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Sprunger ML, Jackrel ME. The role of Matrin-3 in physiology and its dysregulation in disease. Biochem Soc Trans 2024; 52:961-972. [PMID: 38813817 DOI: 10.1042/bst20220585] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
The dysfunction of many RNA-binding proteins (RBPs) that are heavily disordered, including TDP-43 and FUS, are implicated in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). These proteins serve many important roles in the cell, and their capacity to form biomolecular condensates (BMCs) is key to their function, but also a vulnerability that can lead to misregulation and disease. Matrin-3 (MATR3) is an intrinsically disordered RBP implicated both genetically and pathologically in ALS/FTD, though it is relatively understudied as compared with TDP-43 and FUS. In addition to binding RNA, MATR3 also binds DNA and is implicated in many cellular processes including the DNA damage response, transcription, splicing, and cell differentiation. It is unclear if MATR3 localizes to BMCs under physiological conditions, which is brought further into question due to its lack of a prion-like domain. Here, we review recent studies regarding MATR3 and its roles in numerous physiological processes, as well as its implication in a range of diseases.
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Affiliation(s)
- Macy L Sprunger
- Department of Chemistry, Washington University, St. Louis, MO 63130, U.S.A
| | - Meredith E Jackrel
- Department of Chemistry, Washington University, St. Louis, MO 63130, U.S.A
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2
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Santos JR, Park J. MATR3's Role beyond the Nuclear Matrix: From Gene Regulation to Its Implications in Amyotrophic Lateral Sclerosis and Other Diseases. Cells 2024; 13:980. [PMID: 38891112 PMCID: PMC11171696 DOI: 10.3390/cells13110980] [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: 05/13/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024] Open
Abstract
Matrin-3 (MATR3) was initially discovered as a component of the nuclear matrix about thirty years ago. Since then, accumulating studies have provided evidence that MATR3 not only plays a structural role in the nucleus, but that it is also an active protein involved in regulating gene expression at multiple levels, including chromatin organization, DNA transcription, RNA metabolism, and protein translation in the nucleus and cytoplasm. Furthermore, MATR3 may play a critical role in various cellular processes, including DNA damage response, cell proliferation, differentiation, and survival. In addition to the revelation of its biological role, recent studies have reported MATR3's involvement in the context of various diseases, including neurodegenerative and neurodevelopmental diseases, as well as cancer. Moreover, sequencing studies of patients revealed a handful of disease-associated mutations in MATR3 linked to amyotrophic lateral sclerosis (ALS), which further elevated the gene's importance as a topic of study. In this review, we synthesize the current knowledge regarding the diverse functions of MATR3 in DNA- and RNA-related processes, as well as its involvement in various diseases, with a particular emphasis on ALS.
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Affiliation(s)
- Jhune Rizsan Santos
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Genetics and Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeehye Park
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Genetics and Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
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3
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He H, Jamal M, Zeng X, Lei Y, Xiao D, Wei Z, Zhang C, Zhang X, Pan S, Ding Q, Tan H, Xie S, Zhang Q. Matrin-3 acts as a potential biomarker and promotes hepatocellular carcinoma progression by interacting with cell cycle-regulating genes. Cell Cycle 2024; 23:15-35. [PMID: 38252499 PMCID: PMC11005806 DOI: 10.1080/15384101.2024.2305535] [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: 01/15/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. The oncogenic role of Matrin-3 (MATR3), an a nuclear matrix protein, in HCC remains largely unknown. Here, we document the biological function of MATR3 in HCC based on integrated bioinformatics analysis and functional studies. According to the TCGA database, MATR3 expression was found to be positively correlated with clinicopathological characteristics in HCC. The receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) curve displayed the diagnostic and prognostic potentials of MATR3 in HCC patients, respectively. Pathway enrichment analysis represented the enrichment of MATR3 in various molecular pathways, including the regulation of the cell cycle. Functional assays in HCC cell lines showed reduced proliferation of cells with stable silencing of MATR3. At the same time, the suppressive effects of MATR3 depletion on HCC development were verified by xenograft tumor experiments. Moreover, MATR3 repression also resulted in cell cycle arrest by modulating the expression of cell cycle-associated genes. In addition, the interaction of MATR3 with cell cycle-regulating factors in HCC cells was further corroborated with co-immunoprecipitation and mass spectrometry (Co-IP/MS). Furthermore, CIBERSORT and TIMER analyses showed an association between MATR3 and immune infiltration in HCC. In general, this study highlights the novel oncogenic function of MATR3 in HCC, which could comprehensively address how aberrant changes in the cell cycle promote HCC development. MATR3 might serve as a prognostic predictor and therapeutic target for HCC patients.
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Affiliation(s)
- Hengjing He
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Muhammad Jamal
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xingruo Zeng
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yufei Lei
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Di Xiao
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zimeng Wei
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Chengjie Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Shan Pan
- School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Qianshan Ding
- School of Medicine, Northwest University, Xian, China
| | - Haiyan Tan
- Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Songping Xie
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qiuping Zhang
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan, China
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4
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Bollwein H, Malama E. Review: Evaluation of bull fertility. Functional and molecular approaches. Animal 2023; 17 Suppl 1:100795. [PMID: 37567681 DOI: 10.1016/j.animal.2023.100795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 08/13/2023] Open
Abstract
With the term "assisted reproduction technologies" in modern cattle farming, one could imply the collection of techniques that aim at the optimal use of bovine gametes to produce animals of high genetic value in a time- and cost-efficient manner. The accurate characterisation of sperm quality plays a critical role for the efficiency of several assisted reproduction-related procedures, such as sperm processing, in vitro embryo production and artificial insemination. Bull fertility is ultimately a collective projection of the ability of a series of ejaculates to endure sperm processing stress, and achieve fertilisation of the oocyte and production of a viable and well-developing embryo. In this concept, the assessment of sperm functional and molecular characteristics is key to bull fertility diagnostics and prognostics. Among others, functional features linked to sperm plasma membrane, acrosome and DNA integrity are usually assessed as a measure of the ability of sperm to express the phenotypes that will allow them to maintain their homeostasis and orchestrate-in a strict temporal manner-the course of events that will enable the delivery of their genetic content to the oocyte upon fertilisation. Nevertheless, measures of sperm functionality are not always adequate indicators of bull fertility. Nowadays, advancements in the field of molecular biology have facilitated the profiling of several biomolecules in male gametes. The molecular profiling of bovine sperm offers a deeper insight into the mechanisms underlying sperm physiology and, thus, can reveal novel candidate markers for bull fertility prognosis. In this review, the importance of three organelles (the nucleus, the plasma membrane and the acrosome) for the characterisation of sperm fertilising capacity and bull fertility is discussed at functional and molecular levels. In particular, information about sperm head morphometry, chromatin structure, viability as well as the ability of sperm to capacitate and undergo the acrosome reaction are presented in relation to the cryotolerance of male gametes and bull fertility. Finally, major spermatozoal coding and non-coding RNAs, and proteins that are involved in the above-mentioned aspects of sperm functionality are also summarised.
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Affiliation(s)
- H Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland.
| | - E Malama
- Clinic of Reproductive Medicine, Department for Farm Animals, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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de Lima MF, Lisboa MDO, Terceiro LEL, Rangel-Pozzo A, Mai S. Chromosome Territories in Hematological Malignancies. Cells 2022; 11:cells11081368. [PMID: 35456046 PMCID: PMC9028803 DOI: 10.3390/cells11081368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Chromosomes are organized in distinct nuclear areas designated as chromosome territories (CT). The structural formation of CT is a consequence of chromatin packaging and organization that ultimately affects cell function. Chromosome positioning can identify structural signatures of genomic organization, especially for diseases where changes in gene expression contribute to a given phenotype. The study of CT in hematological diseases revealed chromosome position as an important factor for specific chromosome translocations. In this review, we highlight the history of CT theory, current knowledge on possible clinical applications of CT analysis, and the impact of CT in the development of hematological neoplasia such as multiple myeloma, leukemia, and lymphomas. Accumulating data on nuclear architecture in cancer allow one to propose the three-dimensional nuclear genomic landscape as a novel cancer biomarker for the future.
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Affiliation(s)
- Matheus Fabiao de Lima
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Brazil;
| | - Lucas E. L. Terceiro
- Department of Pathology, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
| | - Sabine Mai
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
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Salem A, Wilson CJ, Rutledge BS, Dilliott A, Farhan S, Choy WY, Duennwald ML. Matrin3: Disorder and ALS Pathogenesis. Front Mol Biosci 2022; 8:794646. [PMID: 35083279 PMCID: PMC8784776 DOI: 10.3389/fmolb.2021.794646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons in the brain and spinal cord. ALS is associated with protein misfolding and inclusion formation involving RNA-binding proteins, including TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS). The 125-kDa Matrin3 is a highly conserved nuclear DNA/RNA-binding protein that is implicated in many cellular processes, including binding and stabilizing mRNA, regulating mRNA nuclear export, modulating alternative splicing, and managing chromosomal distribution. Mutations in MATR3, the gene encoding Matrin3, have been identified as causal in familial ALS (fALS). Matrin3 lacks a prion-like domain that characterizes many other ALS-associated RNA-binding proteins, including TDP-43 and FUS, however, our bioinformatics analyses and preliminary studies document that Matrin3 contains long intrinsically disordered regions that may facilitate promiscuous interactions with many proteins and may contribute to its misfolding. In addition, these disordered regions in Matrin3 undergo numerous post-translational modifications, including phosphorylation, ubiquitination and acetylation that modulate the function and misfolding of the protein. Here we discuss the disordered nature of Matrin3 and review the factors that may promote its misfolding and aggregation, two elements that might explain its role in ALS pathogenesis.
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Affiliation(s)
- Ahmed Salem
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Carter J. Wilson
- Department of Applied Mathematics, Western University, London, ON, Canada
| | - Benjamin S. Rutledge
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Allison Dilliott
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
| | - Sali Farhan
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
- Department of Human Genetics, McGill Universty, Montreal, QC, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Martin L. Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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Cha HJ, Uyan Ö, Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan GC, Dekker J, Orkin SH. Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nat Commun 2021; 12:6241. [PMID: 34716321 PMCID: PMC8556400 DOI: 10.1038/s41467-021-26574-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Precise control of gene expression during differentiation relies on the interplay of chromatin and nuclear structure. Despite an established contribution of nuclear membrane proteins to developmental gene regulation, little is known regarding the role of inner nuclear proteins. Here we demonstrate that loss of the nuclear scaffolding protein Matrin-3 (Matr3) in erythroid cells leads to morphological and gene expression changes characteristic of accelerated maturation, as well as broad alterations in chromatin organization similar to those accompanying differentiation. Matr3 protein interacts with CTCF and the cohesin complex, and its loss perturbs their occupancy at a subset of sites. Destabilization of CTCF and cohesin binding correlates with altered transcription and accelerated differentiation. This association is conserved in embryonic stem cells. Our findings indicate Matr3 negatively affects cell fate transitions and demonstrate that a critical inner nuclear protein impacts occupancy of architectural factors, culminating in broad effects on chromatin organization and cell differentiation.
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Affiliation(s)
- Hye Ji Cha
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Özgün Uyan
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yan Kai
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Tianxin Liu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Qian Zhu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Giovanni A Botten
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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Abstract
RNA-binding proteins (RBPs) are essential factors required for the physiological function of neurons, muscle, and other tissue types. In keeping with this, a growing body of genetic, clinical, and pathological evidence indicates that RBP dysfunction and/or gene mutation leads to neurodegeneration and myopathy. Here, we summarize the current understanding of matrin 3 (MATR3), a poorly understood RBP implicated not only in ALS and frontotemporal dementia but also in distal myopathy. We begin by reviewing MATR3's functions, its regulation, and how it may be involved in both sporadic and familial neuromuscular disease. We also discuss insights gleaned from cellular and animal models of MATR3 pathogenesis, the links between MATR3 and other disease-associated RBPs, and the mechanisms underlying RBP-mediated disorders.
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Affiliation(s)
- Ahmed M. Malik
- Medical Scientist Training Program
- Neuroscience Graduate Program, and
| | - Sami J. Barmada
- Neuroscience Graduate Program, and
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
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Fritz AJ, Sehgal N, Pliss A, Xu J, Berezney R. Chromosome territories and the global regulation of the genome. Genes Chromosomes Cancer 2019; 58:407-426. [PMID: 30664301 DOI: 10.1002/gcc.22732] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/29/2022] Open
Abstract
Spatial positioning is a fundamental principle governing nuclear processes. Chromatin is organized as a hierarchy from nucleosomes to Mbp chromatin domains (CD) or topologically associating domains (TADs) to higher level compartments culminating in chromosome territories (CT). Microscopic and sequencing techniques have substantiated chromatin organization as a critical factor regulating gene expression. For example, enhancers loop back to interact with their target genes almost exclusively within TADs, distally located coregulated genes reposition into common transcription factories upon activation, and Mbp CDs exhibit dynamic motion and configurational changes in vivo. A longstanding question in the nucleus field is whether an interactive nuclear matrix provides a direct link between structure and function. The findings of nonrandom radial positioning of CT within the nucleus suggest the possibility of preferential interaction patterns among populations of CT. Sequential labeling up to 10 CT followed by application of computer imaging and geometric graph mining algorithms revealed cell-type specific interchromosomal networks (ICN) of CT that are altered during the cell cycle, differentiation, and cancer progression. It is proposed that the ICN correlate with the global level of genome regulation. These approaches also demonstrated that the large scale 3-D topology of CT is specific for each CT. The cell-type specific proximity of certain chromosomal regions in normal cells may explain the propensity of distinct translocations in cancer subtypes. Understanding how genes are dysregulated upon disruption of the normal "wiring" of the nucleus by translocations, deletions, and amplifications that are hallmarks of cancer, should enable more targeted therapeutic strategies.
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Affiliation(s)
- Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Nitasha Sehgal
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics and the Department of Chemistry, University at Buffalo, Buffalo, New York
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York
| | - Ronald Berezney
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
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Kiselev AM, Stepanova IS, Adonin LS, Batalova FM, Parfenov VN, Bogolyubov DS, Podgornaya OI. The exon junction complex factor Y14 is dynamic in the nucleus of the beetle Tribolium castaneum during late oogenesis. Mol Cytogenet 2017; 10:41. [PMID: 29151891 PMCID: PMC5679382 DOI: 10.1186/s13039-017-0342-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/27/2017] [Indexed: 12/02/2022] Open
Abstract
Background The oocyte chromosomes of the red flour beetle, Tribolium castaneum, are gathered into a knot, forming a karyosphere at the diplotene stage of meiotic prophase. Chromatin rearrangement, which is a characteristic feature of oocyte maturation, is well documented. The T. castaneum karyosphere is surrounded by a complex extrachromosomal structure termed the karyosphere capsule. The capsule contains the vast majority of oocyte RNA. We have previously shown using a BrUTP assay that oocyte chromosomes in T. castaneum maintain residual transcription up to the very end of oocyte maturation. Karyosphere transcription requires evidently not only transcription factors but also mRNA processing factors, including the components of the exon junction complex with its core component, the splicing factor Y14. We employed a gene engineering approach with injection of mRNA derived from the Myc-tagged Y14 plasmid-based construct in order to monitor the newly synthesized fusion protein in the oocyte nuclei. Results Our preliminary data have been presented as a brief correspondence elsewhere. Here, we provide a full-length article including immunoelectron-microscopy localization data on Y14–Myc distribution in the nucleus of previtellogenic and vitellogenic oocytes. The injections of the fusion protein Y14–Myc mRNA into the oocytes showed a dynamic pattern of the protein distribution. At the previtellogenic stage, there are two main locations for the protein: SC35 domains (the analogues of interchromatin granule clusters or nuclear speckles) and the karyosphere capsule. At the vitellogenic stage, SC35 domains were devoid of labels, and Y14–Myc was found in the perichromatin region of the karyosphere, presumably at the places of residual transcription. We show that karyosphere formation is accompanied by the movement of a nuclear protein while the residual transcription occurs during genome inactivation. Conclusions Our data indicate that the karyosphere capsule, being a destination site for a protein involved in mRNA splicing and export, is not only a specializes part of nuclear matrix separating the karyosphere from the products of chromosome activity, as believed previously, but represents a special nuclear compartment involved in the processes of gene expression in the case the karyosphere retains residual transcription activity. Electronic supplementary material The online version of this article (10.1186/s13039-017-0342-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Artem M Kiselev
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia.,Federal Almazov North-West Medical Research Centre, St. Petersburg, 197341 Russia.,ITMO University, Institute of Translational Medicine, St. Petersburg, 197101 Russia
| | - Irina S Stepanova
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Leonid S Adonin
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Florina M Batalova
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Vladimir N Parfenov
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Dmitry S Bogolyubov
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia
| | - Olga I Podgornaya
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064 Russia.,Department of Cytology and Histology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034 Russia.,Far Eastern Federal University, School of Biomedicine, Vladivostok, 690950 Russia
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11
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Pochukalina GN, Ilicheva NV, Podgornaya OI, Voronin AP. Nucleolus-like body of mouse oocytes contains lamin A and B and TRF2 but not actin and topo II. Mol Cytogenet 2016; 9:50. [PMID: 27347007 PMCID: PMC4921027 DOI: 10.1186/s13039-016-0259-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/18/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND During the final stages of oocyte development, all chromosomes join in a limited nuclear volume for the final formation of a single complex chromatin structure - the karyosphere. In the majority of mammalian species, the chromosomes surround a round protein/fibrillar body known as the central body, or nucleolus-like body (NLB). Nothing seems to unite the inner portion of the karyosphere with the nucleolus except position at its remnants. Nevertheless, in this study we will use term NLB as the conventional one for karyosphere with the central body. At the morphological level, NLBs consist of tightly-packed fibres of 6-10 nm. The biochemical structure of this dense, compact NLB fibre centre remains uncertain. RESULTS The aim of this study was to determine which proteins represent the NLB components at final stages of karyosphere formation in mouse oogenesis. To determine this, three antibodies (ABs) have been examined against different actin epitopes. Examination of both ABs against the actin N-end provided similar results: spots inside the nucleus. Double staining with AB against SC35 and actin revealed the colocalization of these proteins in IGCs (interchromatin granule clusters/nuclear speckles/SC35 domains). In contrast, examination of polyclonal AB against peptide at the C-end reveals a different result: actin is localized exclusively in connection with the chromatin. Surprisingly, no forms of actin or topoisomerase II are present as components of the NLB. It was discovered that: (1) lamin B is an NLB component from the beginning of NLB formation, and a major portion of it resides in the NLB at the end of oocyte development; (2) lamin A undergoes rapid movement into the NLB, and a majority of it remains in the NLB; (3) the telomere-binding protein TRF2 resides in the IGCs/nuclear speckles until the end of oocyte development, when significant part of it transfers to the NLB. CONCLUSIONS NLBs do not contain actin or topo II. Lamin B is involved from the beginning of NLB formation. Both Lamin A and TRF2 exhibit rapid movement to the NLB at the end of oogenesis. This dynamic distribution of proteins may reflect the NLB's role in future chromatin organization post-fertilisation.
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Affiliation(s)
| | - Nadya V. Ilicheva
- />Institute of Cytology, Russian Academy of Sciences, St Petersburg, 194064 Russia
| | - Olga I. Podgornaya
- />Institute of Cytology, Russian Academy of Sciences, St Petersburg, 194064 Russia
- />Saint Petersburg State University, St Petersburg, 199034 Russia
- />Far Eastern Federal University, Vladivostok, 690950 Russia
| | - Alexey P. Voronin
- />Institute of Cytology, Russian Academy of Sciences, St Petersburg, 194064 Russia
- />Saint Petersburg State University, St Petersburg, 199034 Russia
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12
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Coelho MB, Attig J, Ule J, Smith CWJ. Matrin3: connecting gene expression with the nuclear matrix. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:303-15. [PMID: 26813864 DOI: 10.1002/wrna.1336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 01/06/2023]
Abstract
As indicated by its name, Matrin3 was discovered as a component of the nuclear matrix, an insoluble fibrogranular network that structurally organizes the nucleus. Matrin3 possesses both DNA- and RNA-binding domains and, consistent with this, has been shown to function at a number of stages in the life cycle of messenger RNAs. These numerous activities indicate that Matrin3, and indeed the nuclear matrix, do not just provide a structural framework for nuclear activities but also play direct functional roles in these activities. Here, we review the structure, functions, and molecular interactions of Matrin3 and of Matrin3-related proteins, and the pathologies that can arise upon mutation of Matrin3. WIREs RNA 2016, 7:303-315. doi: 10.1002/wrna.1336 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Miguel B Coelho
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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13
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Affiliation(s)
- Huy Q. Nguyen
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755;
| | - Giovanni Bosco
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755;
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14
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Erazo A, Goff SP. Nuclear matrix protein Matrin 3 is a regulator of ZAP-mediated retroviral restriction. Retrovirology 2015; 12:57. [PMID: 26129669 PMCID: PMC4487854 DOI: 10.1186/s12977-015-0182-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 06/11/2015] [Indexed: 12/01/2022] Open
Abstract
Background Matrin 3 is a nuclear matrix protein involved in multiple nuclear processes. In HIV-1 infection, Matrin 3 serves as a Rev cofactor important for the cytoplasmic accumulation of HIV-1 transcripts. ZAP is a potent host restriction factor of multiple viruses including retroviruses HIV-1 and MoMuLV. In this study we sought to further characterize Matrin 3 functions in the regulation of HIV gene expression. Results Here we describe a function for Matrin 3 as a negative regulator of the ZAP-mediated restriction of retroviruses. Mass spectrometry analysis of Matrin 3-associated proteins uncovered interactions with proteins of the ZAP degradation complex, DDX17 and EXOSC3. Coimmunoprecipitation studies confirmed Matrin 3 associations with DDX17, EXOSC3 and ZAP, in a largely RNA-dependent manner, indicating that RNA is mediating the Matrin 3 interactions with these components of the ZAP degradation complex. Silencing Matrin 3 expression caused a remarkably enhanced ZAP-driven inhibition of HIV-1 and MoMuLV luciferase reporter viruses. This effect was shared with additional nuclear matrix proteins. ZAP targets multiply-spliced HIV-1 transcripts, but in the context of Matrin 3 suppression, this ZAP restriction was broadened to unspliced and multiply-spliced RNAs. Conclusions Here we reveal an unprecedented role for a nuclear matrix protein, Matrin 3, in the regulation of ZAP’s antiretroviral activity. Suppressing Matrin 3 powers a heightened and broader ZAP restriction of HIV-1 gene expression. This study suggests that this ZAP regulatory mechanism is shared with additional nuclear matrix proteins.
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Affiliation(s)
- Angela Erazo
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY, 10032, USA.
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY, 10032, USA. .,Department of Microbiology and Immunology, Columbia University, New York, NY, 10032, USA.
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15
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Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J, Smith CWJ. Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. EMBO J 2015; 34:653-68. [PMID: 25599992 PMCID: PMC4365034 DOI: 10.15252/embj.201489852] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA metabolism has yet been clearly demonstrated. We identified Matrin3 by its interaction with the second RRM domain of the splicing regulator PTB. Using a combination of RNAi knockdown, transcriptome profiling and iCLIP, we find that Matrin3 is a regulator of hundreds of alternative splicing events, principally acting as a splicing repressor with only a small proportion of targeted events being co-regulated by PTB. In contrast to other splicing regulators, Matrin3 binds to an extended region within repressed exons and flanking introns with no sharply defined peaks. The identification of this clear molecular function of Matrin3 should help to clarify the molecular pathology of ALS and other diseases caused by mutations of Matrin3.
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Affiliation(s)
- Miguel B Coelho
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Nicolás Bellora
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain INIBIOMA CONICET-UNComahue, Bariloche, Argentina
| | - Julian König
- MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Martina Hallegger
- Department of Biochemistry, University of Cambridge, Cambridge, UK Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Eduardo Eyras
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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16
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Qin XY, Fukuda T, Yang L, Zaha H, Akanuma H, Zeng Q, Yoshinaga J, Sone H. Effects of bisphenol A exposure on the proliferation and senescence of normal human mammary epithelial cells. Cancer Biol Ther 2014; 13:296-306. [DOI: 10.4161/cbt.18942] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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17
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Yasui DH, Gonzales ML, Aflatooni JO, Crary FK, Hu DJ, Gavino BJ, Golub MS, Vincent JB, Carolyn Schanen N, Olson CO, Rastegar M, Lasalle JM. Mice with an isoform-ablating Mecp2 exon 1 mutation recapitulate the neurologic deficits of Rett syndrome. Hum Mol Genet 2013; 23:2447-58. [PMID: 24352790 DOI: 10.1093/hmg/ddt640] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mutations in MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT OMIM 312750). Alternative inclusion of MECP2/Mecp2 exon 1 with exons 3 and 4 encodes MeCP2-e1 or MeCP2-e2 protein isoforms with unique amino termini. While most MECP2 mutations are located in exons 3 and 4 thus affecting both isoforms, MECP2 exon 1 mutations but not exon 2 mutations have been identified in RTT patients, suggesting that MeCP2-e1 deficiency is sufficient to cause RTT. As expected, genetic deletion of Mecp2 exons 3 and/or 4 recapitulates RTT-like neurologic defects in mice. However, Mecp2 exon 2 knockout mice have normal neurologic function. Here, a naturally occurring MECP2 exon 1 mutation is recapitulated in a mouse model by genetic engineering. A point mutation in the translational start codon of Mecp2 exon 1, transmitted through the germline, ablates MeCP2-e1 translation while preserving MeCP2-e2 production in mouse brain. The resulting MeCP2-e1 deficient mice developed forelimb stereotypy, hindlimb clasping, excessive grooming and hypo-activity prior to death between 7 and 31 weeks. MeCP2-e1 deficient mice also exhibited abnormal anxiety, sociability and ambulation. Despite MeCP2-e1 and MeCP2-e2 sharing, 96% amino acid identity, differences were identified. A fraction of phosphorylated MeCP2-e1 differed from the bulk of MeCP2 in subnuclear localization and co-factor interaction. Furthermore, MeCP2-e1 exhibited enhanced stability compared with MeCP2-e2 in neurons. Therefore, MeCP2-e1 deficient mice implicate MeCP2-e1 as the sole contributor to RTT with non-redundant functions.
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Affiliation(s)
- Dag H Yasui
- Department of Medical Microbiology and Immunology, UC Davis, Davis, CA, USA
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18
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Nuclear trafficking of retroviral RNAs and Gag proteins during late steps of replication. Viruses 2013; 5:2767-95. [PMID: 24253283 PMCID: PMC3856414 DOI: 10.3390/v5112767] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 10/31/2013] [Accepted: 11/12/2013] [Indexed: 11/16/2022] Open
Abstract
Retroviruses exploit nuclear trafficking machinery at several distinct stages in their replication cycles. In this review, we will focus primarily on nucleocytoplasmic trafficking events that occur after the completion of reverse transcription and proviral integration. First, we will discuss nuclear export of unspliced viral RNA transcripts, which serves two essential roles: as the mRNA template for the translation of viral structural proteins and as the genome for encapsidation into virions. These full-length viral RNAs must overcome the cell's quality control measures to leave the nucleus by co-opting host factors or encoding viral proteins to mediate nuclear export of unspliced viral RNAs. Next, we will summarize the most recent findings on the mechanisms of Gag nuclear trafficking and discuss potential roles for nuclear localization of Gag proteins in retrovirus replication.
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19
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Fritz A, Sinha S, Marella N, Berezney R. Alterations in replication timing of cancer-related genes in malignant human breast cancer cells. J Cell Biochem 2013; 114:1074-83. [PMID: 23161755 DOI: 10.1002/jcb.24447] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 01/13/2023]
Abstract
The replication timing of nine genes commonly involved in cancer was investigated in the MCF10 cell lines for human breast cancer progression. Six of these nine genes are part of a constellation of tumor suppressor genes that play a major role in familial human breast cancer (TP53, ATM, PTEN, CHK2, BRCA1, and BRCA2). Three other genes are involved in a large number of human cancers including breast as either tumor suppressors (RB1 and RAD51) or as an oncogene (cMYC). Five of these nine genes (TP53, RAD51, ATM, PTEN, and cMYC) show significant differences (P < 0.05) in replication timing between MCF10A normal human breast cells and the corresponding malignant MCF10CA1a cells. These differences are specific to the malignant state of the MCF10CA1a cells since there were no significant differences in the replication timing of these genes between normal MCF10A cells and the non-malignant cancer MCF10AT1 cells. Microarray analysis further demonstrated that three of these five genes (TP53, RAD51, and cMYC) showed significant changes in gene expression (≥2-fold) between normal and malignant cells. Our findings demonstrate an alteration in the replication timing of a small subset of cancer-related genes in malignant breast cancer cells. These alterations partially correlate with the major transcriptional changes characteristic of the malignant state in these cells.
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Affiliation(s)
- Andrew Fritz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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20
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Soldi M, Bonaldi T. The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components. Mol Cell Proteomics 2013; 12:764-80. [PMID: 23319141 PMCID: PMC3591667 DOI: 10.1074/mcp.m112.024307] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent mass spectrometry analysis. Here we describe a modified protocol for chromatin immunoprecipitation combined with quantitative proteomics based on stable isotope labeling by amino acids in cell culture to identify known and novel histone modifications, variants, and complexes that specifically associate with silent and active chromatin domains. Our chromatin proteomics strategy revealed unique functional interactions among various chromatin modifiers, suggesting new regulatory pathways, such as a heterochromatin-specific modulation of DNA damage response involving H2A.X and WICH, both enriched in silent domains. Chromatin proteomics expands the arsenal of tools for deciphering how all the distinct protein components act together to enforce a given region-specific chromatin status.
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Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, Milan, Italy
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21
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HIV-1 pre-mRNA commitment to Rev mediated export through PSF and Matrin 3. Virology 2013; 435:329-40. [DOI: 10.1016/j.virol.2012.10.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/16/2012] [Accepted: 10/21/2012] [Indexed: 12/15/2022]
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22
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Pliss A, Malyavantham KS, Bhattacharya S, Berezney R. Chromatin dynamics in living cells: Identification of oscillatory motion. J Cell Physiol 2012; 228:609-16. [DOI: 10.1002/jcp.24169] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 07/31/2012] [Indexed: 01/13/2023]
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23
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Asumda FZ, Chase PB. Nuclear cardiac troponin and tropomyosin are expressed early in cardiac differentiation of rat mesenchymal stem cells. Differentiation 2011; 83:106-15. [PMID: 22364878 DOI: 10.1016/j.diff.2011.10.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 08/31/2011] [Accepted: 10/10/2011] [Indexed: 01/22/2023]
Abstract
Nuclear actin - which is immunologically distinct from cytoplasmic actin - has been documented in a number of differentiated cell types, and cardiac isoforms of troponin I (cTnI) and troponin T (cTnT) have been detected in association with nuclei of adult human cardiac myocytes. It is not known whether these and related proteins are present in undifferentiated stem cells, or when they appear in cardiomyogenic cells following differentiation. We first tested the hypothesis that nuclear actin and cardiac isoforms of troponin C (cTnC) and tropomyosin (cTm) are present along with cTnI and cTnT in nuclei of isolated, neonatal rat cardiomyocytes in culture. We also tested the hypothesis that of these five proteins, only actin is present in nuclei of multipotent, bone marrow-derived mesenchymal stem cells (BM-MSCs) from adult rats in culture, but that cTnC, cTnI, cTnT and cTm appear early and uniquely following cardiomyogenic differentiation. Here we show that nuclear actin is present within nuclei of both ventricular cardiomyocytes and undifferentiated, multipotent BM-MSCs. We furthermore show that cTnC, cTnI, cTnT and cTm are not only present in myofilaments of ventricular cardiomyocytes in culture but are also within their nuclei; significantly, these four proteins appear between days 3 and 5 in both myofilaments and nuclei of BM-MSCs treated to differentiate into cardiomyogenic cells. These observations indicate that cardiac troponin and tropomyosin could have important cellular function(s) beyond Ca(2+)-regulation of contraction. While the roles of nuclear-associated actin, troponin subunits and tropomyosin in cardiomyocytes are not known, we anticipate that the BM-MSC culture system described here will be useful for elucidating their function(s), which likely involve cardiac-specific, Ca(2+)-dependent signaling in the nucleus.
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Affiliation(s)
- Faizal Z Asumda
- Department of Biological Science and Program in Molecular Biophysics, Florida State University, FL 32306-4295, USA.
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24
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Barboro P, Repaci E, Ferrari N, Rubagotti A, Boccardo F, Balbi C. Androgen receptor and heterogeneous nuclear ribonucleoprotein K colocalize in the nucleoplasm and are modulated by bicalutamide and 4-hydroxy-tamoxifen in prostatic cancer cell lines. Prostate 2011; 71:1466-79. [PMID: 21321982 DOI: 10.1002/pros.21366] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 01/24/2011] [Indexed: 01/18/2023]
Abstract
BACKGROUND Bicalutamide (BIC) is widely used in prostate cancer therapy. The dose and schedule employed are well tolerated, but about 50% of patients develop gynecomastia. Several studies have shown a significant reduction of the troublesome effects when Tamoxifen is concomitantly administered with BIC. However, the results reported in the literature seem to be preliminary and possible interferences could be present. In order to clarify the molecular mechanisms of the combination of the two drugs, we have investigated whether the expression of the proteins belonging to nuclear matrix (NM), one modulator of hormone action, is altered by BIC and/or 4-hydroxy-tamoxifen (4OHT) in LNCaP cells. We focused above all on heterogeneous nuclear ribonucleoprotein K (hnRNP K) a NM protein with a key role in prostate carcinoma. METHODS NM proteins were analyzed by two-dimensional gel electrophoresis. Modulation and compartmentalization of the androgen receptor and the hnRNP K were studied by Western blotting, confocal microscopy, and immunoprecipitation. RESULTS Proteomic analysis revealed that there is a similarity in the changes of the NM proteins elicited by drugs alone but that their combination does not result in a simple additive effect. Moreover, we found that in the nucleoplasm the androgen receptor and the hnRNP K colocalize in a complex that is highly proximal to DNA and that both proteins were synchronously modulated by BIC and/or 4OHT treatment. CONCLUSION This study confirm the pivotal role of hnRNP K in prostate carcinoma and suggest that this role might be played by the interaction with the androgen receptor.
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Affiliation(s)
- Paola Barboro
- Istituto Nazionale per la Ricerca sul Cancro, Università di Genova, Largo Rosanna Benzi, Genova, Italy
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Kula A, Guerra J, Knezevich A, Kleva D, Myers MP, Marcello A. Characterization of the HIV-1 RNA associated proteome identifies Matrin 3 as a nuclear cofactor of Rev function. Retrovirology 2011; 8:60. [PMID: 21771346 PMCID: PMC3160904 DOI: 10.1186/1742-4690-8-60] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 07/20/2011] [Indexed: 12/30/2022] Open
Abstract
Background Central to the fully competent replication cycle of the human immunodeficiency virus type 1 (HIV-1) is the nuclear export of unspliced and partially spliced RNAs mediated by the Rev posttranscriptional activator and the Rev response element (RRE). Results Here, we introduce a novel method to explore the proteome associated with the nuclear HIV-1 RNAs. At the core of the method is the generation of cell lines harboring an integrated provirus carrying RNA binding sites for the MS2 bacteriophage protein. Flag-tagged MS2 is then used for affinity purification of the viral RNA. By this approach we found that the viral RNA is associated with the host nuclear matrix component MATR3 (Matrin 3) and that its modulation affected Rev activity. Knockdown of MATR3 suppressed Rev/RRE function in the export of unspliced HIV-1 RNAs. However, MATR3 was able to associate with Rev only through the presence of RRE-containing viral RNA. Conclusions In this work, we exploited a novel proteomic method to identify MATR3 as a cellular cofactor of Rev activity. MATR3 binds viral RNA and is required for the Rev/RRE mediated nuclear export of unspliced HIV-1 RNAs.
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Affiliation(s)
- Anna Kula
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34012 Trieste, Italy
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Yedavalli VSRK, Jeang KT. Matrin 3 is a co-factor for HIV-1 Rev in regulating post-transcriptional viral gene expression. Retrovirology 2011; 8:61. [PMID: 21771347 PMCID: PMC3160905 DOI: 10.1186/1742-4690-8-61] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 07/20/2011] [Indexed: 01/11/2023] Open
Abstract
Post-transcriptional regulation of HIV-1 gene expression is mediated by interactions between viral transcripts and viral/cellular proteins. For HIV-1, post-transcriptional nuclear control allows for the export of intron-containing RNAs which are normally retained in the nucleus. Specific signals on the viral RNAs, such as instability sequences (INS) and Rev responsive element (RRE), are binding sites for viral and cellular factors that serve to regulate RNA-export. The HIV-1 encoded viral Rev protein binds to the RRE found on unspliced and incompletely spliced viral RNAs. Binding by Rev directs the export of these RNAs from the nucleus to the cytoplasm. Previously, Rev co-factors have been found to include cellular factors such as CRM1, DDX3, PIMT and others. In this work, the nuclear matrix protein Matrin 3 is shown to bind Rev/RRE-containing viral RNA. This binding interaction stabilizes unspliced and partially spliced HIV-1 transcripts leading to increased cytoplasmic expression of these viral RNAs.
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Affiliation(s)
- Venkat S R K Yedavalli
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institutes of Allergy and Infectious Diseases, the National Institutes of Health, Bethesda, Maryland 20892-0460, USA
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Stein GS, Stein JL, van Wijnen AJ, Lian JB, Zaidi SK, Nickerson JA, Montecino MA, Young DW. An architectural genetic and epigenetic perspective. Integr Biol (Camb) 2011; 3:297-303. [PMID: 21184003 PMCID: PMC3251170 DOI: 10.1039/c0ib00103a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The organization and intranuclear localization of nucleic acids and regulatory proteins contribute to both genetic and epigenetic parameters of biological control. Regulatory machinery in the cell nucleus is functionally compartmentalized in microenvironments (focally organized sites where regulatory factors reside) that provide threshold levels of factors required for transcription, replication, repair and cell survival. The common denominator for nuclear organization of regulatory machinery is that each component of control is architecturally configured and every component of control is embedded in architecturally organized networks that provide an infrastructure for integration and transduction of regulatory signals. It is realistic to anticipate emerging mechanisms that account for the organization and assembly of regulatory complexes within the cell nucleus can provide novel options for cancer diagnosis and therapy with maximal specificity, reduced toxicity and minimal off-target complications.
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Affiliation(s)
- Gary S Stein
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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Latrasse D, Germann S, Houba-Hérin N, Dubois E, Bui-Prodhomme D, Hourcade D, Juul-Jensen T, Le Roux C, Majira A, Simoncello N, Granier F, Taconnat L, Renou JP, Gaudin V. Control of flowering and cell fate by LIF2, an RNA binding partner of the polycomb complex component LHP1. PLoS One 2011; 6:e16592. [PMID: 21304947 PMCID: PMC3031606 DOI: 10.1371/journal.pone.0016592] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 12/29/2010] [Indexed: 01/31/2023] Open
Abstract
Polycomb Repressive Complexes (PRC) modulate the epigenetic status of key cell fate and developmental regulators in eukaryotes. The chromo domain protein LIKE HETEROCHROMATIN PROTEIN1 (LHP1) is a subunit of a plant PRC1-like complex in Arabidopsis thaliana and recognizes histone H3 lysine 27 trimethylation, a silencing epigenetic mark deposited by the PRC2 complex. We have identified and studied an LHP1-Interacting Factor2 (LIF2). LIF2 protein has RNA recognition motifs and belongs to the large hnRNP protein family, which is involved in RNA processing. LIF2 interacts in vivo, in the cell nucleus, with the LHP1 chromo shadow domain. Expression of LIF2 was detected predominantly in vascular and meristematic tissues. Loss-of-function of LIF2 modifies flowering time, floral developmental homeostasis and gynoecium growth determination. lif2 ovaries have indeterminate growth and produce ectopic inflorescences with severely affected flowers showing proliferation of ectopic stigmatic papillae and ovules in short-day conditions. To look at how LIF2 acts relative to LHP1, we conducted transcriptome analyses in lif2 and lhp1 and identified a common set of deregulated genes, which showed significant enrichment in stress-response genes. By comparing expression of LHP1 targets in lif2, lhp1 and lif2 lhp1 mutants we showed that LIF2 can either antagonize or act with LHP1. Interestingly, repression of the FLC floral transcriptional regulator in lif2 mutant is accompanied by an increase in H3K27 trimethylation at the locus, without any change in LHP1 binding, suggesting that LHP1 is targeted independently from LIF2 and that LHP1 binding does not strictly correlate with gene expression. LIF2, involved in cell identity and cell fate decision, may modulate the activity of LHP1 at specific loci, during specific developmental windows or in response to environmental cues that control cell fate determination. These results highlight a novel link between plant RNA processing and Polycomb regulation.
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Affiliation(s)
- David Latrasse
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Sophie Germann
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- Centre Léon Bérard, Inserm U590, Oncogenèse et progression tumorale, Lyon, France
| | - Nicole Houba-Hérin
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Emeline Dubois
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- Centre de Génétique Moléculaire, CNRS FRE3144, Gif-sur-Yvette, France
| | - Duyen Bui-Prodhomme
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- Biologie du Fruit, UMR 619 INRA Centre de Bordeaux, Villenave-d'Ornon, France
| | - Delphine Hourcade
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Trine Juul-Jensen
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Clémentine Le Roux
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Amel Majira
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Nathalie Simoncello
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Fabienne Granier
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | | | | | - Valérie Gaudin
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- * E-mail:
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Nguyen DK, Yang F, Kaul R, Alkan C, Antonellis A, Friery KF, Zhu B, de Jong PJ, Disteche CM. Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X. Genome Res 2011; 21:402-9. [PMID: 21282478 DOI: 10.1101/gr.108563.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In Mus spretus, the chloride channel 4 gene Clcn4-2 is X-linked and dosage compensated by X up-regulation and X inactivation, while in the closely related mouse species Mus musculus, Clcn4-2 has been translocated to chromosome 7. We sequenced Clcn4-2 in M. spretus and identified the breakpoints of the evolutionary translocation in the Mus lineage. Genetic and epigenetic differences were observed between the 5'ends of the autosomal and X-linked loci. Remarkably, Clcn4-2 introns have been truncated on chromosome 7 in M. musculus as compared with the X-linked loci from seven other eutherian mammals. Intron sequences specifically preserved in the X-linked loci were significantly enriched in AT-rich oligomers. Genome-wide analyses showed an overall enrichment in AT motifs unique to the eutherian X (except for genes that escape X inactivation), suggesting a role for these motifs in regulation of the X chromosome.
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Affiliation(s)
- Di Kim Nguyen
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
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Johnson GD, Lalancette C, Linnemann AK, Leduc F, Boissonneault G, Krawetz SA. The sperm nucleus: chromatin, RNA, and the nuclear matrix. Reproduction 2011; 141:21-36. [PMID: 20876223 PMCID: PMC5358669 DOI: 10.1530/rep-10-0322] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Within the sperm nucleus, the paternal genome remains functionally inert and protected following protamination. This is marked by a structural morphogenesis that is heralded by a striking reduction in nuclear volume. Despite these changes, both human and mouse spermatozoa maintain low levels of nucleosomes that appear non-randomly distributed throughout the genome. These regions may be necessary for organizing higher order genomic structure through interactions with the nuclear matrix. The promoters of this transcriptionally quiescent genome are differentially marked by modified histones that may poise downstream epigenetic effects. This notion is supported by increasing evidence that the embryo inherits these differing levels of chromatin organization. In concert with the suite of RNAs retained in the mature sperm, they may synergistically interact to direct early embryonic gene expression. Irrespective, these features reflect the transcriptional history of spermatogenic differentiation. As such, they may soon be utilized as clinical markers of male fertility. In this review, we explore and discuss how this may be orchestrated.
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Affiliation(s)
- Graham D. Johnson
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Claudia Lalancette
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Amelia K. Linnemann
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Frédéric Leduc
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Guylain Boissonneault
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Stephen A. Krawetz
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Institute for Scientific Computing, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
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Keune WJ, Bultsma Y, Sommer L, Jones D, Divecha N. Phosphoinositide signalling in the nucleus. ACTA ACUST UNITED AC 2010; 51:91-9. [PMID: 21035491 DOI: 10.1016/j.advenzreg.2010.09.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 09/14/2010] [Indexed: 12/11/2022]
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The alphaherpesvirus US3/ORF66 protein kinases direct phosphorylation of the nuclear matrix protein matrin 3. J Virol 2010; 85:568-81. [PMID: 20962082 DOI: 10.1128/jvi.01611-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The protein kinase found in the short region of alphaherpesviruses, termed US3 in herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV) and ORF66 in varicella-zoster virus (VZV), affects several viral and host cell processes, and its specific targets remain an area of active investigation. Reports suggesting that HSV-1 US3 substrates overlap with those of cellular protein kinase A (PKA) prompted the use of an antibody specific for phosphorylated PKA substrates to identify US3/ORF66 targets. HSV-1, VZV, and PRV induced very different substrate profiles that were US3/ORF66 kinase dependent. The predominant VZV-phosphorylated 125-kDa species was identified as matrin 3, one of the major nuclear matrix proteins. Matrin 3 was also phosphorylated by HSV-1 and PRV in a US3 kinase-dependent manner and by VZV ORF66 kinase at a novel residue (KRRRT150EE). Since VZV-directed T150 phosphorylation was not blocked by PKA inhibitors and was not induced by PKA activation, and since PKA predominantly targeted matrin 3 S188, it was concluded that phosphorylation by VZV was PKA independent. However, purified VZV ORF66 kinase did not phosphorylate matrin 3 in vitro, suggesting that additional cellular factors were required. In VZV-infected cells in the absence of the ORF66 kinase, matrin 3 displayed intranuclear changes, while matrin 3 showed a pronounced cytoplasmic distribution in late-stage cells infected with US3-negative HSV-1 or PRV. This work identifies phosphorylation of the nuclear matrix protein matrin 3 as a new conserved target of this kinase group.
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Tili E, Michaille JJ, Liu CG, Alder H, Taccioli C, Volinia S, Calin GA, Croce CM. GAM/ZFp/ZNF512B is central to a gene sensor circuitry involving cell-cycle regulators, TGF{beta} effectors, Drosha and microRNAs with opposite oncogenic potentials. Nucleic Acids Res 2010; 38:7673-88. [PMID: 20639536 PMCID: PMC2995059 DOI: 10.1093/nar/gkq637] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs targeting multiple effectors of cell homeostasis and development, whose malfunctions are associated with major pathologies such as cancer. Herein we show that GAM/ZFp/ZNF512B works within an intricate gene regulatory network involving cell-cycle regulators, TGFβ effectors and oncogenic miRNAs of the miR-17-92 cluster. Thus, GAM impairs the transcriptional activation of the miR-17-92 promoter by c-Myc, downregulates miR-17-92 miRNAs differentially, and limits the activation of genes responsive to TGFβ canonical pathway. In contrast, TGFβ decreases GAM transcripts levels while differentially upregulating miR-17-92 miRNAs. In turn, miR-17, miR-20a and miR-92a-1 target GAM transcripts, thus establishing a feedback autoregulatory loop. GAM transcripts are also targeted by miRNAs of the let-7 family. GAM downregulates Drosha, the main effector of miRNA maturation in the nucleus, and interacts with it in a RNA-dependent manner. Finally, GAM modulates the levels of E2F1 and Ras, and increases apoptosis while reducing cell proliferation. We propose that GAM represents a new kind of vertebrate regulator aimed at balancing the opposite effects of regulators of cell homeostasis by increasing the robustness of gene circuitries controlling cell proliferation, differentiation and development.
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Affiliation(s)
- Esmerina Tili
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Biological Research Tower, Columbus, OH 43210, USA, LBMN-INSERM U866, Université de Bourgogne, Faculté Gabriel, 6 Bd. Gabriel 21000 Dijon, France and Department of Experimental Therapeutics and Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
| | - Jean-Jacques Michaille
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Biological Research Tower, Columbus, OH 43210, USA, LBMN-INSERM U866, Université de Bourgogne, Faculté Gabriel, 6 Bd. Gabriel 21000 Dijon, France and Department of Experimental Therapeutics and Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
- *To whom correspondence should be addressed. Tel: +33 380 39 62 11; Fax: +33 380 39 62 50;
| | - Chang-Gong Liu
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Biological Research Tower, Columbus, OH 43210, USA, LBMN-INSERM U866, Université de Bourgogne, Faculté Gabriel, 6 Bd. Gabriel 21000 Dijon, France and Department of Experimental Therapeutics and Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
| | - Hansjuerg Alder
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Biological Research Tower, Columbus, OH 43210, USA, LBMN-INSERM U866, Université de Bourgogne, Faculté Gabriel, 6 Bd. Gabriel 21000 Dijon, France and Department of Experimental Therapeutics and Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
| | - Cristian Taccioli
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Biological Research Tower, Columbus, OH 43210, USA, LBMN-INSERM U866, Université de Bourgogne, Faculté Gabriel, 6 Bd. Gabriel 21000 Dijon, France and Department of Experimental Therapeutics and Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
| | - Stefano Volinia
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Biological Research Tower, Columbus, OH 43210, USA, LBMN-INSERM U866, Université de Bourgogne, Faculté Gabriel, 6 Bd. Gabriel 21000 Dijon, France and Department of Experimental Therapeutics and Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
| | - George A. Calin
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Biological Research Tower, Columbus, OH 43210, USA, LBMN-INSERM U866, Université de Bourgogne, Faculté Gabriel, 6 Bd. Gabriel 21000 Dijon, France and Department of Experimental Therapeutics and Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
| | - Carlo M. Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Biological Research Tower, Columbus, OH 43210, USA, LBMN-INSERM U866, Université de Bourgogne, Faculté Gabriel, 6 Bd. Gabriel 21000 Dijon, France and Department of Experimental Therapeutics and Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
- Correspondence may also be addressed to Carlo M. Croce. Tel: +614 292 4930; Fax: +614 292 3063;
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Rouquette J, Cremer C, Cremer T, Fakan S. Functional nuclear architecture studied by microscopy: present and future. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 282:1-90. [PMID: 20630466 DOI: 10.1016/s1937-6448(10)82001-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this review we describe major contributions of light and electron microscopic approaches to the present understanding of functional nuclear architecture. The large gap of knowledge, which must still be bridged from the molecular level to the level of higher order structure, is emphasized by differences of currently discussed models of nuclear architecture. Molecular biological tools represent new means for the multicolor visualization of various nuclear components in living cells. New achievements offer the possibility to surpass the resolution limit of conventional light microscopy down to the nanometer scale and require improved bioinformatics tools able to handle the analysis of large amounts of data. In combination with the much higher resolution of electron microscopic methods, including ultrastructural cytochemistry, correlative microscopy of the same cells in their living and fixed state is the approach of choice to combine the advantages of different techniques. This will make possible future analyses of cell type- and species-specific differences of nuclear architecture in more detail and to put different models to critical tests.
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Affiliation(s)
- Jacques Rouquette
- Biocenter, Ludwig Maximilians University (LMU), Martinsried, Germany
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35
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Abstract
While the cell nucleus was described for the first time almost two centuries ago, our modern view of the nuclear architecture is primarily based on studies from the last two decades. This surprising late start coincides with the development of new, powerful strategies to probe for the spatial organization of nuclear activities in both fixed and live cells. As a result, three major principles have emerged: first, the nucleus is not just a bag filled with nucleic acids and proteins. Rather, many distinct functional domains, including the chromosomes, resides within the confines of the nuclear envelope. Second, all these nuclear domains are highly dynamic, with molecules exchanging rapidly between them and the surrounding nucleoplasm. Finally, the motion of molecules within the nucleoplasm appears to be mostly driven by random diffusion. Here, the emerging roles of several subnuclear domains are discussed in the context of the dynamic functions of the cell nucleus.
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Affiliation(s)
- Christopher M Austin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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36
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37
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38
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Zeitz MJ, Mukherjee L, Bhattacharya S, Xu J, Berezney R. A probabilistic model for the arrangement of a subset of human chromosome territories in WI38 human fibroblasts. J Cell Physiol 2009; 221:120-9. [PMID: 19507193 DOI: 10.1002/jcp.21842] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There is growing evidence that chromosome territories have a probabilistic non-random arrangement within the cell nucleus of mammalian cells. Other than their radial positioning, however, our knowledge of the degree and specificity of chromosome territory associations is predominantly limited to studies of pair-wise associations. In this study we have investigated the association profiles of eight human chromosome pairs (numbers 1, 2, 3, 4, 6, 7, 8, 9) in the cell nuclei of G(0)-arrested WI38 diploid lung fibroblasts. Associations between heterologous chromosome combinations ranged from 52% to 78% while the homologous chromosome pairs had much lower levels of association (3-25%). A geometric computational method termed the Generalized Median Graph enabled identification of the most probable arrangement of these eight chromosome pairs. Approximately 41% of the predicted associations are present in any given nucleus. The association levels of several chromosome pairs were very similar in a series of lung fibroblast cell lines but strikingly different in skin and colon derived fibroblast cells. We conclude that a large subset of human chromosomes has a preferred probabilistic arrangement in WI38 cells and that the resulting chromosomal associations show tissue origin specificity.
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Affiliation(s)
- Michael J Zeitz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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Marella NV, Bhattacharya S, Mukherjee L, Xu J, Berezney R. Cell type specific chromosome territory organization in the interphase nucleus of normal and cancer cells. J Cell Physiol 2009; 221:130-8. [PMID: 19496171 DOI: 10.1002/jcp.21836] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Numerous studies indicate that the genome of higher eukaryotes is organized into distinct chromosome territories and that the 3-D arrangement of these territories may be closely connected to genomic function and the global regulation of gene expression. Despite this progress, the degree of non-random arrangement remains unclear and no overall model has been proposed for chromosome territory associations. To address this issue, a re-FISH approach was combined with computational analysis to analysis the pair-wise associations for six pairs of human chromosomes (chr #1, 4, 11, 12, 16, 18) in the G(0) state of normal human WI38 lung fibroblast and MCF10A epithelial breast cells. Similar levels of associations were found in WI38 and MCF10A for several of the chromosomes whereas others showed striking differences. A novel computational geometric approach, the generalized median graph (GMG), revealed a preferred probabilistic arrangement distinct for each cell line. Statistical analysis demonstrated that approximately 50% of the associations depicted in the GMG models are present in each individual nucleus. A nearly twofold increase of chromosome 4/16 associations in a malignant breast cancer cell line (MCFCA1a) compared to the related normal epithelial cell line (MCF10A) further demonstrates cancer related changes in chromosome arrangements. Our findings of highly preferred chromosome association profiles that are cell type specific and undergo alterations in cancer cells, lead us to propose a probabilistic chromosome code whereby the 3-D association profile of chromosomes contributes to the functional landscape of the cell nucleus, the global regulation of gene expression and the epigenetic state of chromatin.
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Affiliation(s)
- Narasimharao V Marella
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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40
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Ameyar-Zazoua M, Souidi M, Fritsch L, Robin P, Thomas A, Hamiche A, Percipalle P, Ait-Si-Ali S, Harel-Bellan A. Physical and functional interaction between heterochromatin protein 1alpha and the RNA-binding protein heterogeneous nuclear ribonucleoprotein U. J Biol Chem 2009; 284:27974-27979. [PMID: 19617346 DOI: 10.1074/jbc.m109.037929] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
By combining biochemical purification and mass spectrometry, we identified proteins associated with human heterochromatin protein 1alpha (HP1alpha) both in the nucleoplasm and in chromatin. Some of these are RNA-binding proteins, and among them is the protein heterogeneous nuclear ribonucleoprotein U (hnRNP U)/SAF-A, which is linked to chromatin organization and transcriptional regulation. Here, we demonstrate that hnRNP U is a bona fide HP1alpha-interacting molecule. More importantly, hnRNP U depletion reduces HP1alpha-dependent gene silencing and disturbs HP1alpha subcellular localization. Thus, our data demonstrate that hnRNP U is involved in HP1alpha function, shedding new light on the mode of action of HP1alpha and on the function of hnRNP U.
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Affiliation(s)
- Maya Ameyar-Zazoua
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Mouloud Souidi
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Lauriane Fritsch
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Philippe Robin
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Audrey Thomas
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Ali Hamiche
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, S-171 77 Stockholm, Sweden
| | - Slimane Ait-Si-Ali
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Annick Harel-Bellan
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France.
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Pliss A, Malyavantham K, Bhattacharya S, Zeitz M, Berezney R. Chromatin dynamics is correlated with replication timing. Chromosoma 2009; 118:459-70. [PMID: 19296120 DOI: 10.1007/s00412-009-0208-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 03/03/2009] [Accepted: 03/03/2009] [Indexed: 01/21/2023]
Abstract
Discrete chromatin domains (ChrD), containing an average of approximately 1 Mbp DNA, represent the basic structural units for the regulation of DNA organization and replication in situ. In this study, a bio-computational approach is employed to simultaneously measure the translational motion of large populations of ChrD in the cell nucleus of living cells. Both movement and configurational changes are strikingly higher in early S-phase replicating ChrD compared to those that replicate in mid and late S-phase. The chromatin dynamics was not sensitive to transcription inhibition by alpha-amanitin but was significantly reduced by actinomycin D treatment. Since a majority of active genes replicate in early S-phase, our results suggest a correlation between levels of chromatin dynamics and chromatin poised for active transcription. Analysis of ChrD colocalization with transcription sites and cDNA with ChrD and transcription sites further supports this proposal.
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Affiliation(s)
- Artem Pliss
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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Wang N, Tytell JD, Ingber DE. Mechanotransduction at a distance: mechanically coupling the extracellular matrix with the nucleus. Nat Rev Mol Cell Biol 2009; 10:75-82. [DOI: 10.1038/nrm2594] [Citation(s) in RCA: 1267] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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43
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Ruiz JF, Juárez R, García-Díaz M, Terrados G, Picher AJ, González-Barrera S, Fernández de Henestrosa AR, Blanco L. Lack of sugar discrimination by human Pol mu requires a single glycine residue. Nucleic Acids Res 2003; 31:4441-9. [PMID: 12888504 PMCID: PMC169901 DOI: 10.1093/nar/gkg637] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA polymerase mu (Pol mu) is a novel family X DNA polymerase that has been suggested to play a role in micro-homology mediated joining and repair of double strand breaks. We show here that human Pol mu is not able to discriminate against the 2'-OH group of the sugar moiety. It inserts rNTPs with an efficiency that is <10-fold lower than that of dNTPs, in sharp contrast with the >1000-fold discrimination characteristic of most DNA-dependent DNA polymerases. The lack of sugar discrimination by Pol mu is demonstrated by its ability to add rNTPs to both DNA and RNA primer strands, and to insert both deoxy- and ribonucleotides on growing nucleic acid chains. 3D-modelling of human Pol mu based on the available Pol beta and TdT structural information allowed us to predict candidate residues involved in sugar discrimination. Thus, a single amino acid substitution in which Gly433 residue of Pol mu was mutated to the consensus tyrosine present in Pol beta, produced a strong increase in the discrimination against ribonucleotides. The unusual capacity to insert both rNTPs and dNTPs will be discussed in the context of the predicted roles of Pol mu in DNA repair.
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Affiliation(s)
- José F Ruiz
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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