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Attar AG, Paturej J, Banigan EJ, Erbaş A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. Nucleus 2024; 15:2351957. [PMID: 38753956 DOI: 10.1080/19491034.2024.2351957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Abnormal cell nuclear shapes are hallmarks of diseases, including progeria, muscular dystrophy, and many cancers. Experiments have shown that disruption of heterochromatin and increases in euchromatin lead to nuclear deformations, such as blebs and ruptures. However, the physical mechanisms through which chromatin governs nuclear shape are poorly understood. To investigate how heterochromatin and euchromatin might govern nuclear morphology, we studied chromatin microphase separation in a composite coarse-grained polymer and elastic shell simulation model. By varying chromatin density, heterochromatin composition, and heterochromatin-lamina interactions, we show how the chromatin phase organization may perturb nuclear shape. Increasing chromatin density stabilizes the lamina against large fluctuations. However, increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations by a "wetting"-like interaction. In contrast, fluctuations are insensitive to heterochromatin's internal structure. Our simulations suggest that peripheral heterochromatin accumulation could perturb nuclear morphology, while nuclear shape stabilization likely occurs through mechanisms other than chromatin microphase organization.
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Affiliation(s)
- Ali Goktug Attar
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
| | | | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
- Institute of Physics, University of Silesia, Chorzów, Poland
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2
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Li G, Pu P, Pan M, Weng X, Qiu S, Li Y, Abbas SJ, Zou L, Liu K, Wang Z, Shao Z, Jiang L, Wu W, Liu Y, Shao R, Liu F, Liu Y. Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer. Front Med 2024; 18:109-127. [PMID: 37721643 DOI: 10.1007/s11684-023-1008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/05/2023] [Indexed: 09/19/2023]
Abstract
Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer. However, knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited. Here, by taking advantage of in situ Hi-C, RNA-sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq), we investigated structural reorganization and functional changes in chromosomal compartments, topologically associated domains (TADs), and CCCTC binding factor (CTCF)-mediated loops in gallbladder cancer (GBC) tissues and cell lines. We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes. Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls. Furthermore, the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial-mesenchymal transition activation were enriched in cancer compared with their control counterparts. Cancer-specific enhancer-promoter loops, which contain multiple transcription factor binding motifs, acted as a central element to regulate aberrant gene expression. Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions. Collectively, our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.
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Affiliation(s)
- Guoqiang Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Peng Pu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Mengqiao Pan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
| | - Xiaoling Weng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
| | - Shimei Qiu
- Department of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200082, China
| | - Yiming Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Sk Jahir Abbas
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
| | - Lu Zou
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Ke Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Zheng Wang
- Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Ziyu Shao
- Department of General Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200082, China
| | - Lin Jiang
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
- Department of General Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200082, China
| | - Wenguang Wu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China
| | - Yun Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China.
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China.
| | - Rong Shao
- Department of Pharmacology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Fatao Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China.
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China.
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, 200127, China.
- Shanghai Key Laboratory of Biliary Tract Disease, Shanghai, 200082, China.
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Chhatwal K, Smith JJ, Bola H, Zahid A, Venkatakrishnan A, Brand T. Uncovering the Genetic Basis of Congenital Heart Disease: Recent Advancements and Implications for Clinical Management. CJC PEDIATRIC AND CONGENITAL HEART DISEASE 2023; 2:464-480. [PMID: 38205435 PMCID: PMC10777202 DOI: 10.1016/j.cjcpc.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/13/2023] [Indexed: 01/12/2024]
Abstract
Congenital heart disease (CHD) is the most prevalent hereditary disorder, affecting approximately 1% of all live births. A reduction in morbidity and mortality has been achieved with advancements in surgical intervention, yet challenges in managing complications, extracardiac abnormalities, and comorbidities still exist. To address these, a more comprehensive understanding of the genetic basis underlying CHD is required to establish how certain variants are associated with the clinical outcomes. This will enable clinicians to provide personalized treatments by predicting the risk and prognosis, which might improve the therapeutic results and the patient's quality of life. We review how advancements in genome sequencing are changing our understanding of the genetic basis of CHD, discuss experimental approaches to determine the significance of novel variants, and identify barriers to use this knowledge in the clinics. Next-generation sequencing technologies are unravelling the role of oligogenic inheritance, epigenetic modification, genetic mosaicism, and noncoding variants in controlling the expression of candidate CHD-associated genes. However, clinical risk prediction based on these factors remains challenging. Therefore, studies involving human-induced pluripotent stem cells and single-cell sequencing help create preclinical frameworks for determining the significance of novel genetic variants. Clinicians should be aware of the benefits and implications of the responsible use of genomics. To facilitate and accelerate the clinical integration of these novel technologies, clinicians should actively engage in the latest scientific and technical developments to provide better, more personalized management plans for patients.
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Affiliation(s)
- Karanjot Chhatwal
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Jacob J. Smith
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Harroop Bola
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Abeer Zahid
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Ashwin Venkatakrishnan
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Thomas Brand
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
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4
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Zhang L, Guan Q, Wang Z, Feng J, Zou J, Gao B. Consequences of Aging on Bone. Aging Dis 2023:AD.2023.1115. [PMID: 38029404 DOI: 10.14336/ad.2023.1115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
With the aging of the global population, the incidence of musculoskeletal diseases has been increasing, seriously affecting people's health. As people age, the microenvironment within skeleton favors bone resorption and inhibits bone formation, accompanied by bone marrow fat accumulation and multiple cellular senescence. Specifically, skeletal stem/stromal cells (SSCs) during aging tend to undergo adipogenesis rather than osteogenesis. Meanwhile, osteoblasts, as well as osteocytes, showed increased apoptosis, decreased quantity, and multiple functional limitations including impaired mechanical sensing, intercellular modulation, and exosome secretion. Also, the bone resorption function of macrophage-lineage cells (including osteoclasts and preosteoclasts) was significantly enhanced, as well as impaired vascularization and innervation. In this study, we systematically reviewed the effect of aging on bone and the within microenvironment (including skeletal cells as well as their intracellular structure variations, vascular structures, innervation, marrow fat distribution, and lymphatic system) caused by aging, and mechanisms of osteoimmune regulation of the bone environment in the aging state, and the causal relationship with multiple musculoskeletal diseases in addition with their potential therapeutic strategy.
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Affiliation(s)
- Lingli Zhang
- College of Athletic Performance, Shanghai University of Sport, Shanghai, China
| | - Qiao Guan
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Zhikun Wang
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Jie Feng
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Jun Zou
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Bo Gao
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
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5
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Saribas AS, Bellizzi A, Wollebo HS, Beer T, Tang HY, Safak M. Human neurotropic polyomavirus, JC virus, late coding region encodes a novel nuclear protein, ORF4, which targets the promyelocytic leukemia nuclear bodies (PML-NBs) and modulates their reorganization. Virology 2023; 587:109866. [PMID: 37741199 PMCID: PMC10602023 DOI: 10.1016/j.virol.2023.109866] [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: 05/10/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 09/25/2023]
Abstract
We previously reported the discovery and characterization of two novel proteins (ORF1 and ORF2) generated by the alternative splicing of the JC virus (JCV) late coding region. Here, we report the discovery and partial characterization of three additional novel ORFs from the same coding region, ORF3, ORF4 and ORF5, which potentially encode 70, 173 and 265 amino acid long proteins respectively. While ORF3 protein exhibits a uniform distribution pattern throughout the cells, we were unable to detect ORF5 expression. Surprisingly, ORF4 protein was determined to be the only JCV protein specifically targeting the promyelocytic leukemia nuclear bodies (PML-NBs) and inducing their reorganization in nucleus. Although ORF4 protein has a modest effect on JCV replication, it is implicated to play major roles during the JCV life cycle, perhaps by regulating the antiviral response of PML-NBs against JCV infections and thus facilitating the progression of the JCV-induced disease in infected individuals.
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Affiliation(s)
- A Sami Saribas
- Department of Microbiology, Immunology, and Inflammation, Laboratory of Molecular Neurovirology, MERB-757, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Anna Bellizzi
- Department of Microbiology, Immunology, and Inflammation, Laboratory of Molecular Neurovirology, MERB-757, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Hassen S Wollebo
- Department of Microbiology, Immunology, and Inflammation, Laboratory of Molecular Neurovirology, MERB-757, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Thomas Beer
- The Wistar Institute Proteomics and Metabolomics Facility Room 252, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Hsin-Yao Tang
- The Wistar Institute Proteomics and Metabolomics Facility Room 252, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Mahmut Safak
- Department of Microbiology, Immunology, and Inflammation, Laboratory of Molecular Neurovirology, MERB-757, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA.
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Wulfridge P, Yan Q, Rell N, Doherty J, Jacobson S, Offley S, Deliard S, Feng K, Phillips-Cremins JE, Gardini A, Sarma K. G-quadruplexes associated with R-loops promote CTCF binding. Mol Cell 2023; 83:3064-3079.e5. [PMID: 37552993 PMCID: PMC10529333 DOI: 10.1016/j.molcel.2023.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/24/2023] [Accepted: 07/07/2023] [Indexed: 08/10/2023]
Abstract
CTCF is a critical regulator of genome architecture and gene expression that binds thousands of sites on chromatin. CTCF genomic localization is controlled by the recognition of a DNA sequence motif and regulated by DNA modifications. However, CTCF does not bind to all its potential sites in all cell types, raising the question of whether the underlying chromatin structure can regulate CTCF occupancy. Here, we report that R-loops facilitate CTCF binding through the formation of associated G-quadruplex (G4) structures. R-loops and G4s co-localize with CTCF at many genomic regions in mouse embryonic stem cells and promote CTCF binding to its cognate DNA motif in vitro. R-loop attenuation reduces CTCF binding in vivo. Deletion of a specific G4-forming motif in a gene reduces CTCF binding and alters gene expression. Conversely, chemical stabilization of G4s results in CTCF gains and accompanying alterations in chromatin organization, suggesting a pivotal role for G4 structures in reinforcing long-range genome interactions through CTCF.
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Affiliation(s)
- Phillip Wulfridge
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qingqing Yan
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel Rell
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Doherty
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Skye Jacobson
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Offley
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra Deliard
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kelly Feng
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer E Phillips-Cremins
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kavitha Sarma
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Canoy RJ, Shmakova A, Karpukhina A, Lomov N, Tiukacheva E, Kozhevnikova Y, André F, Germini D, Vassetzky Y. Specificity of cancer-related chromosomal translocations is linked to proximity after the DNA double-strand break and subsequent selection. NAR Cancer 2023; 5:zcad049. [PMID: 37750169 PMCID: PMC10518054 DOI: 10.1093/narcan/zcad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/01/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Most cancer-related chromosomal translocations appear to be cell type specific. It is currently unknown why different chromosomal translocations occur in different cells. This can be due to either the occurrence of particular translocations in specific cell types or adaptive survival advantage conferred by translocations only in specific cells. We experimentally addressed this question by double-strand break (DSB) induction at MYC, IGH, AML and ETO loci in the same cell to generate chromosomal translocations in different cell lineages. Our results show that any translocation can potentially arise in any cell type. We have analyzed different factors that could affect the frequency of the translocations, and only the spatial proximity between gene loci after the DSB induction correlated with the resulting translocation frequency, supporting the 'breakage-first' model. Furthermore, upon long-term culture of cells with the generated chromosomal translocations, only oncogenic MYC-IGH and AML-ETO translocations persisted over a 60-day period. Overall, the results suggest that chromosomal translocation can be generated after DSB induction in any type of cell, but whether the cell with the translocation would persist in a cell population depends on the cell type-specific selective survival advantage that the chromosomal translocation confers to the cell.
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Affiliation(s)
- Reynand Jay Canoy
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, 1000 Manila, The Philippines
| | - Anna Shmakova
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Laboratory of Molecular Endocrinology, Institute of Experimental Cardiology, Federal State Budgetary Organization ‘National Cardiology Research Center’ of the Ministry of Health of the Russian Federation, 127994 Moscow, Russia
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Anna Karpukhina
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Nikolai Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugenia Tiukacheva
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Yana Kozhevnikova
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Franck André
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Diego Germini
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Yegor Vassetzky
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
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Shin H, Kim Y. Regulation of loop extrusion on the interphase genome. Crit Rev Biochem Mol Biol 2023; 58:1-18. [PMID: 36921088 DOI: 10.1080/10409238.2023.2182273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
In the human cell nucleus, dynamically organized chromatin is the substrate for gene regulation, DNA replication, and repair. A central mechanism of DNA loop formation is an ATPase motor cohesin-mediated loop extrusion. The cohesin complexes load and unload onto the chromosome under the control of other regulators that physically interact and affect motor activity. Regulation of the dynamic loading cycle of cohesin influences not only the chromatin structure but also genome-associated human disorders and aging. This review focuses on the recently spotlighted genome organizing factors and the mechanism by which their dynamic interactions shape the genome architecture in interphase.
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Affiliation(s)
- Hyogyung Shin
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Yoori Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea.,New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
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9
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Heng E, Thanedar S, Heng HH. Challenges and Opportunities for Clinical Cytogenetics in the 21st Century. Genes (Basel) 2023; 14:493. [PMID: 36833419 PMCID: PMC9956237 DOI: 10.3390/genes14020493] [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: 01/28/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
The powerful utilities of current DNA sequencing technology question the value of developing clinical cytogenetics any further. By briefly reviewing the historical and current challenges of cytogenetics, the new conceptual and technological platform of the 21st century clinical cytogenetics is presented. Particularly, the genome architecture theory (GAT) has been used as a new framework to emphasize the importance of clinical cytogenetics in the genomic era, as karyotype dynamics play a central role in information-based genomics and genome-based macroevolution. Furthermore, many diseases can be linked to elevated levels of genomic variations within a given environment. With karyotype coding in mind, new opportunities for clinical cytogenetics are discussed to integrate genomics back into cytogenetics, as karyotypic context represents a new type of genomic information that organizes gene interactions. The proposed research frontiers include: 1. focusing on karyotypic heterogeneity (e.g., classifying non-clonal chromosome aberrations (NCCAs), studying mosaicism, heteromorphism, and nuclear architecture alteration-mediated diseases), 2. monitoring the process of somatic evolution by characterizing genome instability and illustrating the relationship between stress, karyotype dynamics, and diseases, and 3. developing methods to integrate genomic data and cytogenomics. We hope that these perspectives can trigger further discussion beyond traditional chromosomal analyses. Future clinical cytogenetics should profile chromosome instability-mediated somatic evolution, as well as the degree of non-clonal chromosomal aberrations that monitor the genomic system's stress response. Using this platform, many common and complex disease conditions, including the aging process, can be effectively and tangibly monitored for health benefits.
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Affiliation(s)
- Eric Heng
- Stanford University, 450 Jane Stanford Way, Stanford, CA 94305, USA
| | - Sanjana Thanedar
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Henry H. Heng
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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10
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Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:ijms24032658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
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Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
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Abstract
Changes in bone architecture and metabolism with aging increase the likelihood of osteoporosis and fracture. Age-onset osteoporosis is multifactorial, with contributory extrinsic and intrinsic factors including certain medical problems, specific prescription drugs, estrogen loss, secondary hyperparathyroidism, microenvironmental and cellular alterations in bone tissue, and mechanical unloading or immobilization. At the histological level, there are changes in trabecular and cortical bone as well as marrow cellularity, lineage switching of mesenchymal stem cells to an adipogenic fate, inadequate transduction of signals during skeletal loading, and predisposition toward senescent cell accumulation with production of a senescence-associated secretory phenotype. Cumulatively, these changes result in bone remodeling abnormalities that over time cause net bone loss typically seen in older adults. Age-related osteoporosis is a geriatric syndrome due to the multiple etiologies that converge upon the skeleton to produce the ultimate phenotypic changes that manifest as bone fragility. Bone tissue is dynamic but with tendencies toward poor osteoblastic bone formation and relative osteoclastic bone resorption with aging. Interactions with other aging physiologic systems, such as muscle, may also confer detrimental effects on the aging skeleton. Conversely, individuals who maintain their BMD experience a lower risk of fractures, disability, and mortality, suggesting that this phenotype may be a marker of successful aging. © 2023 American Physiological Society. Compr Physiol 13:4355-4386, 2023.
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Affiliation(s)
- Robert J Pignolo
- Department of Medicine, Divisions of Geriatric Medicine and Gerontology, Endocrinology, and Hospital Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA.,The Department of Physiology and Biomedical Engineering, and the Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, Minnesota, USA
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12
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Xu N, Liu Y, Nai S, Tao Y, Ding Y, Jia L, Geng Q, Li J, Bai Y, Wei GH, Dong MQ, Luo L, Zhao M, Xu X, Li XX, Li J, Huang L. UBE3D Is Involved in Blue Light-Induced Retinal Damage by Regulating Double-Strand Break Repair. Invest Ophthalmol Vis Sci 2022; 63:7. [PMID: 36094642 PMCID: PMC9482326 DOI: 10.1167/iovs.63.10.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose Age-related macular degeneration (AMD) is currently the leading cause of blindness worldwide. Previously, we identified ubiquitin-protein ligase E3D (UBE3D) as an AMD-associated protein for East Asian populations, and here we further demonstrate that UBE3D could be associated with DNA damage response. Methods The established I-SceI-inducible GFP reporter system was used to explore the effect of UBE3D on homologous recombination. Immunoprecipitation-mass spectrometry (MS) was used to explore potential UBE3D-interacting proteins and validated with coimmunoprecipitation assays and the pulldown assays. Micrococcal nuclease (MNase) assays were used to investigate the function of UBE3D on heterochromatin de-condensation upon DNA damage. An aged mouse model of blue light-induced eye damage was constructed, and electroretinography (ERG) and optical coherence tomography (OCT) were performed to compare the differences between wild-type and UBE3D+/- mice. Results First, we show that GFP-UBE3D is recruited to damage sites by PCNA, through a PCNA-interacting protein (PIP) box. Furthermore, UBE3D interacts with KAP1 via R377R378 and oxidation of the AMD-associated V379M mutation abolishes KAP1-UBE3D binding. By MNase assays, UBE3D depletion reduces the chromatin relaxation levels upon DNA damage. In addition, UBE3D depletion renders less KAP1 recruitment. Compared with wild type, blue light induces less damage in UBE3D+/- mice as measured by ERG and OCT, consistent with our biochemical results. Conclusions Hence, we propose that one potential mechanism that UBE3D-V379M contributes to AMD pathogenesis might be via defective DNA damage repair linked with oxidative stress and our results offered a potential direction for the treatment of AMD.
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Affiliation(s)
- Ningda Xu
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Yue Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Shanshan Nai
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University, Chaoyang District, Beijing, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing, China
| | - Lemei Jia
- National Institute of Biological Sciences, Beijing, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Jie Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Yujing Bai
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Linyi Luo
- Department of Ophthalmology and Visual Sciences, Affiliated Dongguan Hospital, Southern Medical University, Guangdong, China
| | - Mingwei Zhao
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xiao-Xin Li
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
- Department of Ophthalmology, Xiamen Eye Center of Xiamen University, Xiamen, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Lvzhen Huang
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
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13
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Li Y, Agrawal V, Virk RKA, Roth E, Li WS, Eshein A, Frederick J, Huang K, Almassalha L, Bleher R, Carignano MA, Szleifer I, Dravid VP, Backman V. Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM). Sci Rep 2022; 12:12198. [PMID: 35842472 PMCID: PMC9288481 DOI: 10.1038/s41598-022-16028-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/04/2022] [Indexed: 11/09/2022] Open
Abstract
Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei.
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Affiliation(s)
- Yue Li
- Applied Physics Program, Northwestern University, Evanston, IL, 60208, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Ranya K A Virk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Eric Roth
- Department of Materials Sciences and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Wing Shun Li
- Applied Physics Program, Northwestern University, Evanston, IL, 60208, USA
| | - Adam Eshein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Kai Huang
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen, 518132, China
| | - Luay Almassalha
- Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60611, USA
| | - Reiner Bleher
- Department of Materials Sciences and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Marcelo A Carignano
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Vinayak P Dravid
- Department of Materials Sciences and Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
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14
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Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Nat Methods 2022; 19:938-949. [PMID: 35817938 PMCID: PMC9349046 DOI: 10.1038/s41592-022-01527-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 05/18/2022] [Indexed: 02/07/2023]
Abstract
A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integration approach to produce populations of single-cell genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction and spatial segregation of functionally related chromatin. We demonstrate that multimodal data integration can compensate for systematic errors in some of the data and can greatly increase accuracy and coverage of genome structure models. We also show that alternative combinations of different orthogonal data sources can converge to models with similar predictive power. Moreover, our study reveals the key contributions of low-frequency (‘rare’) interchromosomal contacts to accurately predicting the global nuclear architecture, including the positioning of genes and chromosomes. Overall, our results highlight the benefits of multimodal data integration for genome structure analysis, available through the Integrative Genome Modeling software package. The Integrative Genome Modeling platform is a tool for population-based three-dimensional genome structure modeling and analysis by integrating various experimental data sources.
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15
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Özturan D, Morova T, Lack NA. Androgen Receptor-Mediated Transcription in Prostate Cancer. Cells 2022; 11:cells11050898. [PMID: 35269520 PMCID: PMC8909478 DOI: 10.3390/cells11050898] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Androgen receptor (AR)-mediated transcription is critical in almost all stages of prostate cancer (PCa) growth and differentiation. This process involves a complex interplay of coregulatory proteins, chromatin remodeling complexes, and other transcription factors that work with AR at cis-regulatory enhancer regions to induce the spatiotemporal transcription of target genes. This enhancer-driven mechanism is remarkably dynamic and undergoes significant alterations during PCa progression. In this review, we discuss the AR mechanism of action in PCa with a focus on how cis-regulatory elements modulate gene expression. We explore emerging evidence of genetic variants that can impact AR regulatory regions and alter gene transcription in PCa. Finally, we highlight several outstanding questions and discuss potential mechanisms of this critical transcription factor.
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Affiliation(s)
- Doğancan Özturan
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
| | - Nathan A. Lack
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
- Correspondence: ; Tel.: +1-604-875-4411 (ext. 6417)
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16
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Peze-Heidsieck E, Bonnifet T, Znaidi R, Ravel-Godreuil C, Massiani-Beaudoin O, Joshi RL, Fuchs J. Retrotransposons as a Source of DNA Damage in Neurodegeneration. Front Aging Neurosci 2022; 13:786897. [PMID: 35058771 PMCID: PMC8764243 DOI: 10.3389/fnagi.2021.786897] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
The etiology of aging-associated neurodegenerative diseases (NDs), such as Parkinson’s disease (PD) and Alzheimer’s disease (AD), still remains elusive and no curative treatment is available. Age is the major risk factor for PD and AD, but the molecular link between aging and neurodegeneration is not fully understood. Aging is defined by several hallmarks, some of which partially overlap with pathways implicated in NDs. Recent evidence suggests that aging-associated epigenetic alterations can lead to the derepression of the LINE-1 (Long Interspersed Element-1) family of transposable elements (TEs) and that this derepression might have important implications in the pathogenesis of NDs. Almost half of the human DNA is composed of repetitive sequences derived from TEs and TE mobility participated in shaping the mammalian genomes during evolution. Although most TEs are mutated and no longer mobile, more than 100 LINE-1 elements have retained their full coding potential in humans and are thus retrotransposition competent. Uncontrolled activation of TEs has now been reported in various models of neurodegeneration and in diseased human brain tissues. We will discuss in this review the potential contribution of LINE-1 elements in inducing DNA damage and genomic instability, which are emerging pathological features in NDs. TEs might represent an important molecular link between aging and neurodegeneration, and a potential target for urgently needed novel therapeutic disease-modifying interventions.
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Affiliation(s)
- Eugenie Peze-Heidsieck
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Tom Bonnifet
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Rania Znaidi
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Rajiv L Joshi
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
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17
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Boninsegna L, Yildirim A, Zhan Y, Alber F. Integrative approaches in genome structure analysis. Structure 2021; 30:24-36. [PMID: 34963059 DOI: 10.1016/j.str.2021.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/13/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
Abstract
New technological advances in integrated imaging, sequencing-based assays, and computational analysis have revolutionized our view of genomes in terms of their structure and dynamics in space and time. These advances promise a deeper understanding of genome functions and mechanistic insights into how the nucleus is spatially organized and functions. These wide arrays of complementary data provide an opportunity to produce quantitative integrative models of nuclear organization. In this article, we highlight recent key developments and discuss the outlook for these fields.
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Affiliation(s)
- Lorenzo Boninsegna
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Asli Yildirim
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yuxiang Zhan
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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18
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Aho V, Salminen S, Mattola S, Gupta A, Flomm F, Sodeik B, Bosse JB, Vihinen-Ranta M. Infection-induced chromatin modifications facilitate translocation of herpes simplex virus capsids to the inner nuclear membrane. PLoS Pathog 2021; 17:e1010132. [PMID: 34910768 PMCID: PMC8673650 DOI: 10.1371/journal.ppat.1010132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/19/2021] [Indexed: 01/04/2023] Open
Abstract
Herpes simplex virus capsids are assembled and packaged in the nucleus and move by diffusion through the nucleoplasm to the nuclear envelope for egress. Analyzing their motion provides conclusions not only on capsid transport but also on the properties of the nuclear environment during infection. We utilized live-cell imaging and single-particle tracking to characterize capsid motion relative to the host chromatin. The data indicate that as the chromatin was marginalized toward the nuclear envelope it presented a restrictive barrier to the capsids. However, later in infection this barrier became more permissive and the probability of capsids to enter the chromatin increased. Thus, although chromatin marginalization initially restricted capsid transport to the nuclear envelope, a structural reorganization of the chromatin counteracted that to promote capsid transport later. Analyses of capsid motion revealed that it was subdiffusive, and that the diffusion coefficients were lower in the chromatin than in regions lacking chromatin. In addition, the diffusion coefficient in both regions increased during infection. Throughout the infection, the capsids were never enriched at the nuclear envelope, which suggests that instead of nuclear export the transport through the chromatin is the rate-limiting step for the nuclear egress of capsids. This provides motivation for further studies by validating the importance of intranuclear transport to the life cycle of HSV-1.
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Affiliation(s)
- Vesa Aho
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Sami Salminen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Salla Mattola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Alka Gupta
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Felix Flomm
- HPI, Leibniz-Institute for Experimental Virology, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Beate Sodeik
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Jens B. Bosse
- HPI, Leibniz-Institute for Experimental Virology, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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Feric M, Misteli T. Phase separation in genome organization across evolution. Trends Cell Biol 2021; 31:671-685. [PMID: 33771451 PMCID: PMC8286288 DOI: 10.1016/j.tcb.2021.03.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023]
Abstract
Phase separation is emerging as a paradigm to explain the self-assembly and organization of membraneless bodies in the cell. Recent advances show that this principle also extends to nucleoprotein complexes, including DNA-based structures. We discuss here recent observations on the role of phase separation in genome organization across the evolutionary spectrum from bacteria to mammals. These findings suggest that molecular interactions amongst DNA-binding proteins evolved to form a variety of biomolecular condensates with distinct material properties that affect genome organization and function. We suggest that phase separation contributes to genome organization across evolution and that the resulting phase behavior of genomes may underlie regulatory mechanisms and disease.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA; National Institute of General Medical Sciences, NIH, Bethesda, MD, USA.
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA.
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20
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Sajid A, Lalani EN, Chen B, Hashimoto T, Griffin DK, Bhartiya A, Thompson G, Robinson IK, Yusuf M. Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus. Int J Mol Sci 2021; 22:ijms22115987. [PMID: 34206020 PMCID: PMC8198510 DOI: 10.3390/ijms22115987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/18/2022] Open
Abstract
Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.
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Affiliation(s)
- Atiqa Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - Bo Chen
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
- Key Laboratory of Performance Evolution and Control for Engineering Structures of the Ministry of Education, Tongji University, Shanghai 200092, China
| | - Teruo Hashimoto
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | | | - Archana Bhartiya
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
| | - George Thompson
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | - Ian K. Robinson
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mohammed Yusuf
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Correspondence:
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21
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Abstract
Genomic information is encoded on long strands of DNA, which are folded into chromatin and stored in a tiny nucleus. Nuclear chromatin is a negatively charged polymer composed of DNA, histones, and various nonhistone proteins. Because of its highly charged nature, chromatin structure varies greatly depending on the surrounding environment (e.g., cations, molecular crowding, etc.). New technologies to capture chromatin in living cells have been developed over the past 10 years. Our view on chromatin organization has drastically shifted from a regular and static one to a more variable and dynamic one. Chromatin forms numerous compact dynamic domains that act as functional units of the genome in higher eukaryotic cells and locally appear liquid-like. By changing DNA accessibility, these domains can govern various functions. Based on new evidences from versatile genomics and advanced imaging studies, we discuss the physical nature of chromatin in the crowded nuclear environment and how it is regulated.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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22
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Pignolo RJ, Law SF, Chandra A. Bone Aging, Cellular Senescence, and Osteoporosis. JBMR Plus 2021; 5:e10488. [PMID: 33869998 PMCID: PMC8046105 DOI: 10.1002/jbm4.10488] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
Changes in aging bone that lead to osteoporosis are mediated at multiple levels, including hormonal alterations, skeletal unloading, and accumulation of senescent cells. This pathological interplay is superimposed upon medical conditions, potentially bone-wasting medications, modifiable and unmodifiable personal risk factors, and genetic predisposition that accelerate bone loss with aging. In this study, the focus is on bone hemostasis and its dysregulation with aging. The major physiological changes with aging in bone and the role of cellular senescence in contributing to age-related osteoporosis are summarized. The aspects of bone aging are reviewed including remodeling deficits, uncoupling phenomena, inducers of cellular senescence related to bone aging, roles of the senescence-associated secretory phenotype, radiation-induced bone loss as a model for bone aging, and the accumulation of senescent cells in the bone microenvironment as a predominant mechanism for age-related osteoporosis. The study also addresses the rationale and potential for therapeutic interventions based on the clearance of senescent cells or suppression of the senescence-associated secretory phenotype. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Robert J Pignolo
- Department of MedicineMayo ClinicRochesterMNUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMNUSA
| | - Susan F Law
- Department of MedicineMayo ClinicRochesterMNUSA
| | - Abhishek Chandra
- Department of MedicineMayo ClinicRochesterMNUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMNUSA
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23
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Lee BH, Rhie SK. Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Epigenetics Chromatin 2021; 14:14. [PMID: 33741028 PMCID: PMC7980343 DOI: 10.1186/s13072-021-00390-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetic marks do not change the sequence of DNA but affect gene expression in a cell-type specific manner by altering the activities of regulatory elements. Development of new molecular biology assays, sequencing technologies, and computational approaches enables us to profile the human epigenome in three-dimensional structure genome-wide. Here we describe various molecular biology techniques and bioinformatic tools that have been developed to measure the activities of regulatory elements and their chromatin interactions. Moreover, we list currently available three-dimensional epigenomic data sets that are generated in various human cell types and tissues to assist in the design and analysis of research projects.
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Affiliation(s)
- Beoung Hun Lee
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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24
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Botchway SW, Farooq S, Sajid A, Robinson IK, Yusuf M. Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure. Chromosome Res 2021; 29:19-36. [PMID: 33686484 DOI: 10.1007/s10577-021-09654-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 01/07/2023]
Abstract
The organization of chromatin into higher-order structures and its condensation process represent one of the key challenges in structural biology. This is important for elucidating several disease states. To address this long-standing problem, development of advanced imaging methods has played an essential role in providing understanding into mitotic chromosome structure and compaction. Amongst these are two fast evolving fluorescence imaging technologies, specifically fluorescence lifetime imaging (FLIM) and super-resolution microscopy (SRM). FLIM in particular has been lacking in the application of chromosome research while SRM has been successfully applied although not widely. Both these techniques are capable of providing fluorescence imaging with nanometer information. SRM or "nanoscopy" is capable of generating images of DNA with less than 50 nm resolution while FLIM when coupled with energy transfer may provide less than 20 nm information. Here, we discuss the advantages and limitations of both methods followed by their contribution to mitotic chromosome studies. Furthermore, we highlight the future prospects of how advancements in new technologies can contribute in the field of chromosome science.
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Affiliation(s)
- S W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, UK
| | - S Farooq
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - A Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - I K Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.,Brookhaven National Lab, Upton, NY, 11973, USA
| | - M Yusuf
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan. .,London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
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25
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Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains. Nat Commun 2021; 12:1419. [PMID: 33658503 PMCID: PMC7930052 DOI: 10.1038/s41467-021-21707-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.
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26
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McArthur E, Capra JA. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. Am J Hum Genet 2021; 108:269-283. [PMID: 33545030 PMCID: PMC7895846 DOI: 10.1016/j.ajhg.2021.01.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/29/2020] [Indexed: 12/22/2022] Open
Abstract
Topologically associating domains (TADs) are fundamental units of three-dimensional (3D) nuclear organization. The regions bordering TADs-TAD boundaries-contribute to the regulation of gene expression by restricting interactions of cis-regulatory sequences to their target genes. TAD and TAD-boundary disruption have been implicated in rare-disease pathogenesis; however, we have a limited framework for integrating TADs and their variation across cell types into the interpretation of common-trait-associated variants. Here, we investigate an attribute of 3D genome architecture-the stability of TAD boundaries across cell types-and demonstrate its relevance to understanding how genetic variation in TADs contributes to complex disease. By synthesizing TAD maps across 37 diverse cell types with 41 genome-wide association studies (GWASs), we investigate the differences in disease association and evolutionary pressure on variation in TADs versus TAD boundaries. We demonstrate that genetic variation in TAD boundaries contributes more to complex-trait heritability, especially for immunologic, hematologic, and metabolic traits. We also show that TAD boundaries are more evolutionarily constrained than TADs. Next, stratifying boundaries by their stability across cell types, we find substantial variation. Compared to boundaries unique to a specific cell type, boundaries stable across cell types are further enriched for complex-trait heritability, evolutionary constraint, CTCF binding, and housekeeping genes. Thus, considering TAD boundary stability across cell types provides valuable context for understanding the genome's functional landscape and enabling variant interpretation that takes 3D structure into account.
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Affiliation(s)
- Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158; Bakar Institute for Computational Health Sciences, University of California, San Francisco, CA, 94158.
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27
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Falk M, Hausmann M. A Paradigm Revolution or Just Better Resolution-Will Newly Emerging Superresolution Techniques Identify Chromatin Architecture as a Key Factor in Radiation-Induced DNA Damage and Repair Regulation? Cancers (Basel) 2020; 13:E18. [PMID: 33374540 PMCID: PMC7793109 DOI: 10.3390/cancers13010018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023] Open
Abstract
DNA double-strand breaks (DSBs) have been recognized as the most serious lesions in irradiated cells. While several biochemical pathways capable of repairing these lesions have been identified, the mechanisms by which cells select a specific pathway for activation at a given DSB site remain poorly understood. Our knowledge of DSB induction and repair has increased dramatically since the discovery of ionizing radiation-induced foci (IRIFs), initiating the possibility of spatiotemporally monitoring the assembly and disassembly of repair complexes in single cells. IRIF exploration revealed that all post-irradiation processes-DSB formation, repair and misrepair-are strongly dependent on the characteristics of DSB damage and the microarchitecture of the whole affected chromatin domain in addition to the cell status. The microscale features of IRIFs, such as their morphology, mobility, spatiotemporal distribution, and persistence kinetics, have been linked to repair mechanisms. However, the influence of various biochemical and structural factors and their specific combinations on IRIF architecture remains unknown, as does the hierarchy of these factors in the decision-making process for a particular repair mechanism at each individual DSB site. New insights into the relationship between the physical properties of the incident radiation, chromatin architecture, IRIF architecture, and DSB repair mechanisms and repair efficiency are expected from recent developments in optical superresolution microscopy (nanoscopy) techniques that have shifted our ability to analyze chromatin and IRIF architectures towards the nanoscale. In the present review, we discuss this relationship, attempt to correlate still rather isolated nanoscale studies with already better-understood aspects of DSB repair at the microscale, and consider whether newly emerging "correlated multiscale structuromics" can revolutionarily enhance our knowledge in this field.
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Affiliation(s)
- Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany;
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28
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Hu M, Cherkaoui I, Misra S, Rutter GA. Functional Genomics in Pancreatic β Cells: Recent Advances in Gene Deletion and Genome Editing Technologies for Diabetes Research. Front Endocrinol (Lausanne) 2020; 11:576632. [PMID: 33162936 PMCID: PMC7580382 DOI: 10.3389/fendo.2020.576632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
The inheritance of variants that lead to coding changes in, or the mis-expression of, genes critical to pancreatic beta cell function can lead to alterations in insulin secretion and increase the risk of both type 1 and type 2 diabetes. Recently developed clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) gene editing tools provide a powerful means of understanding the impact of identified variants on cell function, growth, and survival and might ultimately provide a means, most likely after the transplantation of genetically "corrected" cells, of treating the disease. Here, we review some of the disease-associated genes and variants whose roles have been probed up to now. Next, we survey recent exciting developments in CRISPR/Cas9 technology and their possible exploitation for β cell functional genomics. Finally, we will provide a perspective as to how CRISPR/Cas9 technology may find clinical application in patients with diabetes.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ines Cherkaoui
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shivani Misra
- Metabolic Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
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29
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Shao LW, Peng Q, Dong M, Gao K, Li Y, Li Y, Li CY, Liu Y. Histone deacetylase HDA-1 modulates mitochondrial stress response and longevity. Nat Commun 2020; 11:4639. [PMID: 32934238 PMCID: PMC7493924 DOI: 10.1038/s41467-020-18501-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/24/2020] [Indexed: 01/06/2023] Open
Abstract
The ability to detect, respond and adapt to mitochondrial stress ensures the development and survival of organisms. Caenorhabditis elegans responds to mitochondrial stress by activating the mitochondrial unfolded protein response (UPRmt) to buffer the mitochondrial folding environment, rewire the metabolic state, and promote innate immunity and lifespan extension. Here we show that HDA-1, the C. elegans ortholog of mammalian histone deacetylase (HDAC) is required for mitochondrial stress-mediated activation of UPRmt. HDA-1 interacts and coordinates with the genome organizer DVE-1 to induce the transcription of a broad spectrum of UPRmt, innate immune response and metabolic reprogramming genes. In rhesus monkey and human tissues, HDAC1/2 transcript levels correlate with the expression of UPRmt genes. Knocking down or pharmacological inhibition of HDAC1/2 disrupts the activation of the UPRmt and the mitochondrial network in mammalian cells. Our results underscore an evolutionarily conserved mechanism of HDAC1/2 in modulating mitochondrial homeostasis and regulating longevity.
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Affiliation(s)
- Li-Wa Shao
- Beijing Advanced Innovation Center for Genomics, State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Qi Peng
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China
| | - Mingyue Dong
- Beijing Advanced Innovation Center for Genomics, State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Kaiyu Gao
- Beijing Advanced Innovation Center for Genomics, State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China
| | - Yumei Li
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China
| | - Yi Li
- Beijing Advanced Innovation Center for Genomics, State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China.
| | - Ying Liu
- Beijing Advanced Innovation Center for Genomics, State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China.
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30
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Vo TV, Dhakshnamoorthy J, Larkin M, Zofall M, Thillainadesan G, Balachandran V, Holla S, Wheeler D, Grewal SIS. CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing. Cell Rep 2020; 28:267-281.e5. [PMID: 31269446 DOI: 10.1016/j.celrep.2019.05.107] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/16/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023] Open
Abstract
In eukaryotic genomes, heterochromatin is targeted by RNAi machinery and/or by pathways requiring RNA elimination and transcription termination factors. However, a direct connection between termination machinery and RNA polymerase II (RNAPII) transcriptional activity at heterochromatic loci has remained elusive. Here, we show that, in fission yeast, the conserved cleavage and polyadenylation factor (CPF) is a key component involved in RNAi-independent assembly of constitutive and facultative heterochromatin domains and that CPF is broadly required to silence genes regulated by Clr4SUV39H. Remarkably, CPF is recruited to non-canonical termination sites within the body of genes by the YTH family RNA-binding protein Mmi1 and is required for RNAPII transcription termination and facultative heterochromatin assembly. CPF loading by Mmi1 also promotes the selective termination of long non-coding RNAs that regulate gene expression in cis. These analyses delineate a mechanism in which CPF loaded onto non-canonical termination sites specifies targets of heterochromatin assembly and gene silencing.
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Affiliation(s)
- Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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31
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Grizzi F, Castello A, Qehajaj D, Russo C, Lopci E. The Complexity and Fractal Geometry of Nuclear Medicine Images. Mol Imaging Biol 2020; 21:401-409. [PMID: 30003453 DOI: 10.1007/s11307-018-1236-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Irregularity in shape and behavior is the main feature of every anatomical system, including human organs, tissues, cells, and sub-cellular entities. It has been shown that this property cannot be quantified by means of the classical Euclidean geometry, which is only able to describe regular geometrical objects. In contrast, fractal geometry has been widely applied in several scientific fields. This rapid growth has also produced substantial insights in the biomedical imaging. Consequently, particular attention has been given to the identification of pathognomonic patterns of "shape" in anatomical entities and their changes from natural to pathological states. Despite the advantages of fractal mathematics and several studies demonstrating its applicability to oncological research, many researchers and clinicians remain unaware of its potential. Therefore, this review aims to summarize the complexity and fractal geometry of nuclear medicine images.
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Affiliation(s)
- Fabio Grizzi
- Department of Immunology and Inflammation, Humanitas Clinical and Research Hospital, Via Manzoni 56 - Rozzano, 20089, Milan, Italy.,Humanitas University, Via Rita Levi Montalcini, Pieve Emanuele, 20090, Milan, Italy
| | - Angelo Castello
- Department of Nuclear Medicine, Humanitas Clinical and Research Hospital, Via Manzoni 56 - Rozzano, 20089, Milan, Italy
| | - Dorina Qehajaj
- Department of Immunology and Inflammation, Humanitas Clinical and Research Hospital, Via Manzoni 56 - Rozzano, 20089, Milan, Italy
| | - Carlo Russo
- "Michele Rodriguez" Foundation, Via Ludovico di Breme, 79, 20156, Milan, Italy
| | - Egesta Lopci
- Department of Nuclear Medicine, Humanitas Clinical and Research Hospital, Via Manzoni 56 - Rozzano, 20089, Milan, Italy.
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32
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Cresswell KG, Dozmorov MG. TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains. Front Genet 2020; 11:158. [PMID: 32211023 PMCID: PMC7076128 DOI: 10.3389/fgene.2020.00158] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 02/11/2020] [Indexed: 12/02/2022] Open
Abstract
Recent research using chromatin conformation capture technologies, such as Hi-C, has demonstrated the importance of topologically associated domains (TADs) and smaller chromatin loops, collectively referred hereafter as "interacting domains." Many such domains change during development or disease, and exhibit cell- and condition-specific differences. Quantification of the dynamic behavior of interacting domains will help to better understand genome regulation. Methods for comparing interacting domains between cells and conditions are highly limited. We developed TADCompare, a method for differential analysis of boundaries of interacting domains between two or more Hi-C datasets. TADCompare is based on a spectral clustering-derived measure called the eigenvector gap, which enables a loci-by-loci comparison of boundary differences. Using this measure, we introduce methods for identifying differential and consensus boundaries of interacting domains and tracking boundary changes over time. We further propose a novel framework for the systematic classification of boundary changes. Colocalization- and gene enrichment analysis of different types of boundary changes demonstrated distinct biological functionality associated with them. TADCompare is available on https://github.com/dozmorovlab/TADCompare and Bioconductor (submitted).
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33
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Oneto M, Scipioni L, Sarmento MJ, Cainero I, Pelicci S, Furia L, Pelicci PG, Dellino GI, Bianchini P, Faretta M, Gratton E, Diaspro A, Lanzanò L. Nanoscale Distribution of Nuclear Sites by Super-Resolved Image Cross-Correlation Spectroscopy. Biophys J 2019; 117:2054-2065. [PMID: 31732142 PMCID: PMC6895719 DOI: 10.1016/j.bpj.2019.10.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/21/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
Deciphering the spatiotemporal coordination between nuclear functions is important to understand its role in the maintenance of human genome. In this context, super-resolution microscopy has gained considerable interest because it can be used to probe the spatial organization of functional sites in intact single-cell nuclei in the 20-250 nm range. Among the methods that quantify colocalization from multicolor images, image cross-correlation spectroscopy (ICCS) offers several advantages, namely it does not require a presegmentation of the image into objects and can be used to detect dynamic interactions. However, the combination of ICCS with super-resolution microscopy has not been explored yet. Here, we combine dual-color stimulated emission depletion (STED) nanoscopy with ICCS (STED-ICCS) to quantify the nanoscale distribution of functional nuclear sites. We show that super-resolved ICCS provides not only a value of the colocalized fraction but also the characteristic distances associated to correlated nuclear sites. As a validation, we quantify the nanoscale spatial distribution of three different pairs of functional nuclear sites in MCF10A cells. As expected, transcription foci and a transcriptionally repressive histone marker (H3K9me3) are not correlated. Conversely, nascent DNA replication foci and the proliferating cell nuclear antigen(PCNA) protein have a high level of proximity and are correlated at a nanometer distance scale that is close to the limit of our experimental approach. Finally, transcription foci are found at a distance of 130 nm from replication foci, indicating a spatial segregation at the nanoscale. Overall, our data demonstrate that STED-ICCS can be a powerful tool for the analysis of the nanoscale distribution of functional sites in the nucleus.
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Affiliation(s)
- Michele Oneto
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Lorenzo Scipioni
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Maria J Sarmento
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Isotta Cainero
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy
| | - Simone Pelicci
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy
| | - Laura Furia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Pier G Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Gaetano I Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy.
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34
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Pelicci S, Diaspro A, Lanzanò L. Chromatin nanoscale compaction in live cells visualized by acceptor-to-donor ratio corrected Förster resonance energy transfer between DNA dyes. JOURNAL OF BIOPHOTONICS 2019; 12:e201900164. [PMID: 31365191 PMCID: PMC7065635 DOI: 10.1002/jbio.201900164] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/14/2019] [Accepted: 07/29/2019] [Indexed: 05/04/2023]
Abstract
@Chromatin nanoscale architecture in live cells can be studied by Förster resonance energy transfer (FRET) between fluorescently labeled chromatin components, such as histones. A higher degree of nanoscale compaction is detected as a higher FRET level, since this corresponds to a higher degree of proximity between donor and acceptor molecules. However, in such a system, the stoichiometry of the donors and acceptors engaged in the FRET process is not well defined and, in principle, FRET variations could be caused by variations in the acceptor-to-donor ratio rather than distance. Here, to get a FRET level independent of the acceptor-to-donor ratio, we combine fluorescence lifetime imaging detection of FRET with a normalization of the FRET level to a pixel-wise estimation of the acceptor-to-donor ratio. We use this method to study FRET between two DNA binding dyes staining the nuclei of live cells. We show that this acceptor-to-donor ratio corrected FRET imaging reveals variations of nanoscale compaction in different chromatin environments. As an application, we monitor the rearrangement of chromatin in response to laser-induced microirradiation and reveal that DNA is rapidly decompacted, at the nanoscale, in response to DNA damage induction.
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Affiliation(s)
- Simone Pelicci
- Nanoscopy and Nikon Imaging Center, Istituto Italiano di TecnologiaGenoaItaly
- Department of PhysicsUniversity of GenoaGenoaItaly
| | - Alberto Diaspro
- Nanoscopy and Nikon Imaging Center, Istituto Italiano di TecnologiaGenoaItaly
- Department of PhysicsUniversity of GenoaGenoaItaly
| | - Luca Lanzanò
- Nanoscopy and Nikon Imaging Center, Istituto Italiano di TecnologiaGenoaItaly
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Structural and Dynamical Signatures of Local DNA Damage in Live Cells. Biophys J 2019; 118:2168-2180. [PMID: 31818467 DOI: 10.1016/j.bpj.2019.10.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/12/2019] [Accepted: 10/15/2019] [Indexed: 02/06/2023] Open
Abstract
The dynamic organization of chromatin inside the cell nucleus plays a key role in gene regulation and genome replication, as well as maintaining genome integrity. Although the static folded state of the genome has been extensively studied, dynamical signatures of processes such as transcription or DNA repair remain an open question. Here, we investigate the interphase chromatin dynamics in human cells in response to local DNA damage, specifically, DNA double-strand breaks (DSBs). Using simultaneous two-color spinning-disk confocal microscopy, we monitor the DSB dynamics and the compaction of the surrounding chromatin, visualized by fluorescently labeled 53BP1 and histone H2B, respectively. Our study reveals a surprising difference between the mobility of DSBs located in the nuclear interior versus periphery (less than 1 μm from the nuclear envelope), with the interior DSBs being almost twice as mobile as the periphery DSBs. Remarkably, we find that the DSB sites possess a robust structural signature in a form of a unique chromatin compaction profile. Moreover, our data show that the DSB motion is subdiffusive and ATP-dependent and exhibits unique dynamical signatures, different from those of undamaged chromatin. Our findings reveal that the DSB mobility follows a universal relationship defined solely by the physical parameters describing the DSBs and their local environment, such as the DSB focus size (represented by the local accumulation of 53BP1), DSB density, and the local chromatin compaction. This suggests that the DSB-related repair processes are robust and likely deterministic because the observed dynamical signatures (DSB mobility) can be explained solely by their structural features (DSB focus size, local chromatin compaction). Such knowledge might help in detecting local DNA damage in live cells, as well as in aiding our biophysical understanding of genome integrity in health and disease.
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Sauerwald N, Singhal A, Kingsford C. Analysis of the structural variability of topologically associated domains as revealed by Hi-C. NAR Genom Bioinform 2019; 2. [PMID: 31687663 PMCID: PMC6824515 DOI: 10.1093/nargab/lqz008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze 137 Hi-C samples from 9 studies under 3 measures to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and provide initial evidence that this variability does not come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of key factors influencing comparisons of chromosome structure, suggesting significant variability and the potential for cell-type-specific structural features, which has previously not been systematically explored. The lack of observed influence of heredity and genetic differences on chromosome structure suggests that factors other than the genetic sequence are driving this structure, which plays an important role in human disease and cellular functioning.
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Affiliation(s)
- Natalie Sauerwald
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Akshat Singhal
- Department of Computer Science, Stony Brook University, Stony Brook, NY 11790, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Sauerwald N, Kingsford C. Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinformatics 2019; 34:i475-i483. [PMID: 29949963 PMCID: PMC6022623 DOI: 10.1093/bioinformatics/bty265] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Motivation Three-dimensional chromosome structure has been increasingly shown to influence various levels of cellular and genomic functions. Through Hi-C data, which maps contact frequency on chromosomes, it has been found that structural elements termed topologically associating domains (TADs) are involved in many regulatory mechanisms. However, we have little understanding of the level of similarity or variability of chromosome structure across cell types and disease states. In this study, we present a method to quantify resemblance and identify structurally similar regions between any two sets of TADs. Results We present an analysis of 23 human Hi-C samples representing various tissue types in normal and cancer cell lines. We quantify global and chromosome-level structural similarity, and compare the relative similarity between cancer and non-cancer cells. We find that cancer cells show higher structural variability around commonly mutated pan-cancer genes than normal cells at these same locations. Availability and implementation Software for the methods and analysis can be found at https://github.com/Kingsford-Group/localtadsim
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Affiliation(s)
- Natalie Sauerwald
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- To whom correspondence should be addressed.
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Chromatin fiber structural motifs as regulatory hubs of genome function? Essays Biochem 2019; 63:123-132. [PMID: 30967476 PMCID: PMC6484786 DOI: 10.1042/ebc20180065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 02/07/2023]
Abstract
Nucleosomes cover eukaryotic genomes like beads on a string and play a central role in regulating genome function. Isolated strings of nucleosomes have the potential to compact and form higher order chromatin structures, such as the well-characterized 30-nm fiber. However, despite tremendous advances in observing chromatin fibers in situ it has not been possible to confirm that regularly ordered fibers represent a prevalent structural level in the folding of chromosomes. Instead, it appears that folding at a larger scale than the nucleosome involves a variety of random structures with fractal characteristics. Nevertheless, recent progress provides evidence for the existence of structural motifs in chromatin fibers, potentially localized to strategic sites in the genome. Here we review the current understanding of chromatin fiber folding and the emerging roles that oligonucleosomal motifs play in the regulation of genome function.
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Pignolo RJ, Samsonraj RM, Law SF, Wang H, Chandra A. Targeting Cell Senescence for the Treatment of Age-Related Bone Loss. Curr Osteoporos Rep 2019; 17:70-85. [PMID: 30806947 DOI: 10.1007/s11914-019-00504-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We review cell senescence in the context of age-related bone loss by broadly discussing aging mechanisms in bone, currently known inducers and markers of senescence, the senescence-associated secretory phenotype (SASP), and the emerging roles of senescence in bone homeostasis and pathology. RECENT FINDINGS Cellular senescence is a state of irreversible cell cycle arrest induced by insults or stressors including telomere attrition, oxidative stress, DNA damage, oncogene activation, and other intrinsic or extrinsic triggers and there is mounting evidence for the role of senescence in aging bone. Cellular aging also instigates a SASP that exerts detrimental paracrine and likely systemic effects. With aging, multiple cell types in the bone microenvironment become senescent, with osteocytes and myeloid cells as primary contributors to the SASP. Targeting undesired senescent cells may be a favorable strategy to promote bone anabolic and anti-resorptive functions in aging bone, with the possibility of improving bone quality and function with normal aging and/or disease.
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Affiliation(s)
- Robert J Pignolo
- Department of Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.
- Division of Geriatric Medicine & Gerontology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA.
| | | | - Susan F Law
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Haitao Wang
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Division of Geriatric Medicine & Gerontology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Abhishek Chandra
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Division of Geriatric Medicine & Gerontology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
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Sandoz J, Nagy Z, Catez P, Caliskan G, Geny S, Renaud JB, Concordet JP, Poterszman A, Tora L, Egly JM, Le May N, Coin F. Functional interplay between TFIIH and KAT2A regulates higher-order chromatin structure and class II gene expression. Nat Commun 2019; 10:1288. [PMID: 30894545 PMCID: PMC6426930 DOI: 10.1038/s41467-019-09270-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
The TFIIH subunit XPB is involved in combined Xeroderma Pigmentosum and Cockayne syndrome (XP-B/CS). Our analyses reveal that XPB interacts functionally with KAT2A, a histone acetyltransferase (HAT) that belongs to the hSAGA and hATAC complexes. XPB interacts with KAT2A-containing complexes on chromatin and an XP-B/CS mutation specifically elicits KAT2A-mediated large-scale chromatin decondensation. In XP-B/CS cells, the abnormal recruitment of TFIIH and KAT2A to chromatin causes inappropriate acetylation of histone H3K9, leading to aberrant formation of transcription initiation complexes on the promoters of several hundred genes and their subsequent overexpression. Significantly, this cascade of events is similarly sensitive to KAT2A HAT inhibition or to the rescue with wild-type XPB. In agreement, the XP-B/CS mutation increases KAT2A HAT activity in vitro. Our results unveil a tight connection between TFIIH and KAT2A that controls higher-order chromatin structure and gene expression and provide new insights into transcriptional misregulation in a cancer-prone DNA repair-deficient disorder.
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Affiliation(s)
- Jérémy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Zita Nagy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Philippe Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Gizem Caliskan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Sylvain Geny
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Jean-Baptiste Renaud
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Nicolas Le May
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France.
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
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Zada D, Bronshtein I, Lerer-Goldshtein T, Garini Y, Appelbaum L. Sleep increases chromosome dynamics to enable reduction of accumulating DNA damage in single neurons. Nat Commun 2019; 10:895. [PMID: 30837464 PMCID: PMC6401120 DOI: 10.1038/s41467-019-08806-w] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/30/2019] [Indexed: 11/09/2022] Open
Abstract
Sleep is essential to all animals with a nervous system. Nevertheless, the core cellular function of sleep is unknown, and there is no conserved molecular marker to define sleep across phylogeny. Time-lapse imaging of chromosomal markers in single cells of live zebrafish revealed that sleep increases chromosome dynamics in individual neurons but not in two other cell types. Manipulation of sleep, chromosome dynamics, neuronal activity, and DNA double-strand breaks (DSBs) showed that chromosome dynamics are low and the number of DSBs accumulates during wakefulness. In turn, sleep increases chromosome dynamics, which are necessary to reduce the amount of DSBs. These results establish chromosome dynamics as a potential marker to define single sleeping cells, and propose that the restorative function of sleep is nuclear maintenance.
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Affiliation(s)
- D Zada
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - I Bronshtein
- Department of Physics and the Institute for Nanotechnology, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - T Lerer-Goldshtein
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Y Garini
- Department of Physics and the Institute for Nanotechnology, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - L Appelbaum
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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Nucleolar Expression and Chromosomal Associations in Robertsonian Spermatocytes of Mus musculus domesticus. Genes (Basel) 2019; 10:genes10020120. [PMID: 30736350 PMCID: PMC6410149 DOI: 10.3390/genes10020120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 02/08/2023] Open
Abstract
We studied and compared the nucleolar expression or nucleoli from specific bivalents in spermatocytes of the standard Mus musculus domesticus 2n=40, of Robertsonian (Rb) homozygotes 2n = 24 and heterozygotes 2n = 32. We analyzed 200 nuclear microspreads of each specific nucleolar chromosome and spermatocyte karyotype, using FISH to identify specific nucleolar bivalents, immunofluorescence for both fibrillarin of the nucleolus and the synaptonemal complex of the bivalents, and DAPI for heterochromatin. There was nucleolar expression in all the chromosomal conditions studied. By specific nucleolar bivalent, the quantitative relative nucleolar expression was higher in the bivalent 12 than in its derivatives, lower in the bivalent 15 than in its derivatives and higher in the bivalent 16 than its Rb derivatives. In the interactions between non-homologous chromosomal domains, the nucleolar bivalents were preferentially associated through pericentromeric heterochromatin with other bivalents of similar morphology and sometimes with other nucleolar bivalents. We suggest that the nucleolar expression in Rb nucleolar chromosomes is modified as a consequence of different localization of ribosomal genes (NOR) in the Rb chromosomes, its proximity to heterochromatin and its associations with chromosomes of the same morphology.
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Yang S, Lee JY, Hur H, Oh JH, Kim MH. Up-regulation of HOXB cluster genes are epigenetically regulated in tamoxifen-resistant MCF7 breast cancer cells. BMB Rep 2018; 51:450-455. [PMID: 29804556 PMCID: PMC6177504 DOI: 10.5483/bmbrep.2018.51.9.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Indexed: 12/17/2022] Open
Abstract
Tamoxifen (TAM) is commonly used to treat estrogen receptor (ER)-positive breast cancer. Despite the remarkable benefits, resistance to TAM presents a serious therapeutic challenge. Since several HOX transcription factors have been proposed as strong candidates in the development of resistance to TAM therapy in breast cancer, we generated an in vitro model of acquired TAM resistance using ER-positive MCF7 breast cancer cells (MCF7-TAMR), and analyzed the expression pattern and epigenetic states of HOX genes. HOXB cluster genes were uniquely up-regulated in MCF7-TAMR cells. Survival analysis of in slico data showed the correlation of high expression of HOXB genes with poor response to TAM in ER-positive breast cancer patients treated with TAM. Gain- and loss-of-function experiments showed that the overexpression of multi HOXB genes in MCF7 renders cancer cells more resistant to TAM, whereas the knockdown restores TAM sensitivity. Furthermore, activation of HOXB genes in MCF7-TAMR was associated with histone modifications, particularly the gain of H3K9ac. These findings imply that the activation of HOXB genes mediate the development of TAM resistance, and represent a target for development of new strategies to prevent or reverse TAM resistance.
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Affiliation(s)
- Seoyeon Yang
- Department of Anatomy, Embryology Laboratory, and 2Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Laboratory, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ho Hur
- Department of Surgery, National Health Insurance Service Ilsan Hospital, Goyang 10444, Korea
| | - Ji Hoon Oh
- Department of Anatomy, Embryology Laboratory, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Laboratory, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
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Szalaj P, Plewczynski D. Three-dimensional organization and dynamics of the genome. Cell Biol Toxicol 2018; 34:381-404. [PMID: 29568981 PMCID: PMC6133016 DOI: 10.1007/s10565-018-9428-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/11/2018] [Indexed: 12/30/2022]
Abstract
Genome is a complex hierarchical structure, and its spatial organization plays an important role in its function. Chromatin loops and topological domains form the basic structural units of this multiscale organization and are essential to orchestrate complex regulatory networks and transcription mechanisms. They also form higher-order structures such as chromosomal compartments and chromosome territories. Each level of this intrinsic architecture is governed by principles and mechanisms that we only start to understand. In this review, we summarize the current view of the genome architecture on the scales ranging from chromatin loops to the whole genome. We describe cell-to-cell variability, links between genome reorganization and various genomic processes, such as chromosome X inactivation and cell differentiation, and the interplay between different experimental techniques.
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Affiliation(s)
- Przemyslaw Szalaj
- Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland.
- I-BioStat, Hasselt University, Hasselt, Belgium.
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.
| | - Dariusz Plewczynski
- Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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Abdollahi E, Taucher-Scholz G, Jakob B. Application of fluorescence lifetime imaging microscopy of DNA binding dyes to assess radiation-induced chromatin compaction changes. Int J Mol Sci 2018; 19:E2399. [PMID: 30110966 PMCID: PMC6121443 DOI: 10.3390/ijms19082399] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/02/2018] [Accepted: 08/10/2018] [Indexed: 01/19/2023] Open
Abstract
In recent years several approaches have been developed to address the chromatin status and its changes in eukaryotic cells under different conditions-but only few are applicable in living cells. Fluorescence lifetime imaging microscopy (FLIM) is a functional tool that can be used for the inspection of the molecular environment of fluorophores in living cells. Here, we present the use of single organic minor groove DNA binder dyes in FLIM for measuring chromatin changes following modulation of chromatin structure in living cells. Treatment with histone deacetylase inhibitors led to an increased fluorescence lifetime indicating global chromatin decompaction, whereas hyperosmolarity decreased the lifetime of the used dyes, thus reflecting the expected compaction. In addition, we demonstrate that time domain FLIM data based on single photon counting should be optimized using pile-up and counting loss correction, which affect the readout even at moderate average detector count rates in inhomogeneous samples. Using these corrections and utilizing Hoechst 34580 as chromatin compaction probe, we measured a pan nuclear increase in the lifetime following irradiation with X-rays in living NIH/3T3 cells thus providing a method to measure radiation-induced chromatin decompaction.
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Affiliation(s)
- Elham Abdollahi
- Department of Biophysics, GSI Helmholzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany.
| | - Gisela Taucher-Scholz
- Department of Biophysics, GSI Helmholzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany.
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany.
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Bridger JM, Brindley PJ, Knight M. The snail Biomphalaria glabrata as a model to interrogate the molecular basis of complex human diseases. PLoS Negl Trop Dis 2018; 12:e0006552. [PMID: 30091971 PMCID: PMC6084811 DOI: 10.1371/journal.pntd.0006552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Joanna M. Bridger
- Institute of Environment, Health, and Societies, Brunel University London, Uxbridge, United Kingdom
| | - Paul J. Brindley
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
| | - Matty Knight
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Division of Science and Mathematics, University of the District of Columbia, Washington DC, United States of America
- * E-mail: ,
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Shelkovnikova TA, Kukharsky MS, An H, Dimasi P, Alexeeva S, Shabir O, Heath PR, Buchman VL. Protective paraspeckle hyper-assembly downstream of TDP-43 loss of function in amyotrophic lateral sclerosis. Mol Neurodegener 2018; 13:30. [PMID: 29859124 PMCID: PMC5984788 DOI: 10.1186/s13024-018-0263-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/25/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Paraspeckles are subnuclear bodies assembled on a long non-coding RNA (lncRNA) NEAT1. Their enhanced formation in spinal neurons of sporadic amyotrophic lateral sclerosis (ALS) patients has been reported but underlying mechanisms are unknown. The majority of ALS cases are characterized by TDP-43 proteinopathy. In current study we aimed to establish whether and how TDP-43 pathology may augment paraspeckle assembly. METHODS Paraspeckle formation in human samples was analysed by RNA-FISH and laser capture microdissection followed by qRT-PCR. Mechanistic studies were performed in stable cell lines, mouse primary neurons and human embryonic stem cell-derived neurons. Loss and gain of function for TDP-43 and other microRNA pathway factors were modelled by siRNA-mediated knockdown and protein overexpression. RESULTS We show that de novo paraspeckle assembly in spinal neurons and glial cells is a hallmark of both sporadic and familial ALS with TDP-43 pathology. Mechanistically, loss of TDP-43 but not its cytoplasmic accumulation or aggregation augments paraspeckle assembly in cultured cells. TDP-43 is a component of the microRNA machinery, and recently, paraspeckles have been shown to regulate pri-miRNA processing. Consistently, downregulation of core protein components of the miRNA pathway also promotes paraspeckle assembly. In addition, depletion of these proteins or TDP-43 results in accumulation of endogenous dsRNA and activation of type I interferon response which also stimulates paraspeckle formation. We demonstrate that human or mouse neurons in vitro lack paraspeckles, but a synthetic dsRNA is able to trigger their de novo formation. Finally, paraspeckles are protective in cells with compromised microRNA/dsRNA metabolism, and their assembly can be promoted by a small-molecule microRNA enhancer. CONCLUSIONS Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.
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Affiliation(s)
| | - Michail S Kukharsky
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
| | - Haiyan An
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Pasquale Dimasi
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Svetlana Alexeeva
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Osman Shabir
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Paul R Heath
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Vladimir L Buchman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
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Chang P, Gohain M, Yen MR, Chen PY. Computational Methods for Assessing Chromatin Hierarchy. Comput Struct Biotechnol J 2018; 16:43-53. [PMID: 29686798 PMCID: PMC5910504 DOI: 10.1016/j.csbj.2018.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/29/2018] [Accepted: 02/11/2018] [Indexed: 12/27/2022] Open
Abstract
The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects. Experimental requirements and considerations specific for each method were highlighted. For computational analysis, we summarized a common analysis strategy for both levels of chromatin assessment, focusing on the characteristic computing steps and the tools. The recently developed single-cell level techniques based on Hi-C and ATAC-seq present great potential to reveal cell-to-cell variability in chromosome architecture. A brief discussion on these methods in terms of experimental and data analysis features is included. We also touch upon the biological relevance of chromatin organization and how the combination with other techniques uncovers the underlying mechanisms. We conclude with a summary and our prospects on necessary improvements of currently available methods in order to advance understanding of chromatin hierarchy. Our review brings together the analyses of both higher- and primary-order chromatin structures, and serves as a roadmap when choosing appropriate experimental and computational methods for assessing chromatin hierarchy.
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Affiliation(s)
- Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Moloya Gohain
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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50
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Yang T, Zhang F, Yardımcı GG, Song F, Hardison RC, Noble WS, Yue F, Li Q. HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Genome Res 2017; 27:1939-1949. [PMID: 28855260 PMCID: PMC5668950 DOI: 10.1101/gr.220640.117] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 08/07/2017] [Indexed: 01/07/2023]
Abstract
Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach.
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Affiliation(s)
- Tao Yang
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Feipeng Zhang
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Galip Gürkan Yardımcı
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Fan Song
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ross C Hardison
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA.,Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98105, USA
| | - Feng Yue
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Qunhua Li
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Statistics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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