an important source of abortive TOP2 activity. However, transcription does not contribute significantly to apoptosis or cell death promoted by TOP2-induced DSBs. On the contrary: transcription-dependent breaks greatly contribute to deleterious mutations and translocations, and can promote oncogenic rearrangements. Importantly, we show that TOP2-induced genome instability is mediated by mutagenic canonical non-homologous end joining whereas homologous recombination protects cells against these insults. Collectively, these results uncover mechanisms behind deleterious effects of TOP2 abortive activity during transcription, with relevant implications for chemotherapy.
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Affiliation(s)
- Joaquín Olmedo-Pelayo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, 41080 Seville, Spain
| | - Diana Rubio-Contreras
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, 41080 Seville, Spain
| | - Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, 41080 Seville, Spain
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12
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Fragola G, Mabb AM, Taylor-Blake B, Niehaus JK, Chronister WD, Mao H, Simon JM, Yuan H, Li Z, McConnell MJ, Zylka MJ. Deletion of Topoisomerase 1 in excitatory neurons causes genomic instability and early onset neurodegeneration. Nat Commun 2020; 11:1962. [PMID: 32327659 PMCID: PMC7181881 DOI: 10.1038/s41467-020-15794-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 03/28/2020] [Indexed: 12/14/2022] Open
Abstract
Topoisomerase 1 (TOP1) relieves torsional stress in DNA during transcription and facilitates the expression of long (>100 kb) genes, many of which are important for neuronal functions. To evaluate how loss of Top1 affected neurons in vivo, we conditionally deleted (cKO) Top1 in postmitotic excitatory neurons in the mouse cerebral cortex and hippocampus. Top1 cKO neurons develop properly, but then show biased transcriptional downregulation of long genes, signs of DNA damage, neuroinflammation, increased poly(ADP-ribose) polymerase-1 (PARP1) activity, single-cell somatic mutations, and ultimately degeneration. Supplementation of nicotinamide adenine dinucleotide (NAD+) with nicotinamide riboside partially blocked neurodegeneration, and increased the lifespan of Top1 cKO mice by 30%. A reduction of p53 also partially rescued cortical neuron loss. While neurodegeneration was partially rescued, behavioral decline was not prevented. These data indicate that reducing neuronal loss is not sufficient to limit behavioral decline when TOP1 function is disrupted. Topoisomerase 1 (TOP1) relieves DNA torsional stress during transcription and facilitates the expression of long neuronal genes. Here we show that deletion of Top1 in excitatory neurons leads to early onset neurodegeneration that is partially dependent on p53/PARP1 activation and NAD+ depletion.
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Affiliation(s)
- Giulia Fragola
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Angela M Mabb
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA
| | - Bonnie Taylor-Blake
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jesse K Niehaus
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - William D Chronister
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hanqian Mao
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Hong Yuan
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Biomedical Imaging Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Zibo Li
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Biomedical Imaging Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, 22908, USA
| | - Mark J Zylka
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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13
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Garro HA, Pungitore CR. DNA Related Enzymes as Molecular Targets for Antiviral and Antitumoral Chemotherapy. A Natural Overview of the Current Perspectives. Curr Drug Targets 2020; 20:70-80. [PMID: 29697027 DOI: 10.2174/1389450119666180426103558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The discovery of new chemotherapeutic agents still remains a continuous goal to achieve. DNA polymerases and topoisomerases act in nucleic acids metabolism modulating different processes like replication, mitosis, damage repair, DNA topology and transcription. It has been widely documented that Polymerases serve as molecular targets for antiviral and antitumoral chemotherapy. Furthermore, telomerase is a ribonucleoprotein with exacerbated activity in most of the tumor cell lines, becoming as an emergent target in Cancer treatment. METHODS We undertook an exhaustive search of bibliographic databases for peer-reviewed research literature related to the last decade. The characteristics of screened bibliography describe structure activity relationships and show the principal moieties involved. This work tries to summarize the investigation about natural and semi-synthetic products with natural origin with the faculty to inhibit key enzymes that play a crucial role in DNA metabolism. RESULTS Eighty-five data references were included in this review, showing natural products widely distributed throughout the plant kingdom and their bioactive properties such as tumor growing inhibitory effects, and anti-AIDS activity. CONCLUSION The findings of this review confirm the importance to find new drugs and biologically active natural products, and their potential medicinally useful benefits.
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Affiliation(s)
- Hugo A Garro
- Intequi-Conicet, Fac. Qca., Bioqca. y Fcia., Univ. Nac. de San Luis (U.N.S.L), Chacabuco y Pedernera, 5700 San Luis, Argentina
| | - Carlos R Pungitore
- Intequi-Conicet, Fac. Qca., Bioqca. y Fcia., Univ. Nac. de San Luis (U.N.S.L), Chacabuco y Pedernera, 5700 San Luis, Argentina
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14
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Roles of Topoisomerases in Heterochromatin, Aging, and Diseases. Genes (Basel) 2019; 10:genes10110884. [PMID: 31683993 PMCID: PMC6896002 DOI: 10.3390/genes10110884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/23/2019] [Accepted: 10/26/2019] [Indexed: 12/11/2022] Open
Abstract
Heterochromatin is a transcriptionally repressive chromatin architecture that has a low abundance of genes but an enrichment of transposons. Defects in heterochromatin can cause the de-repression of genes and transposons, leading to deleterious physiological changes such as aging, cancer, and neurological disorders. While the roles of topoisomerases in many DNA-based processes have been investigated and reviewed, their roles in heterochromatin formation and function are only beginning to be understood. In this review, we discuss recent findings on how topoisomerases can promote heterochromatin organization and impact the transcription of genes and transposons. We will focus on two topoisomerases: Top2α, which catenates and decatenates double-stranded DNA, and Top3β, which can change the topology of not only DNA, but also RNA. Both enzymes are required for normal heterochromatin formation and function, as the inactivation of either protein by genetic mutations or chemical inhibitors can result in defective heterochromatin formation and the de-silencing of transposons. These defects may contribute to the shortened lifespan and neurological disorders observed in individuals carrying mutations of Top3β. We propose that topological stress may be generated in both DNA and RNA during heterochromatin formation and function, which depend on multiple topoisomerases to resolve.
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15
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Splicing regulator SRSF1-3 that controls somatic hypermutation of IgV genes interacts with topoisomerase 1 and AID. Mol Immunol 2019; 116:63-72. [PMID: 31622795 DOI: 10.1016/j.molimm.2019.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/24/2019] [Accepted: 10/01/2019] [Indexed: 01/27/2023]
Abstract
Somatic hypermutation (SHM) of Ig genes is initiated by activation-induced cytidine deaminase (AID) and requires target gene transcription. A splice isoform of SRSF1, SRSF1-3, is necessary for AID-dependent SHM of IgV genes. Nevertheless, its exact molecular mechanism of action in SHM remains unknown. Our in silico studies show that, unlike SRSF1, SRSF1-3 lacks a strong nuclear localization domain. We show that the absence of RS domain in SRSF1-3 affects its nuclear localization, as compared to SRSF1. Consequently, SRSF1-3 is predominantly present in the cytoplasm. Remarkably, co-immunoprecipitation studies showed that SRSF1-3 interacts with Topoisomerase 1 (TOP1), a crucial regulator of SHM that assists in generating ssDNA for AID activity. Moreover, the immunofluorescence studies confirmed that SRSF1-3 and TOP1 are co-localized in the nucleus. Furthermore, Proximity Ligation Assay corroborated the direct interaction between SRSF1-3 and TOP1. An interaction between SRSF1-3 and TOP1 suggests that SRSF1-3 likely influences the TOP1 activity and consequently can aid in SHM. Accordingly, SRSF1-3 probably acts as a link between TOP1 and SHM, by spatially regulating TOP1 activity at the Ig locus. We also confirmed the interaction between SRSF1-3 and AID in chicken B-cells. Thus, SRSF1-3 shows dual-regulation of SHM, via interacting with AID as well as TOP1.
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16
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Economides MP, McCue D, Borthakur G, Pemmaraju N. Topoisomerase II inhibitors in AML: past, present, and future. Expert Opin Pharmacother 2019; 20:1637-1644. [PMID: 31136213 DOI: 10.1080/14656566.2019.1621292] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: Topoisomerase II inhibitors have long been used in the frontline and as salvage therapy for AML, with daunorubicin and idarubicin being prototypical agents in this therapeutic class, classically in combination with nucleoside analogs, e.g. cytarabine. Most recently, several other compounds from this drug class have or are being investigated. Areas covered: The current paper reviews older and newer topoisomerase II inhibitors in clinical development for the treatment of AML. The authors discuss the clinical use of these agents, current trials involving them as well as their safety profile. Important side effects of these medications including therapy-related AML (t-AML) are also covered. Expert opinion: Topoisomerase II inhibitors have helped improve outcomes in AML. Recently, the FDA approved several agents including CPX-351 for the treatment of secondary and t-AML. CPX-351 may have applicability in other high-risk myeloid diseases. Future directions include a combination of these agents with other targeted therapies. Finally, the authors believe that small molecule inhibitors, such as venetoclax and possibly immunotherapy options could also be incorporated to our treatment paradigm in selected patients.
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Affiliation(s)
- Minas P Economides
- Department of Internal Medicine, The University of Texas School of Health Sciences at Houston , Houston , TX , USA
| | - Deborah McCue
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Gautam Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Naveen Pemmaraju
- Department of Leukemia, The University of Texas MD Anderson Cancer Center , Houston , TX , USA
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17
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Jing X, Loskot P, Yu J. How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting? Phys Biol 2018; 15:066007. [PMID: 30091721 DOI: 10.1088/1478-3975/aad933] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Transcription plays an essential role in gene expression. The transcription bursting in bacteria has been suggested to be regulated by positive supercoiling accumulation in front of a transcribing RNA polymerase (RNAP) together with gyrase binding on DNA to release the supercoiling. In this work, we study the supercoiling regulation in the case of a battery of RNAPs working together on DNA by constructing a multi-state quantitative model, which allows gradual and stepwise supercoiling accumulation and release in the RNAP transcription. We solved for transcription characteristics under the multi-state bursting model for a single RNAP transcription, and then simulated for a battery of RNAPs on DNA with T7 and Escherichia coli RNAP types of traffic, respectively, probing both the average and fluctuation impacts of the supercoiling regulation. Our studies show that due to the supercoiling accumulation and release, the number of RNAP molecules loaded onto the DNA vary significantly along time in the traffic condition. Though multiple RNAPs in transcription promote the mRNA production, they also enhance the supercoiling accumulation to suppress the production. In particular, the fluctuations of the mRNA transcripts become highly pronounced for a battery of RNAPs transcribing together under the supercoiling regulation, especially for a long process of transcription elongation. In such an elongation process, though a single RNAP can work at a high duty ratio, multiple RNAPs are hardly able to do so. Our multi-state model thus provides a systematical characterization of the quantitative features of the bacterial transcription bursting; it also supports improved physical examinations on top of this general modeling framework.
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Affiliation(s)
- Xiaobo Jing
- Beijing Computational Science Research Center, 100193, Beijing, People's Republic of China
| | - Pavel Loskot
- Beijing Computational Science Research Center, 100193, Beijing, People's Republic of China
- Systems and Process Engineering Centre, Swansea University, Swansea, SA28PP, United Kingdom
| | - Jin Yu
- Beijing Computational Science Research Center, 100193, Beijing, People's Republic of China
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18
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Manzo SG, Hartono SR, Sanz LA, Marinello J, De Biasi S, Cossarizza A, Capranico G, Chedin F. DNA Topoisomerase I differentially modulates R-loops across the human genome. Genome Biol 2018; 19:100. [PMID: 30060749 PMCID: PMC6066927 DOI: 10.1186/s13059-018-1478-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Co-transcriptional R-loops are abundant non-B DNA structures in mammalian genomes. DNA Topoisomerase I (Top1) is often thought to regulate R-loop formation owing to its ability to resolve both positive and negative supercoils. How Top1 regulates R-loop structures at a global level is unknown. RESULTS Here, we perform high-resolution strand-specific R-loop mapping in human cells depleted for Top1 and find that Top1 depletion results in both R-loop gains and losses at thousands of transcribed loci, delineating two distinct gene classes. R-loop gains are characteristic for long, highly transcribed, genes located in gene-poor regions anchored to Lamin B1 domains and in proximity to H3K9me3-marked heterochromatic patches. R-loop losses, by contrast, occur in gene-rich regions overlapping H3K27me3-marked active replication initiation regions. Interestingly, Top1 depletion coincides with a block of the cell cycle in G0/G1 phase and a trend towards replication delay. CONCLUSIONS Our findings reveal new properties of Top1 in regulating R-loop homeostasis in a context-dependent manner and suggest a potential role for Top1 in modulating the replication process via R-loop formation.
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Affiliation(s)
- Stefano G Manzo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Present address: Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, USA
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, USA
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Frederic Chedin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, USA.
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19
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Daudee R, Gonen R, German U, Orion I, Alfassi ZB, Priel E. DNA Topoisomerase IB as a Potential Ionizing Radiation Exposure and Dose Biomarker. Radiat Res 2018; 189:652-660. [PMID: 29633912 DOI: 10.1667/rr14859.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In radiation exposure scenarios where physical dosimetry is absent or inefficient, dose estimation must rely on biological markers. A reliable biomarker is of utmost importance in correlating biological system changes with radiation exposure. Human DNA topoisomerase ІB (topo І) is a ubiquitous nuclear enzyme, which is involved in essential cellular processes, including transcription, DNA replication and DNA repair, and is the target of anti-cancer drugs. It has been shown that the cellular activity of this enzyme is significantly sensitive to various DNA lesions, including radiation-induced DNA damages. Therefore, we investigated the potential of topo I as a biomarker of radiation exposure and dose. We examined the effect of exposure of different human cells to beta, X-ray and gamma radiation on the cellular catalytic activity of topo I. The results demonstrate a significant reduction in the DNA relaxation activity of topo I after irradiation and the level of the reduction was correlated with radiation dose. In normal human peripheral blood lymphocytes, exposure for 3 h to an integral dose of 0.065 mGy from tritium reduced the enzyme activity to less than 25%. In MG-63 osteoblast-like cells and in human pulmonary fibroblast (HPF) cells exposed to gamma radiation from a 60Co source (up to 2 Gy) or to X rays (up to 2.8 Gy), a significant decrease in topo I catalytic activity was also observed. We observed that the enzyme-protein level was not altered but was partially posttranslational modified by ADP-ribosylation of the enzyme protein that is known to reduce topo I activity. The results of this study suggest that the decrease in the cellular topo I catalytic activity after low-dose exposure to different radiation types may be considered as a novel biomarker of ionizing radiation exposure and dose. For this purpose, a suitable ELISA-based method for large-scale analysis of radiation-induced topo I modification is under development.
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Affiliation(s)
- Rotem Daudee
- a The Shraga Segal Department of Immunology, Microbiology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,b Department of Nuclear Engineering, Faculty of Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel.,c Nuclear Research Center, Negev, Beer Sheva, Israel
| | - Rafi Gonen
- a The Shraga Segal Department of Immunology, Microbiology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,b Department of Nuclear Engineering, Faculty of Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel.,c Nuclear Research Center, Negev, Beer Sheva, Israel
| | - Uzi German
- c Nuclear Research Center, Negev, Beer Sheva, Israel
| | - Itzhak Orion
- b Department of Nuclear Engineering, Faculty of Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Zeev B Alfassi
- b Department of Nuclear Engineering, Faculty of Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Esther Priel
- a The Shraga Segal Department of Immunology, Microbiology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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20
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Björkegren C, Baranello L. DNA Supercoiling, Topoisomerases, and Cohesin: Partners in Regulating Chromatin Architecture? Int J Mol Sci 2018; 19:E884. [PMID: 29547555 PMCID: PMC5877745 DOI: 10.3390/ijms19030884] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 01/25/2023] Open
Abstract
Although our knowledge of chromatin organization has advanced significantly in recent years, much about the relationships between different features of genome architecture is still unknown. Folding of mammalian genomes into spatial domains is thought to depend on architectural proteins, other DNA-binding proteins, and different forms of RNA. In addition, emerging evidence points towards the possibility that the three-dimensional organisation of the genome is controlled by DNA topology. In this scenario, cohesin, CCCTC-binding factor (CTCF), transcription, DNA supercoiling, and topoisomerases are integrated to dictate different layers of genome organization, and the contribution of all four to gene control is an important direction of future studies. In this perspective, we review recent studies that give new insight on how DNA supercoiling shape chromatin structure.
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Affiliation(s)
- Camilla Björkegren
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 43 Huddinge, Sweden.
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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21
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Bansal K, Yoshida H, Benoist C, Mathis D. The transcriptional regulator Aire binds to and activates super-enhancers. Nat Immunol 2017; 18:263-273. [PMID: 28135252 PMCID: PMC5310976 DOI: 10.1038/ni.3675] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/21/2016] [Indexed: 12/15/2022]
Abstract
Aire is a transcription factor that controls T cell tolerance by inducing the expression of a large repertoire of genes specifically in thymic stromal cells. It interacts with scores of protein partners of diverse functional classes. We found that Aire and some of its partners, notably those implicated in the DNA-damage response, preferentially localized to and activated long chromatin stretches that were overloaded with transcriptional regulators, known as super-enhancers. We also identified topoisomerase 1 as a cardinal Aire partner that colocalized on super-enhancers and was required for the interaction of Aire with all of its other associates. We propose a model that entails looping of super-enhancers to efficiently deliver Aire-containing complexes to local and distal transcriptional start sites.
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Affiliation(s)
- Kushagra Bansal
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
| | - Hideyuki Yoshida
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
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22
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Cestrum nocturnum Flower Extracts Attenuate Proliferation and Induce Apoptosis in Malignant Cells through Inducing DNA Damage and Inhibiting Topoisomerase II Activity. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:1456786. [PMID: 28250789 PMCID: PMC5307125 DOI: 10.1155/2017/1456786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 12/20/2016] [Indexed: 11/18/2022]
Abstract
Most of the existing chemotherapeutic drugs have plenty of side effects. Chinese herbal medicine has been used for pharmaceutical and dietary therapy for thousands of years with more effective and fewer side effects. Cestrum nocturnum (CN) has long been used to treat digestive diseases for centuries in China. Our previous study first proved that the n-butanol part isolated from the flowers of CN produced an inhibitory effect on the proliferation of malignant cells. However, the fractions responsible for the antiproliferation effect of n-butanol part from CN flowers and related mechanisms remain unknown. Thus, in this study, we extracted fractions C4 and C5 from n-butanol part of CN flowers and investigated their immune toxicity and antitumor activities. It was found that fractions C4 and C5 exhibited great cytotoxicity to cancer cell lines but had low immune toxicity towards T and B lymphocytes in vitro. The tested fractions also attenuated proliferation and induced apoptosis at G0/G1 and G2/M phases in Bel-7404 cells through inducing DNA damage and inhibiting topoisomerase II relaxation activity. These results suggest that fractions C4 and C5 may represent important sources of potential antitumor agents due to their pronounced antitumor effects and low immune toxicity.
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23
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Affiliation(s)
- Giovanni Capranico
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Jessica Marinello
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Giovanni Chillemi
- SCAI
SuperComputing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185 Rome, Italy
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24
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Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophys Rev 2016; 8:23-32. [PMID: 28510218 DOI: 10.1007/s12551-016-0243-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/11/2016] [Indexed: 12/22/2022] Open
Abstract
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.
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25
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Levens D, Baranello L, Kouzine F. Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophys Rev 2016; 8:259-268. [PMID: 28510225 DOI: 10.1007/s12551-016-0216-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.
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Affiliation(s)
- David Levens
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Laura Baranello
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fedor Kouzine
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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26
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Vutey V, Castelli S, D'Annessa I, Sâmia LBP, Souza-Fagundes EM, Beraldo H, Desideri A. Human topoisomerase IB is a target of a thiosemicarbazone copper(II) complex. Arch Biochem Biophys 2016; 606:34-40. [PMID: 27431056 DOI: 10.1016/j.abb.2016.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/30/2016] [Accepted: 07/12/2016] [Indexed: 02/03/2023]
Abstract
The human topoisomerase IB inhibition and the antiproliferative activity of 3-(4-bromophenyl)-1-pyridin-2-ylprop-2-en-1-one thiosemicarbazone HPyCT4BrPh alone and its copper(II) complex [Cu(PyCT4BrPh)Cl] was investigated. [Cu(PyCT4BrPh)Cl] inhibits both the DNA cleavage and religation step of the enzyme, whilst the ligand alone does not display any effect. In addition we show that coordination to copper(II) improves the cytotoxicity of HPyCT4BrPh against THP-1 leukemia and MCF-7 breast cancer cells. The data indicate that the copper(II) thiosemicarbazone complex may hit human topoisomerase IB and that metal coordination can be useful to improve cytotoxicity of this versatile class of compounds.
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Affiliation(s)
- Venn Vutey
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Castelli
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Ilda D'Annessa
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Luciana B P Sâmia
- Departamento de Química, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine M Souza-Fagundes
- Departamento de Química, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Heloisa Beraldo
- Departamento de Química, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, Minas Gerais, Brazil
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27
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Ang RP, Teoh LS, Chan MK, Miswan N, Khoo BY. Comparing the expression of human DNA topoisomerase I in KM71H and X33 strains of Pichia pastoris. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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28
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Qian C, Wu J, Ji L, Chao H. Topoisomerase IIα poisoning and DNA double-strand breaking by chiral ruthenium(ii) complexes containing 2-furanyl-imidazo[4,5-f][1,10]phenanthroline derivatives. Dalton Trans 2016; 45:10546-55. [DOI: 10.1039/c6dt01422d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Some chiral ruthenium(ii) complexes bearing furan ligands were developed to act as topoisomerase IIα poisons and caused DNA double-strand damage that could lead to apoptosis.
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Affiliation(s)
- Chen Qian
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Jingheng Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou
- P. R. China
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29
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ChIP bias as a function of cross-linking time. Chromosome Res 2015; 24:175-81. [PMID: 26685864 DOI: 10.1007/s10577-015-9509-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 11/12/2015] [Accepted: 11/18/2015] [Indexed: 01/01/2023]
Abstract
The chromatin immunoprecipitation (ChIP) assay is widely used to capture interactions between chromatin and regulatory proteins in vivo. Formaldehyde cross-linking of DNA and proteins is a critical step required to trap their interactions inside the cells before immunoprecipitation and analysis. Yet insufficient attention has been given to variables that might give rise to artifacts in this procedure, such as the duration of cross-linking. We analyzed the dependence of the ChIP signal on the duration of formaldehyde cross-linking time for two proteins: DNA topoisomerase 1 (Top1) that is functionally associated with the double helix in vivo, especially with active chromatin, and green fluorescent protein (GFP) that has no known bona fide interactions with DNA. With short time of formaldehyde fixation, only Top1 immunoprecipation efficiently recovered DNA from active promoters, whereas prolonged fixation augmented non-specific recovery of GFP dramatizing the need to optimize ChIP protocols to minimize the time of cross-linking, especially for abundant nuclear proteins. Thus, ChIP is a powerful approach to study the localization of protein on the genome when care is taken to manage potential artifacts.
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30
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Zubovych IO, Sethi A, Kulkarni A, Tagal V, Roth MG. A Novel Inhibitor of Topoisomerase I Is Selectively Toxic for a Subset of Non-Small Cell Lung Cancer Cell Lines. Mol Cancer Ther 2015; 15:23-36. [PMID: 26668189 DOI: 10.1158/1535-7163.mct-15-0458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/05/2015] [Indexed: 12/16/2022]
Abstract
SW044248, identified through a screen for chemicals that are selectively toxic for non-small cell lung cancer (NSCLC) cell lines, was found to rapidly inhibit macromolecular synthesis in sensitive, but not in insensitive, cells. SW044248 killed approximately 15% of a panel of 74 NSCLC cell lines and was nontoxic to immortalized human bronchial cell lines. The acute transcriptional response to SW044248 in sensitive HCC4017 cells correlated significantly with inhibitors of topoisomerases and SW044248 inhibited topoisomerase 1 (Top1) but not topoisomerase 2. SW044248 inhibited Top1 differently from camptothecin and camptothecin did not show the same selective toxicity as SW044248. Elimination of Top1 by siRNA partially protected cells from SW044248, although removing Top1 was itself eventually toxic. Cells resistant to SW044248 responded to the compound by upregulating CDKN1A and siRNA to CDKN1A sensitized those cells to SW044248. Thus, at least part of the differential sensitivity of NSCLC cells to SW044248 is the ability to upregulate CDKN1A.
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Affiliation(s)
- Iryna O Zubovych
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Anirudh Sethi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Aditya Kulkarni
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Vural Tagal
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Michael G Roth
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas.
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31
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Sutthibutpong T, Harris SA, Noy A. Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA. J Chem Theory Comput 2015; 11:2768-75. [PMID: 26575569 DOI: 10.1021/acs.jctc.5b00035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thana Sutthibutpong
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
| | - Sarah A. Harris
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
| | - Agnes Noy
- Polymer
IRC, School of Physics
and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds LS2 9JT, U.K
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32
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Tacrine derivatives as dual topoisomerase I and II catalytic inhibitors. Bioorg Chem 2015; 59:168-76. [DOI: 10.1016/j.bioorg.2015.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022]
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33
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Maul RW, Saribasak H, Cao Z, Gearhart PJ. Topoisomerase I deficiency causes RNA polymerase II accumulation and increases AID abundance in immunoglobulin variable genes. DNA Repair (Amst) 2015; 30:46-52. [PMID: 25869824 DOI: 10.1016/j.dnarep.2015.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/03/2015] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
Abstract
Activation-induced deaminase (AID) is a DNA cytosine deaminase that diversifies immunoglobulin genes in B cells. Recent work has shown that RNA polymerase II (Pol II) accumulation correlates with AID recruitment. However, a direct link between Pol II and AID abundance has not been tested. We used the DT40 B-cell line to manipulate levels of Pol II by decreasing topoisomerase I (Top1), which relaxes DNA supercoiling in front of the transcription complex. Top1 was decreased by stable transfection of a short hairpin RNA against Top1, which produced an accumulation of Pol II in transcribed genes, compared to cells transfected with sh-control RNA. The increased Pol II density enhanced AID recruitment to variable genes in the λ light chain locus, and resulted in higher levels of somatic hypermutation and gene conversion. It has been proposed by another lab that AID itself might directly suppress Top1 to increase somatic hypermutation. However, we found that in both AID(+/+) and AID(-/-) B cells from DT40 and mice, Top1 protein levels were identical, indicating that the presence or absence of AID did not decrease Top1 expression. Rather, our results suggest that the mechanism for increased diversity when Top1 is reduced is that Pol II accumulates and recruits AID to variable genes.
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Affiliation(s)
- Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Huseyin Saribasak
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Zheng Cao
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States.
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34
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Landes Highlights. Nucleus 2014. [DOI: 10.4161/nucl.27495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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35
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DNA break mapping reveals topoisomerase II activity genome-wide. Int J Mol Sci 2014; 15:13111-22. [PMID: 25056547 PMCID: PMC4139894 DOI: 10.3390/ijms150713111] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 07/09/2014] [Accepted: 07/14/2014] [Indexed: 11/17/2022] Open
Abstract
Genomic DNA is under constant assault by endogenous and exogenous DNA damaging agents. DNA breakage can represent a major threat to genome integrity but can also be necessary for genome function. Here we present approaches to map DNA double-strand breaks (DSBs) and single-strand breaks (SSBs) at the genome-wide scale by two methods called DSB- and SSB-Seq, respectively. We tested these methods in human colon cancer cells and validated the results using the Topoisomerase II (Top2)-poisoning agent etoposide (ETO). Our results show that the combination of ETO treatment with break-mapping techniques is a powerful method to elaborate the pattern of Top2 enzymatic activity across the genome.
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36
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Fujita T, Fujii H. Identification of proteins associated with an IFNγ-responsive promoter by a retroviral expression system for enChIP using CRISPR. PLoS One 2014; 9:e103084. [PMID: 25051498 PMCID: PMC4106880 DOI: 10.1371/journal.pone.0103084] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 06/27/2014] [Indexed: 12/26/2022] Open
Abstract
Isolation of specific genomic regions retaining molecular interactions is essential for comprehensive identification of molecules associated with the genomic regions. Recently, we developed the engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) technology for purification of specific genomic regions. Here, we developed a retroviral expression system for enChIP using CRISPR. We showed that the target genomic locus can be purified with high efficiency by using this system. We also showed that contamination of potential off-target sites is negligible by using this system if the guide RNA (gRNA) for the target site has a sufficiently long unique sequence in its seed sequence. enChIP combined with stable isotope labeling using amino acids in cell culture (SILAC) analysis identified proteins whose association with the interferon (IFN) regulatory factor-1 (IRF-1) promoter region increases in response to IFNγ stimulation. The list of the associated proteins contained many novel proteins in the context of IFNγ-induced gene expression as well as proteins related to histone deacetylase complexes whose involvement has been suggested in IFNγ-mediated gene expression. Finally, we confirmed IFNγ-induced increased association of the identified proteins with the IRF-1 promoter by ChIP. Thus, our results showed that the retroviral enChIP system using CRISPR would be useful for biochemical analysis of genome functions including transcription and epigenetic regulation.
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Affiliation(s)
- Toshitsugu Fujita
- Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Hodaka Fujii
- Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- * E-mail:
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Abstract
Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions.
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Affiliation(s)
- Fedor Kouzine
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| | - David Levens
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| | - Laura Baranello
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
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38
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Wiedermannová J, Sudzinová P, Kovaľ T, Rabatinová A, Šanderova H, Ramaniuk O, Rittich Š, Dohnálek J, Fu Z, Halada P, Lewis P, Krásny L. Characterization of HelD, an interacting partner of RNA polymerase from Bacillus subtilis. Nucleic Acids Res 2014; 42:5151-63. [PMID: 24520113 PMCID: PMC4005671 DOI: 10.1093/nar/gku113] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bacterial RNA polymerase (RNAP) is an essential multisubunit protein complex required for gene expression. Here, we characterize YvgS (HelD) from Bacillus subtilis, a novel binding partner of RNAP. We show that HelD interacts with RNAP-core between the secondary channel of RNAP and the alpha subunits. Importantly, we demonstrate that HelD stimulates transcription in an ATP-dependent manner by enhancing transcriptional cycling and elongation. We demonstrate that the stimulatory effect of HelD can be amplified by a small subunit of RNAP, delta. In vivo, HelD is not essential but it is required for timely adaptations of the cell to changing environment. In summary, this study establishes HelD as a valid component of the bacterial transcription machinery.
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Affiliation(s)
- Jana Wiedermannová
- Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 12843, Czech Republic, Department of Structure Analysis of Biomacromolecules, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Prague 16206, Czech Republic, Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia and Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
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Baranello L, Kouzine F, Levens D. CTCF and cohesin cooperate to organize the 3D structure of the mammalian genome. Proc Natl Acad Sci U S A 2014; 111:889-90. [PMID: 24398527 PMCID: PMC3903212 DOI: 10.1073/pnas.1321957111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Laura Baranello
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Fedor Kouzine
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - David Levens
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
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40
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