1
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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 PMCID: PMC11209761 DOI: 10.1042/bst20220585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [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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Khan M, Chen XXL, Dias M, Santos JR, Kour S, You J, van Bruggen R, Youssef MMM, Wan YW, Liu Z, Rosenfeld JA, Tan Q, Pandey UB, Yalamanchili HK, Park J. MATR3 pathogenic variants differentially impair its cryptic splicing repression function. FEBS Lett 2024; 598:415-436. [PMID: 38320753 DOI: 10.1002/1873-3468.14806] [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: 12/06/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
Matrin-3 (MATR3) is an RNA-binding protein implicated in neurodegenerative and neurodevelopmental diseases. However, little is known regarding the role of MATR3 in cryptic splicing within the context of functional genes and how disease-associated variants impact this function. We show that loss of MATR3 leads to cryptic exon inclusion in many transcripts. We reveal that ALS-linked S85C pathogenic variant reduces MATR3 solubility but does not impair RNA binding. In parallel, we report a novel neurodevelopmental disease-associated M548T variant, located in the RRM2 domain, which reduces protein solubility and impairs RNA binding and cryptic splicing repression functions of MATR3. Altogether, our research identifies cryptic events within functional genes and demonstrates how disease-associated variants impact MATR3 cryptic splicing repression function.
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Affiliation(s)
- Mashiat Khan
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Xiao Xiao Lily Chen
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Michelle Dias
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jhune Rizsan Santos
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Justin You
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Rebekah van Bruggen
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Mohieldin M M Youssef
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Qiumin Tan
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jeehye Park
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
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4
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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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5
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Matr3 reshapes m6A modification complex to alleviate macrophage inflammation during atherosclerosis. Clin Immunol 2022; 245:109176. [DOI: 10.1016/j.clim.2022.109176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
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Sprunger ML, Lee K, Sohn BS, Jackrel ME. Molecular determinants and modifiers of Matrin-3 toxicity, condensate dynamics, and droplet morphology. iScience 2022; 25:103900. [PMID: 35252808 PMCID: PMC8889142 DOI: 10.1016/j.isci.2022.103900] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Matrin-3 (MATR3) is a DNA- and RNA-binding protein implicated in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and distal myopathy. Here, we report the development of a yeast model of MATR3 proteotoxicity and aggregation. MATR3 is toxic and forms dynamic shell-like nuclear condensates in yeast. Disease-associated mutations in MATR3 impair condensate dynamics and disrupt condensate morphology. MATR3 toxicity is largely driven by its RNA-recognitions motifs (RRMs). Further, deletion of one or both RRMs drives coalescence of these condensates. Aberrant phase separation of several different RBPs underpins ALS/FTD, and we have engineered Hsp104 variants to reverse this misfolding. Here, we demonstrate that these same variants also counter MATR3 toxicity. We suggest that these Hsp104 variants which rescue MATR3, TDP-43, and FUS toxicity might be employed against a range of ALS/FTD-associated proteins. We anticipate that our yeast model could be a useful platform to screen for modulators of MATR3 misfolding.
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Affiliation(s)
- Macy L. Sprunger
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Ken Lee
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Brian S. Sohn
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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7
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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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8
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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: 25] [Impact Index Per Article: 8.3] [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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9
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Creamer KM, Kolpa HJ, Lawrence JB. Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction. Mol Cell 2021; 81:3509-3525.e5. [PMID: 34320406 DOI: 10.1016/j.molcel.2021.07.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 12/17/2022]
Abstract
Nuclear chromosomes transcribe far more RNA than required to encode protein. Here we investigate whether non-coding RNA broadly contributes to cytological-scale chromosome territory architecture. We develop a procedure that depletes soluble proteins, chromatin, and most nuclear RNA from the nucleus but does not delocalize XIST, a known architectural RNA, from an insoluble chromosome "scaffold." RNA-seq analysis reveals that most RNA in the nuclear scaffold is repeat-rich, non-coding, and derived predominantly from introns of nascent transcripts. Insoluble, repeat-rich (C0T-1) RNA co-distributes with known scaffold proteins including scaffold attachment factor A (SAF-A), and distribution of these components inversely correlates with chromatin compaction in normal and experimentally manipulated nuclei. We further show that RNA is required for SAF-A to interact with chromatin and for enrichment of structurally embedded "scaffold attachment regions" prevalent in euchromatin. Collectively, the results indicate that long nascent transcripts contribute a dynamic structural role that promotes the open architecture of active chromosome territories.
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Affiliation(s)
- Kevin Michael Creamer
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Heather Jill Kolpa
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jeanne Bentley Lawrence
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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10
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Zhou L, Han YF, Yuan C, Duan ZQ. Screening and bioinformatics analysis of cellular proteins interacting with chicken bromodomain-containing protein 2 in DF-1 cells. Br Poult Sci 2021; 62:810-819. [PMID: 34152239 DOI: 10.1080/00071668.2021.1943311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
1. Bromodomain-containing protein 2 (BRD2) is an important member of the BET protein family, which can specifically bind histone acetylated lysine to participate in gene transcriptional regulation, chromatin remodelling, cell proliferation and apoptosis. The following investigation of cellular proteins interacting with chBRD2 will be helpful in understanding the new functions of chBRD2 and the mechanism of NDV replication.2. The recombinant eukaryotic expression vector pEGFP-chBRD2 and empty vector pEGFP-C1 were transfected into DF-1 cells to overexpress GFP-chBRD2 and GFP, respectively. GO annotation, KEGG pathway, and protein-protein interaction network were used to analyse the cellular proteins interacting with chBRD2. In addition, one targeted protein was selected to verify its interaction with chBRD2 using fluorescent co-localisation and Co-IP.3. A total of 225 cellular proteins were identified that potentially interact with chBRD2. GO analysis showed that these play key roles in gene transcriptional regulation, cell cycle and development, immunity and viral infection. Further KEGG pathway analysis showed that these proteins were mainly involved in genetic information processing, immune system, cellular processes and translation. In addition, one targeted cellular protein chicken matrin 3 (chMATR3) was also identified as chBRD2 complex using both fluorescence co-localisation and Co-IP analysis.4. This study presents the interactome data of chBRD2 protein in DF-1 cells, which provides new information to understand the functions of chBRD2 and new targets for further investigating the replication and pathogenesis of NDV.
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Affiliation(s)
- L Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountains Region, Ministry of Education (Guizhou University)/Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, Guiyang, China.,College of Animal Sciences, Guizhou University, Guiyang, China
| | - Y F Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountains Region, Ministry of Education (Guizhou University)/Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, Guiyang, China.,College of Animal Sciences, Guizhou University, Guiyang, China
| | - C Yuan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountains Region, Ministry of Education (Guizhou University)/Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, Guiyang, China.,College of Animal Sciences, Guizhou University, Guiyang, China
| | - Z Q Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountains Region, Ministry of Education (Guizhou University)/Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, Guiyang, China.,College of Animal Sciences, Guizhou University, Guiyang, China
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11
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Identification of Potential Prognostic Biomarkers for Breast Cancer Based on lncRNA-TF-Associated ceRNA Network and Functional Module. BIOMED RESEARCH INTERNATIONAL 2021; 2020:5257896. [PMID: 32802855 PMCID: PMC7411464 DOI: 10.1155/2020/5257896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 11/17/2022]
Abstract
Breast cancer leads to most of cancer deaths among women worldwide. Systematically analyzing the competing endogenous RNA (ceRNA) network and their functional modules may provide valuable insight into the pathogenesis of breast cancer. In this study, we constructed a lncRNA-TF-associated ceRNA network via combining all the significant lncRNA-TF ceRNA pairs and TF-TF PPI pairs. We computed important topological features of the network, such as degree and average path length. Hub nodes in the lncRNA-TF-associated ceRNA network were extracted to detect differential expression in different subtypes and tumor stages of breast cancer. MCODE was used for identifying the closely connected modules from the ceRNA network. Survival analysis was further used for evaluating whether the modules had prognosis effects on breast cancer. TF motif searching analysis was performed for investigating the binding potentials between lncRNAs and TFs. As a result, a lncRNA-TF-associated ceRNA network in breast cancer was constructed, which had a scale-free property. Hub nodes such as MDM4, ZNF410, AC0842-19, and CTB-89H12 were differentially expressed between cancer and normal sample in different subtypes and tumor stages. Two closely connected modules were identified to significantly classify patients into a low-risk group and high-risk group with different clinical outcomes. TF motif searching analysis suggested that TFs, such as NFAT5, might bind to the promoter and enhancer regions of hub lncRNAs and function in breast cancer biology. The results demonstrated that the synergistic, competitive lncRNA-TF ceRNA network and their functional modules played important roles in the biological processes and molecular functions of breast cancer.
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12
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Pollini D, Loffredo R, Maniscalco F, Cardano M, Micaelli M, Bonomo I, Licata NV, Peroni D, Tomaszewska W, Rossi A, Crippa V, Dassi E, Viero G, Quattrone A, Poletti A, Conti L, Provenzani A. Multilayer and MATR3-dependent regulation of mRNAs maintains pluripotency in human induced pluripotent stem cells. iScience 2021; 24:102197. [PMID: 33733063 PMCID: PMC7940987 DOI: 10.1016/j.isci.2021.102197] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/22/2020] [Accepted: 02/11/2021] [Indexed: 10/28/2022] Open
Abstract
Matrin3 (MATR3) is a nuclear RNA/DNA-binding protein that plays pleiotropic roles in gene expression regulation by directly stabilizing target RNAs and supporting the activity of transcription factors by modulating chromatin architecture. MATR3 is involved in the differentiation of neural cells, and, here, we elucidate its critical functions in regulating pluripotent circuits in human induced pluripotent stem cells (hiPSCs). MATR3 downregulation affects hiPSCs' differentiation potential by altering key pluripotency regulators' expression levels, including OCT4, NANOG, and LIN28A by pleiotropic mechanisms. MATR3 binds to the OCT4 and YTHDF1 promoters favoring their expression. YTHDF1, in turn, binds the m6A-modified OCT4 mRNA. Furthermore, MATR3 is recruited on ribosomes and controls pluripotency regulating the translation of specific transcripts, including NANOG and LIN28A, by direct binding and favoring their stabilization. These results show that MATR3 orchestrates the pluripotency circuitry by regulating the transcription, translational efficiency, and epitranscriptome of specific transcripts.
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Affiliation(s)
- Daniele Pollini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Rosa Loffredo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Maniscalco
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
- Institute of Biophysics, CNR, Trento, Italy
| | - Marina Cardano
- Cell Technology Core Facility, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Mariachiara Micaelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Isabelle Bonomo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Daniele Peroni
- Mass Spectrometry Core Facility, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Weronika Tomaszewska
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Annalisa Rossi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Valeria Crippa
- Laboratorio di Biologia Applicata, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Angelo Poletti
- Laboratorio di Biologia Applicata, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Luciano Conti
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
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13
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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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14
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Yang J, Lee SJ, Kwon Y, Ma L, Kim J. Tumor suppressive function of Matrin 3 in the basal-like breast cancer. Biol Res 2020; 53:42. [PMID: 32977861 PMCID: PMC7519516 DOI: 10.1186/s40659-020-00310-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Basal-like breast cancer (BLBC) or triple-negative breast cancer (TNBC) is an aggressive and highly metastatic subtype of human breast cancer. The present study aimed to elucidate the potential tumor-suppressive function of MATR3, an abundant nuclear protein, in BLBC/TNBC, whose cancer-relevance has not been characterized. METHODS We analyzed in vitro tumorigenecity by cell proliferation and soft agar colony formation assays, apoptotic cell death by flow cytometry and Poly (ADP-ribose) polymerase (PARP) cleavage, epithelial-mesenchymal transition (EMT) by checking specific EMT markers with real-time quantitative PCR and in vitro migration and invasion by Boyden Chamber assays. To elucidate the underlying mechanism by which MATR3 functions as a tumor suppressor, we performed Tandem affinity purification followed by mass spectrometry (TAP-MS) and pathway analysis. We also scrutinized MATR3 expression levels in the different subtypes of human breast cancer and the correlation between MATR3 expression and patient survival by bioinformatic analyses of publicly available transcriptome datasets. RESULTS MATR3 suppressed in vitro tumorigenecity, promoted apoptotic cell death and inhibited EMT, migration, and invasion in BLBC/TNBC cells. Various proteins regulating apoptosis were identified as MATR3-binding proteins, and YAP/TAZ pathway was suppressed by MATR3. MATR3 expression was inversely correlated with the aggressive and metastatic nature of breast cancer. Moreover, high expression levels of MATR3 were associated with a good prognosis of breast cancer patients. CONCLUSIONS Our data demonstrate that MATR3 functions as a putative tumor suppressor in BLBC/TNBC cells. Also, MATR3 potentially plays a role as a biomarker in predicting chemotherapy-sensitivity and patient survival in breast cancer patients.
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Affiliation(s)
- Jaehyuk Yang
- Department of Life Sciences, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul, Republic of Korea
| | - Seung Jun Lee
- Department of Life Sciences, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul, Republic of Korea
| | - Yongseok Kwon
- Department of Chemistry, Sogang University, Seoul, Republic of Korea
| | - Li Ma
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jongchan Kim
- Department of Life Sciences, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul, Republic of Korea.
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15
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Cappellini A, Mongiorgi S, Finelli C, Fazio A, Ratti S, Marvi MV, Curti A, Salvestrini V, Pellagatti A, Billi AM, Suh PG, McCubrey JA, Boultwood J, Manzoli L, Cocco L, Follo MY. Phospholipase C beta1 (PI-PLCbeta1)/Cyclin D3/protein kinase C (PKC) alpha signaling modulation during iron-induced oxidative stress in myelodysplastic syndromes (MDS). FASEB J 2020; 34:15400-15416. [PMID: 32959428 DOI: 10.1096/fj.202000933rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/31/2020] [Accepted: 09/09/2020] [Indexed: 01/10/2023]
Abstract
MDS are characterized by anemia and transfusion requirements. Transfused patients frequently show iron overload that negatively affects hematopoiesis. Iron chelation therapy can be effective in these MDS cases, but the molecular consequences of this treatment need to be further investigated. That is why we studied the molecular features of iron effect and Deferasirox therapy on PI-PLCbeta1 inositide signaling, using hematopoietic cells and MDS samples. At baseline, MDS patients showing a positive response after iron chelation therapy displayed higher levels of PI-PLCbeta1/Cyclin D3/PKCalpha expression. During treatment, these responder patients, as well as hematopoietic cells treated with FeCl3 and Deferasirox, showed a specific reduction of PI-PLCbeta1/Cyclin D3/PKCalpha expression, indicating that this signaling pathway is targeted by Deferasirox. The treatment was also able to specifically decrease the production of ROS. This effect correlated with a reduction of IL-1A and IL-2, as well as Akt/mTOR phosphorylation. In contrast, cells exposed only to FeCl3 and cells from MDS patients refractory to Deferasirox showed a specific increase of ROS and PI-PLCbeta1/Cyclin D3/PKCalpha expression. All in all, our data show that PI-PLCbeta1 signaling is a target for iron-induced oxidative stress and suggest that baseline PI-PLCbeta1 quantification could predict iron chelation therapy response in MDS.
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Affiliation(s)
- Alessandra Cappellini
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Sara Mongiorgi
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Carlo Finelli
- Department of Hematology and Oncology, Institute of Hematology "L. and A. Seràgnoli, University-Hospital S.Orsola-Malpighi, Bologna, Italy
| | - Antonietta Fazio
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Stefano Ratti
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Vittoria Marvi
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Antonio Curti
- Department of Hematology and Oncology, Institute of Hematology "L. and A. Seràgnoli, University-Hospital S.Orsola-Malpighi, Bologna, Italy
| | - Valentina Salvestrini
- Department of Hematology and Oncology, Institute of Hematology "L. and A. Seràgnoli, University-Hospital S.Orsola-Malpighi, Bologna, Italy
| | - Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Anna Maria Billi
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Pann-Ghill Suh
- Korea Brain Research Institute, Daegu, Republic of Korea.,School of Life Sciences, UNIST, Ulsan, Republic of Korea
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Lucia Manzoli
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Lucio Cocco
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Matilde Y Follo
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
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16
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Li M, Gan J, Sun Y, Xu Z, Yang J, Sun Y, Li C. Architectural proteins for the formation and maintenance of the 3D genome. SCIENCE CHINA. LIFE SCIENCES 2020; 63:795-810. [PMID: 32249389 DOI: 10.1007/s11427-019-1613-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 12/26/2019] [Indexed: 12/20/2022]
Abstract
Eukaryotic genomes are densely packaged into hierarchical three-dimensional (3D) structures that contain information about gene regulation and many other biological processes. With the development of imaging and sequencing-based technologies, 3D genome studies have revealed that the high-order chromatin structure is composed of hierarchical levels, including chromosome territories, A/B compartments, topologically associated domains, and chromatin loops. However, how this chromatin architecture is formed and maintained is not completely clear. In this review, we introduce experimental methods to investigate the 3D genome, review major architectural proteins that regulate 3D chromatin organization in mammalian cells, such as CTCF (CCCTC-binding factor), cohesin, lamins, and transcription factors, and discuss relevant mechanisms such as phase separation.
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Affiliation(s)
- Mengfan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jingbo Gan
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yuao Sun
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Zihan Xu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Junsheng Yang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Cheng Li
- Center for Statistical Science, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China.
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17
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Picchiarelli G, Dupuis L. Role of RNA Binding Proteins with prion-like domains in muscle and neuromuscular diseases. Cell Stress 2020; 4:76-91. [PMID: 32292882 PMCID: PMC7146060 DOI: 10.15698/cst2020.04.217] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A number of neuromuscular and muscular diseases, including amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and several myopathies, are associated to mutations in related RNA-binding proteins (RBPs), including TDP-43, FUS, MATR3 or hnRNPA1/B2. These proteins harbor similar modular primary sequence with RNA binding motifs and low complexity domains, that enables them to phase separate and create liquid microdomains. These RBPs have been shown to critically regulate multiple events of RNA lifecycle, including transcriptional events, splicing and RNA trafficking and sequestration. Here, we review the roles of these disease-related RBPs in muscle and motor neurons, and how their dysfunction in these cell types might contribute to disease.
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Affiliation(s)
- Gina Picchiarelli
- Université de Strasbourg, INSERM, Mécanismes Centraux et Périphériques de la Neurodégénérescence, UMR_S 1118, Strasbourg, France
| | - Luc Dupuis
- Université de Strasbourg, INSERM, Mécanismes Centraux et Périphériques de la Neurodégénérescence, UMR_S 1118, Strasbourg, France
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18
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Liu CH, Chien MJ, Chang YC, Cheng YH, Li FA, Mou KY. Combining Proximity Labeling and Cross-Linking Mass Spectrometry for Proteomic Dissection of Nuclear Envelope Interactome. J Proteome Res 2020; 19:1109-1118. [DOI: 10.1021/acs.jproteome.9b00609] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Cheng-Hao Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Jou Chien
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - You-Chiun Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Hsiang Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Fu-An Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kurt Yun Mou
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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19
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The Nuclear Matrix Protein SAFA Surveils Viral RNA and Facilitates Immunity by Activating Antiviral Enhancers and Super-enhancers. Cell Host Microbe 2020; 26:369-384.e8. [PMID: 31513772 DOI: 10.1016/j.chom.2019.08.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 05/23/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022]
Abstract
Pathogen pattern recognition receptors (PRRs) trigger innate immune responses to invading pathogens. All known PRRs for viral RNA have extranuclear localization. However, for many viruses, replication generates dsRNA in the nucleus. Here, we show that the nuclear matrix protein SAFA (also known as HnRNPU) functions as a nuclear viral dsRNA sensor for both DNA and RNA viruses. Upon recognition of viral dsRNA, SAFA oligomerizes and activates the enhancers of antiviral genes, including IFNB1. Moreover, SAFA is required for the activation of super-enhancers, which direct vigorous immune gene transcription to establish the antiviral state. Myeloid-specific SAFA-deficient mice were more susceptible to lethal HSV-1 and VSV infection, with decreased type I IFNs. Thus, SAFA functions as a nuclear viral RNA sensor and trans-activator to bridge innate sensing with chromatin remodeling and potentiate robust antiviral responses.
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20
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Shi L, Sun J, Kinomura A, Fukuto A, Horikoshi Y, Tashiro S. Matrin3 promotes homologous recombinational repair by regulation of RAD51. J Biochem 2019; 166:343-351. [PMID: 31119278 DOI: 10.1093/jb/mvz041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/15/2019] [Indexed: 01/19/2023] Open
Abstract
Matrin3 is a highly conserved inner nuclear matrix protein involved in multiple stages of RNA metabolism. Although Matrin3 may also play a role in DNA repair, its precise roles have remained unclear. In this study, we showed that the depletion of Matrin3 led to decreased homologous recombination (HR) efficiency and increased radiation sensitivity of cells. Matrin3-depleted cells showed impaired DNA damage-dependent focus formation of RAD51, a key protein in HR. These findings suggest that Matrin3 promotes HR by regulating RAD51.
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Affiliation(s)
- Lin Shi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Aiko Kinomura
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Atsuhiko Fukuto
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
- Department of Ophthalmology and Visual Science, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
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21
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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: 53] [Impact Index Per Article: 10.6] [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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22
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Nho SH, Yoon G, Seo JH, Oh HN, Cho SS, Kim H, Choi HW, Shim JH, Chae JI. Licochalcone H induces the apoptosis of human oral squamous cell carcinoma cells via regulation of matrin 3. Oncol Rep 2018; 41:333-340. [PMID: 30320347 PMCID: PMC6278573 DOI: 10.3892/or.2018.6784] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
Licochalcone H (LCH) is a chemical compound that is a positional isomer of licochalcone C (LCC), a chalconoid isolated from the root of Glycyrrhiza inflata, which has various pharmacological properties including anti-inflammatory, antioxidant, antitumor, and anticancer effects. However, the efficacy of LCH on cancer cells has not been investigated. The present study examined the effects of LCH on cell proliferation, induction of apoptosis, and the regulation of matrin 3 (Matr3) protein in oral squamous cell carcinoma (OSCC) cells by Annexin V/propidium iodide (PI) staining and western blot analysis. LCH reduced cell viability and colony forming ability, and induced cell cycle arrest and apoptosis in HSC2 and HSC3 cells through the suppression of Matr3. It was also found that LCH directly bound to Matr3 in a Sepharose 4B pull-down assay. Consequently, the results of the present study suggest that LCH may be used as an anticancer drug in combination with conventional chemotherapy for the treatment of OSCC, and that Matr3 may be a potential effective therapeutic target.
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Affiliation(s)
- Su-Hyun Nho
- Department of Dental Pharmacology, School of Dentistry and Institute of Oral Bioscience, BK21 Plus, Chonbuk National University, Jeonju, Jeollabuk 54896, Republic of Korea
| | - Goo Yoon
- Department of Pharmacy, College of Pharmacy and Natural Medicine Research Institute, Mokpo National University, Muan, Jeonnam 58554, Republic of Korea
| | - Ji-Hye Seo
- Department of Dental Pharmacology, School of Dentistry and Institute of Oral Bioscience, BK21 Plus, Chonbuk National University, Jeonju, Jeollabuk 54896, Republic of Korea
| | - Ha-Na Oh
- Department of Pharmacy, College of Pharmacy and Natural Medicine Research Institute, Mokpo National University, Muan, Jeonnam 58554, Republic of Korea
| | - Seung-Sik Cho
- Department of Pharmacy, College of Pharmacy and Natural Medicine Research Institute, Mokpo National University, Muan, Jeonnam 58554, Republic of Korea
| | - Hangun Kim
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Jeonnam 57922, Republic of Korea
| | - Hyun Woo Choi
- Department of Animal Science, Chonbuk National University, Jeonju, Jeollabuk 54896, Republic of Korea
| | - Jung-Hyun Shim
- Department of Pharmacy, College of Pharmacy and Natural Medicine Research Institute, Mokpo National University, Muan, Jeonnam 58554, Republic of Korea
| | - Jung-Il Chae
- Department of Dental Pharmacology, School of Dentistry and Institute of Oral Bioscience, BK21 Plus, Chonbuk National University, Jeonju, Jeollabuk 54896, Republic of Korea
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23
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RNA sequencing of Xp11 translocation-associated cancers reveals novel gene fusions and distinctive clinicopathologic correlations. Mod Pathol 2018; 31:1346-1360. [PMID: 29713041 DOI: 10.1038/s41379-018-0051-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/20/2022]
Abstract
Both Xp11 translocation renal cell carcinomas and the corresponding mesenchymal neoplasms are characterized by a variety of gene fusions involving TFE3. It has been known that tumors with different gene fusions may have different clinicopathologic features; however, further in-depth investigations of subtyping Xp11 translocation-associated cancers are needed in order to explore more meaningful clinicopathologic correlations. A total of 22 unusual cases of Xp11 translocation-associated cancers were selected for the current study; 20 cases were further analyzed by RNA sequencing to explore their TFE3 gene fusion partners. RNA sequencing identified 17 of 20 cases (85%) with TFE3-associated gene fusions, including 4 ASPSCR1/ASPL-TFE3, 3 PRCC-TFE3, 3 SFPQ/PSF-TFE3, 1 NONO-TFE3, 4 MED15-TFE3, 1 MATR3-TFE3, and 1 FUBP1-TFE3. The results have been verified by fusion fluorescence in situ hybridization (FISH) assays or reverse transcriptase polymerase chain reaction (RT-PCR). The remaining 2 cases with specific pathologic features highly suggestive of MED15-TFE3 renal cell carcinoma were identified by fusion FISH assay. We provide the detailed morphologic and immunophenotypic description of the MED15-TFE3 renal cell carcinomas, which frequently demonstrate extensively cystic architecture, similar to multilocular cystic renal neoplasm of low malignant potential, and expressed cathepsin K and melanotic biomarker Melan A. This is the first time to correlate the MED15-TFE3 renal cell carcinoma with specific clinicopathologic features. We also report the first case of the corresponding mesenchymal neoplasm with MED15-TFE3 gene fusion. Additional novel TFE3 gene fusion partners, MATR3 and FUBP1, were identified. Cases with ASPSCR1-TFE3, SFPQ-TFE3, PRCC-TFE3, and NONO-TFE3 gene fusion showed a wide variability in morphologic features, including invasive tubulopapillary pattern simulating collecting duct carcinoma, extensive calcification and ossification, and overlapping and high columnar cells with nuclear grooves mimicking tall cell variant of papillary thyroid carcinoma. Furthermore, we respectively evaluated the ability of TFE3 immunohistochemistry, TFE3 FISH, RT-PCR, and RNA sequencing to subclassify Xp11 translocation-associated cancers. In summary, our study expands the list of TFE3 gene fusion partners and the clinicopathologic features of Xp11 translocation-associated cancers, and highlights the importance of subtyping Xp11 translocation-associated cancers combining morphology, immunohistochemistry, and multiple molecular techniques.
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24
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Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy. Sci Rep 2018; 8:4049. [PMID: 29511296 PMCID: PMC5840295 DOI: 10.1038/s41598-018-21371-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 02/02/2018] [Indexed: 02/08/2023] Open
Abstract
To understand how mutations in Matrin 3 (MATR3) cause amyotrophic lateral sclerosis (ALS) and distal myopathy, we used transcriptome and interactome analysis, coupled with microscopy. Over-expression of wild-type (WT) or F115C mutant MATR3 had little impact on gene expression in neuroglia cells. Only 23 genes, expressed at levels of >100 transcripts showed ≥1.6-fold changes in expression by transfection with WT or mutant MATR3:YFP vectors. We identified ~123 proteins that bound MATR3, with proteins associated with stress granules and RNA processing/splicing being prominent. The interactome of myopathic S85C and ALS-variant F115C MATR3 were virtually identical to WT protein. Deletion of RNA recognition motif (RRM1) or Zn finger motifs (ZnF1 or ZnF2) diminished the binding of a subset of MATR3 interacting proteins. Remarkably, deletion of the RRM2 motif caused enhanced binding of >100 hundred proteins. In live cells, MATR3 lacking RRM2 (ΔRRM2) formed intranuclear spherical structures that fused over time into large structures. Our findings in the cell models used here suggest that MATR3 with disease-causing mutations is not dramatically different from WT protein in modulating gene regulation or in binding to normal interacting partners. The intra-nuclear localization and interaction network of MATR3 is strongly modulated by its RRM2 domain.
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25
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Burla R, Carcuro M, Torre ML, Fratini F, Crescenzi M, D'Apice MR, Spitalieri P, Raffa GD, Astrologo L, Lattanzi G, Cundari E, Raimondo D, Biroccio A, Gatti M, Saggio I. The telomeric protein AKTIP interacts with A- and B-type lamins and is involved in regulation of cellular senescence. Open Biol 2017; 6:rsob.160103. [PMID: 27512140 PMCID: PMC5008010 DOI: 10.1098/rsob.160103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/08/2016] [Indexed: 01/07/2023] Open
Abstract
AKTIP is a shelterin-interacting protein required for replication of telomeric DNA. Here, we show that AKTIP biochemically interacts with A- and B-type lamins and affects lamin A, but not lamin C or B, expression. In interphase cells, AKTIP localizes at the nuclear rim and in discrete regions of the nucleoplasm just like lamins. Double immunostaining revealed that AKTIP partially co-localizes with lamin B1 and lamin A/C in interphase cells, and that proper AKTIP localization requires functional lamin A. In mitotic cells, AKTIP is enriched at the spindle poles and at the midbody of late telophase cells similar to lamin B1. AKTIP-depleted cells show senescence-associated markers and recapitulate several aspects of the progeroid phenotype. Collectively, our results indicate that AKTIP is a new player in lamin-related processes, including those that govern nuclear architecture, telomere homeostasis and cellular senescence.
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Affiliation(s)
- Romina Burla
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, 00185, Italy Istituto Pasteur Fondazione Cenci Bolognetti, Rome 00185, Italy Istituto di Biologia e Patologia Molecolari CNR Roma, 00185, Italy
| | - Mariateresa Carcuro
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, 00185, Italy
| | - Mattia La Torre
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, 00185, Italy
| | | | | | | | - Paola Spitalieri
- Dipartimento di Biomedicina e Prevenzione, Università di Roma Tor Vergata, Roma 00133, Italy
| | - Grazia Daniela Raffa
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, 00185, Italy
| | - Letizia Astrologo
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, 00185, Italy
| | | | - Enrico Cundari
- Istituto di Biologia e Patologia Molecolari CNR Roma, 00185, Italy
| | - Domenico Raimondo
- Dipartimento di Medicina Molecolare, Sapienza, Università di Roma, Rome 00185, Italy
| | - Annamaria Biroccio
- Unità di Oncogenomica ed Epigenetica, Istituto Nazionale Tumori Regina Elena, Roma 00144, Italy
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, 00185, Italy Istituto di Biologia e Patologia Molecolari CNR Roma, 00185, Italy
| | - Isabella Saggio
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, 00185, Italy Istituto di Biologia e Patologia Molecolari CNR Roma, 00185, Italy
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Matrin 3 Is a Component of Neuronal Cytoplasmic Inclusions of Motor Neurons in Sporadic Amyotrophic Lateral Sclerosis. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:507-514. [PMID: 29128563 DOI: 10.1016/j.ajpath.2017.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 12/12/2022]
Abstract
Mutations in the MATR3 gene have been identified as a cause of familial amyotrophic lateral sclerosis, but involvement of the matrin 3 (MATR3) protein in sporadic amyotrophic lateral sclerosis (SALS) pathology has not been fully assessed. We immunohistochemically analyzed MATR3 pathology in the spinal cords of SALS and control autopsy specimens. MATR3 immunostaining of the motor neuron nuclei revealed two distinct patterns: mild and strong staining. There were no differences in the ratio of mild versus strong nuclear staining between the SALS and control cases. MATR3-containing neuronal cytoplasmic inclusions (NCIs) were observed in 60% of SALS cases. Most motor neurons with MATR3-positive NCIs exhibited a mild nuclear staining pattern. Although 16.8% of NCIs positive for transactivating response region DNA-binding protein 43 (TDP-43) were estimated as double-labeled by MATR3, no MATR3-positive or TDP-43-negative NCIs were observed. Although a previous study found that MATR3-positive NCIs are present only in cases with C9orf72 hexanucleotide repeat expansion, ubiquitin-positive granular NCIs were not observed in the cerebellum, which have been reported as specific to C9orf72-related ALS. Six ALS cases were confirmed to be negative for the GGGGCC hexanucleotide. Our results reveal that MATR3 is a component of TDP-43-positive NCIs in motor neurons, even in SALS, and indicate the broader involvement of MATR3 in ALS pathology and the heterogeneity of TDP-43-positive NCIs.
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Banerjee A, Vest KE, Pavlath GK, Corbett AH. Nuclear poly(A) binding protein 1 (PABPN1) and Matrin3 interact in muscle cells and regulate RNA processing. Nucleic Acids Res 2017; 45:10706-10725. [PMID: 28977530 PMCID: PMC5737383 DOI: 10.1093/nar/gkx786] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/27/2017] [Indexed: 01/01/2023] Open
Abstract
The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of muscular dystrophy termed oculopharyngeal muscular dystrophy (OPMD). Despite the tissue-specific pathology that occurs in this disease, only recently have studies of PABPN1 begun to explore the role of this protein in skeletal muscle. We have used co-immunoprecipitation and mass spectrometry to identify proteins that interact with PABPN1 in mouse skeletal muscles. Among the interacting proteins we identified Matrin 3 (MATR3) as a novel protein interactor of PABPN1. The MATR3 gene is mutated in a form of distal myopathy and amyotrophic lateral sclerosis (ALS). We demonstrate, that like PABPN1, MATR3 is critical for myogenesis. Furthermore, MATR3 controls critical aspects of RNA processing including alternative polyadenylation and intron retention. We provide evidence that MATR3 also binds and regulates the levels of long non-coding RNA (lncRNA) Neat1 and together with PABPN1 is required for normal paraspeckle function. We demonstrate that PABPN1 and MATR3 are required for paraspeckles, as well as for adenosine to inosine (A to I) RNA editing of Ctn RNA in muscle cells. We provide a functional link between PABPN1 and MATR3 through regulation of a common lncRNA target with downstream impact on paraspeckle morphology and function. We extend our analysis to a mouse model of OPMD and demonstrate altered paraspeckle morphology in the presence of endogenous levels of alanine-expanded PABPN1. In this study, we report protein-binding partners of PABPN1, which could provide insight into novel functions of PABPN1 in skeletal muscle and identify proteins that could be sequestered with alanine-expanded PABPN1 in the nuclear aggregates found in OPMD.
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Affiliation(s)
- Ayan Banerjee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Katherine E Vest
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins. Biochem Soc Trans 2017; 44:1058-65. [PMID: 27528752 DOI: 10.1042/bst20160080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Indexed: 02/04/2023]
Abstract
Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and with various proteins containing PRI ligands.
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The increasing diversity of functions attributed to the SAFB family of RNA-/DNA-binding proteins. Biochem J 2016; 473:4271-4288. [DOI: 10.1042/bcj20160649] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/28/2016] [Accepted: 09/02/2016] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins play a central role in cellular metabolism by orchestrating the complex interactions of coding, structural and regulatory RNA species. The SAFB (scaffold attachment factor B) proteins (SAFB1, SAFB2 and SAFB-like transcriptional modulator, SLTM), which are highly conserved evolutionarily, were first identified on the basis of their ability to bind scaffold attachment region DNA elements, but attention has subsequently shifted to their RNA-binding and protein–protein interactions. Initial studies identified the involvement of these proteins in the cellular stress response and other aspects of gene regulation. More recently, the multifunctional capabilities of SAFB proteins have shown that they play crucial roles in DNA repair, processing of mRNA and regulatory RNA, as well as in interaction with chromatin-modifying complexes. With the advent of new techniques for identifying RNA-binding sites, enumeration of individual RNA targets has now begun. This review aims to summarise what is currently known about the functions of SAFB proteins.
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Yamaguchi A, Takanashi K. FUS interacts with nuclear matrix-associated protein SAFB1 as well as Matrin3 to regulate splicing and ligand-mediated transcription. Sci Rep 2016; 6:35195. [PMID: 27731383 PMCID: PMC5059712 DOI: 10.1038/srep35195] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/26/2016] [Indexed: 11/23/2022] Open
Abstract
FUS (Fused-in-Sarcoma) is a multifunctional DNA/RNA binding protein linked to familial amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Since FUS is localized mainly in the nucleus with nucleo-cytoplasmic shuttling, it is critical to understand physiological functions in the nucleus to clarify pathogenesis. Here we report a yeast two-hybrid screening identified FUS interaction with nuclear matrix-associated protein SAFB1 (scaffold attachment factor B1). FUS and SAFB1, abundant in chromatin-bound fraction, interact in a DNA-dependent manner. N-terminal SAP domain of SAFB1, a DNA-binding motif, was required for its localization to chromatin-bound fraction and splicing regulation. In addition, depletion of SAFB1 reduced FUS’s localization to chromatin-bound fraction and splicing activity, suggesting SAFB1 could tether FUS to chromatin compartment thorough N-terminal DNA-binding motif. FUS and SAFB1 also interact with Androgen Receptor (AR) regulating ligand-dependent transcription. Moreover, FUS interacts with another nuclear matrix-associated protein Matrin3, which is muted in a subset of familial ALS cases and reportedly interacts with TDP-43. Interestingly, ectopic ALS-linked FUS mutant sequestered endogenous Matrin3 and SAFB1 in the cytoplasmic aggregates. These findings indicate SAFB1 could be a FUS’s functional platform in chromatin compartment to regulate RNA splicing and ligand-dependent transcription and shed light on the etiological significance of nuclear matrix-associated proteins in ALS pathogenesis.
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Affiliation(s)
- Atsushi Yamaguchi
- Department of Neurobiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Takanashi
- Department of Neurobiology, Graduate School of Medicine, Chiba University, Chiba, Japan
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31
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Rajgor D, Hanley JG, Shanahan CM. Identification of novel nesprin-1 binding partners and cytoplasmic matrin-3 in processing bodies. Mol Biol Cell 2016; 27:3894-3902. [PMID: 27733621 PMCID: PMC5170611 DOI: 10.1091/mbc.e16-06-0346] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/20/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022] Open
Abstract
Several new nesprin-1 binding partners were identified, of which many are well-characterized RNA-binding proteins involved in various forms of nuclear RNA-processing events. Matrin-3 was one such protein identified, and a new cytoplasmic localization for matrin-3 is shown. Nesprins are highly conserved spectrin repeat–containing scaffold proteins predominantly known to function at the nuclear envelope (NE). However, nesprin isoforms are emerging with localizations and scaffolding functions at sites away from the NE, suggesting their functions are more diverse than originally thought. In this study, we combined nesprin-1 coimmunoprecipitations with mass spectrometry to identify novel nesprin-1 binding partners for isoforms that localize to subcellular compartments beyond the NE. We show that one of these interactors, matrin-3 (matr3), localizes to mRNA processing bodies (PBs), where we have previously shown a nesprin-1 isoform to localize. Furthermore, we show that Matr3 is part of PB mRNP complexes, is a regulator of miRNA-mediated gene silencing, and possibly shuttles to stress granules in stressed cells. More importantly, we identify a new C-terminally truncated Matr3 isoform that is likely to be involved in these functions and PB localization. This study highlights several novel nesprin-1 binding partners and a new function and localization for Matr3 in cytoplasmic RNA granules.
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Affiliation(s)
- Dipen Rajgor
- Cardiovascular Division, King's College London, London SE5 9NU, United Kingdom .,Department of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Jonathan G Hanley
- Department of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
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Sullivan AE, Peet DJ, Whitelaw ML. MAGED1 is a novel regulator of a select subset of bHLH PAS transcription factors. FEBS J 2016; 283:3488-502. [PMID: 27472814 DOI: 10.1111/febs.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/19/2016] [Accepted: 07/27/2016] [Indexed: 01/04/2023]
Abstract
Transcription factors of the basic helix-loop-helix (bHLH) PER-ARNT-SIM (PAS) family generally have critical and nonredundant biological roles, but some bHLH PAS proteins compete for common cofactors or recognise similar DNA elements. Identifying factors that regulate function of bHLH PAS proteins, particularly in cells where multiple family members are coexpressed, is important for understanding bHLH PAS factor biology. This study identifies and characterises a novel interaction between melanoma-associated antigen D1 (MAGED1) and select members of the bHLH PAS transcription factor family. MAGED1 binds and positively regulates the transcriptional activity of family members SIM1, SIM2, NPAS4 and ARNT2, but does not interact with AhR, HIF1α and ARNT. This interaction is mediated by PAS repeat regions which also form the interface for bHLH PAS dimerisation, and accordingly MAGED1 is not found in complex with bHLH PAS dimers. We show that MAGED1 does not affect bHLH PAS protein levels and cannot be acting as a coactivator of transcriptionally active heterodimers, but rather appears to interact with nascent bHLH PAS proteins in the cytoplasm to enhance their function prior to nuclear import. As a selective regulator, MAGED1 may play an important role in the biology of these specific factors and in general bHLH PAS protein dynamics.
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Affiliation(s)
- Adrienne E Sullivan
- Department of Molecular and Cellular Biology, University of Adelaide, Australia.
| | - Daniel J Peet
- Department of Molecular and Cellular Biology, University of Adelaide, Australia
| | - Murray L Whitelaw
- Department of Molecular and Cellular Biology, University of Adelaide, Australia
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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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Theme 10 Molecular Cell Biology. Amyotroph Lateral Scler Frontotemporal Degener 2015; 16 Suppl 1:176-85. [PMID: 26517031 DOI: 10.3109/21678421.2015.1098815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Leblond CS, Gan-Or Z, Spiegelman D, Laurent SB, Szuto A, Hodgkinson A, Dionne-Laporte A, Provencher P, de Carvalho M, Orrù S, Brunet D, Bouchard JP, Awadalla P, Dupré N, Dion PA, Rouleau GA. Replication study of MATR3 in familial and sporadic amyotrophic lateral sclerosis. Neurobiol Aging 2015; 37:209.e17-209.e21. [PMID: 26493020 DOI: 10.1016/j.neurobiolaging.2015.09.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/03/2015] [Accepted: 09/19/2015] [Indexed: 12/28/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder characterized by an extensive loss of motor neurons in the primary motor cortex, brainstem, and spinal cord. Genetic studies report a high heritability of ALS. Recently, whole-exome sequencing analysis of familial ALS (FALS) patients allowed the identification of missense variations within the MATR3 gene. MATR3 was previously associated to distal myopathy 2 and encodes for a nuclear matrix and DNA/RNA binding protein that has been shown to interact with TDP43 in an RNA-dependent manner. Here, we assessed the MATR3 mutation frequency in French-Canadian ALS and control individuals (nFALS = 83, sporadic ALS [nSALS] = 164, and ncontrols = 162) and showed that MATR3 mutations were found in 0%, 1.8%, and 0% of FALS, SALS, and controls, respectively. Interestingly, among the mutations identified in SALS, the splicing mutation c.48+1G>T was found to result in the insertion of 24 amino acids in MATR3 protein. These findings further support the role of MATR3 in ALS, and more studies are needed to shed more light on MATR3 proteinopathy.
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Affiliation(s)
- Claire S Leblond
- Department of Human Genetics, McGill University, Montreal, Québec, Canada; Montreal Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montreal, Québec, Canada; Montreal Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada
| | - Sandra B Laurent
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada
| | - Anna Szuto
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada
| | - Alan Hodgkinson
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Québec, Canada
| | - Alexandre Dionne-Laporte
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada
| | - Pierre Provencher
- Department of Medicine, University of Laval, Quebec City, Québec, Canada
| | - Mamede de Carvalho
- Faculty of Medicine, Department of Neurosciences, University of Lisbon, Hospital de Santa Maria-CHLN, Lisbon, Portugal
| | - Sandro Orrù
- Medical Genetics, Department of Medical Sciences, University of Cagliari, Cagliari, Italy
| | - Denis Brunet
- Department of Medicine, University of Laval, Quebec City, Québec, Canada; Neuromuscular and Neurogenetic Disease Clinic, Centre Hospitalier Universitaire de Québec, Quebec City, Québec, Canada
| | - Jean-Pierre Bouchard
- Department of Medicine, University of Laval, Quebec City, Québec, Canada; Neuromuscular and Neurogenetic Disease Clinic, Centre Hospitalier Universitaire de Québec, Quebec City, Québec, Canada
| | - Philip Awadalla
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Québec, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nicolas Dupré
- Department of Medicine, University of Laval, Quebec City, Québec, Canada; Neuromuscular and Neurogenetic Disease Clinic, Centre Hospitalier Universitaire de Québec, Quebec City, Québec, Canada
| | - Patrick A Dion
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada.
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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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Cremer T, Cremer M, Hübner B, Strickfaden H, Smeets D, Popken J, Sterr M, Markaki Y, Rippe K, Cremer C. The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments. FEBS Lett 2015; 589:2931-43. [PMID: 26028501 DOI: 10.1016/j.febslet.2015.05.037] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 02/04/2023]
Abstract
Recent methodological advancements in microscopy and DNA sequencing-based methods provide unprecedented new insights into the spatio-temporal relationships between chromatin and nuclear machineries. We discuss a model of the underlying functional nuclear organization derived mostly from electron and super-resolved fluorescence microscopy studies. It is based on two spatially co-aligned, active and inactive nuclear compartments (ANC and INC). The INC comprises the compact, transcriptionally inactive core of chromatin domain clusters (CDCs). The ANC is formed by the transcriptionally active periphery of CDCs, called the perichromatin region (PR), and the interchromatin compartment (IC). The IC is connected to nuclear pores and serves nuclear import and export functions. The ANC is the major site of RNA synthesis. It is highly enriched in epigenetic marks for transcriptionally competent chromatin and RNA Polymerase II. Marks for silent chromatin are enriched in the INC. Multi-scale cross-correlation spectroscopy suggests that nuclear architecture resembles a random obstacle network for diffusing proteins. An increased dwell time of proteins and protein complexes within the ANC may help to limit genome scanning by factors or factor complexes to DNA exposed within the ANC.
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Affiliation(s)
- Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany.
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Hilmar Strickfaden
- University of Alberta, Cross Cancer Institute Dept. of Oncology, Edmonton, AB, Canada
| | - Daniel Smeets
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Jens Popken
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Michael Sterr
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Yolanda Markaki
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) & BioQuant Center, Research Group Genome Organization & Function, Heidelberg, Germany.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Mainz and Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Germany.
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Razin SV, Borunova VV, Iarovaia OV, Vassetzky YS. Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus. BIOCHEMISTRY (MOSCOW) 2015; 79:608-18. [PMID: 25108324 DOI: 10.1134/s0006297914070037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Becoming popular at the end of the 20th century, the concept of the nuclear matrix implies the existence of a nuclear skeleton that organizes functional elements in the cell nucleus. This review presents a critical analysis of the results obtained in the study of nuclear matrix in the light of current views on the organization of the cell nucleus. Numerous studies of nuclear matrix have failed to provide evidence of the existence of such a structure. Moreover, the existence of a filamentous structure that supports the nuclear compartmentalization appears to be unnecessary, since this function is performed by the folded genome itself.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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Lin KP, Tsai PC, Liao YC, Chen WT, Tsai CP, Soong BW, Lee YC. Mutational analysis of MATR3 in Taiwanese patients with amyotrophic lateral sclerosis. Neurobiol Aging 2015; 36:2005.e1-4. [PMID: 25771394 DOI: 10.1016/j.neurobiolaging.2015.02.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/01/2015] [Accepted: 02/07/2015] [Indexed: 11/26/2022]
Abstract
Mutations in the MATR3 gene were just recently identified to cause familial amyotrophic lateral sclerosis, and their role in amyotrophic lateral sclerosis (ALS) in various populations remains unclear. The aim of this study was to determine the frequency and spectrum of mutations in MATR3 in a Taiwanese ALS cohort of Han Chinese origin. Mutational analyses of MATR3 were carried out by direct nucleotide sequencing in a cohort of 207 unrelated patients with ALS. Among them, the genetic diagnoses of 169 patients remained elusive after mutations in SOD1, C9ORF72, TARDBP, FUS, ATXN2, OPTN, VCP, UBQLN2, SQSTM1, PFN1, HNRNPA1, and HNRNPA2B1 had been excluded. We identified 1 heterozygous missense mutation, p.Ala72Thr (c.214G>A), in 1 patient with bulbar-onset and apparently sporadic ALS. The frequency of MATR3 mutations in ALS patients in Taiwan is, therefore, approximately 0.5% (1 of 207). This study reports a novel MATR3 mutation and stresses on the importance to consider MATR3 mutation as a possible etiology of ALS.
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Affiliation(s)
- Kon-Ping Lin
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Pei-Chien Tsai
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chu Liao
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Wei-Ting Chen
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ching-Piao Tsai
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Bing-Wen Soong
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan; Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan; Brain Research Center, National Yang-Ming University, Taipei, Taiwan.
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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: 109] [Impact Index Per Article: 12.1] [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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SUI WEIGUO, ZHANG RUOHAN, CHEN JIEJING, HE HUIYAN, CUI ZHENZHEN, OU MINGLIN, LI WUXIAN, QI SUWEN, WEN JINGLI, LIN XIUHUA, DAI YONG. Quantitative proteomic analysis of Down syndrome in the umbilical cord blood using iTRAQ. Mol Med Rep 2014; 11:1391-9. [DOI: 10.3892/mmr.2014.2828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 05/22/2014] [Indexed: 11/06/2022] Open
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Müller TJ, Kraya T, Stoltenburg-Didinger G, Hanisch F, Kornhuber M, Stoevesandt D, Senderek J, Weis J, Baum P, Deschauer M, Zierz S. Phenotype of matrin-3-related distal myopathy in 16 German patients. Ann Neurol 2014; 76:669-80. [DOI: 10.1002/ana.24255] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/21/2014] [Accepted: 08/21/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Tobias J. Müller
- Department of Neurology; Martin Luther University of Halle-Wittenberg; Halle Germany
| | - Torsten Kraya
- Department of Neurology; Martin Luther University of Halle-Wittenberg; Halle Germany
| | - Gisela Stoltenburg-Didinger
- Department of Neurology; Martin Luther University of Halle-Wittenberg; Halle Germany
- Institute of Cell and Neurobiology; Charité University Medicine Berlin; Berlin Germany
| | - Frank Hanisch
- Department of Neurology; Martin Luther University of Halle-Wittenberg; Halle Germany
| | - Malte Kornhuber
- Department of Neurology; Martin Luther University of Halle-Wittenberg; Halle Germany
| | - Dietrich Stoevesandt
- Department of Diagnostic Radiology; Martin Luther University of Halle-Wittenberg; Halle Germany
| | - Jan Senderek
- Friedrich Bauer Institute; Ludwig Maximilian University of Munich; Munich Germany
| | - Joachim Weis
- Institute of Neuropathology; RWTH Aachen University Hospital; Aachen Germany
| | - Petra Baum
- Clinic and Polyclinic for Neurology; University of Leipzig; Leipzig Germany
| | - Marcus Deschauer
- Department of Neurology; Martin Luther University of Halle-Wittenberg; Halle Germany
| | - Stephan Zierz
- Department of Neurology; Martin Luther University of Halle-Wittenberg; Halle Germany
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Required enhancer-matrin-3 network interactions for a homeodomain transcription program. Nature 2014; 514:257-61. [PMID: 25119036 PMCID: PMC4358797 DOI: 10.1038/nature13573] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 06/10/2014] [Indexed: 11/17/2022]
Abstract
Homeodomain proteins, described 30 years ago1,2, exert essential roles in development as regulators of target gene expression3,4, however the molecular mechanism underlying transcriptional activity of homeodomain factors remains poorly understood. Here, investigation of a developmentally-required POU-homeodomain transcription factor, Pit1/Pou1f1, has revealed that, unexpectedly, binding of Pit1-occupied enhancers5 to a nuclear matrin-3-rich network/architecture6,7 is a key event in effective activation of the Pit1-regulated enhancer/coding gene transcriptional program. Pit1 association with Satb18 and β-catenin is required for this tethering event. A naturally-occurring, dominant negative, point mutation in human Pit1 (R271W), causing combined pituitary hormone deficiency (CPDH)9, results in loss of Pit1 association with β-catenin and Satb1 and therefore the matrin-3-rich network, blocking Pit1-dependent enhancer/coding target gene activation. This defective activation can be rescued by artificial tethering of the mutant R271W Pit1 protein to the matrin-3 network, bypassing the prerequisite association with β-catenin and Satb1 otherwise required. The matrin-3 network-tethered R271W Pit1 mutant, but not the untethered protein, restores Pit1-dependent activation of the enhancers and recruitment of co-activators, exemplified by p300, causing both eRNA transcription and target gene activation. These studies have thus revealed an unanticipated homeodomain factor/β-catenin/Satb1-dependent localization of target gene regulatory enhancer regions to a subnuclear architectural structure that serves as an underlying mechanism by which an enhancer-bound homeodomain factor effectively activates developmental gene transcriptional programs.
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Razin SV, Iarovaia OV, Vassetzky YS. A requiem to the nuclear matrix: from a controversial concept to 3D organization of the nucleus. Chromosoma 2014; 123:217-24. [PMID: 24664318 DOI: 10.1007/s00412-014-0459-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/10/2014] [Accepted: 03/14/2014] [Indexed: 12/13/2022]
Abstract
The first papers coining the term "nuclear matrix" were published 40 years ago. Here, we review the data obtained during the nuclear matrix studies and discuss the contribution of this controversial concept to our current understanding of nuclear architecture and three-dimensional organization of genome.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334, Moscow, Russia
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Nuclear Nox4-derived reactive oxygen species in myelodysplastic syndromes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:456937. [PMID: 24719867 PMCID: PMC3955662 DOI: 10.1155/2014/456937] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/21/2014] [Indexed: 12/25/2022]
Abstract
A role for intracellular ROS production has been recently implicated in the pathogenesis and progression of a wide variety of neoplasias. ROS sources, such as NAD(P)H oxidase (Nox) complexes, are frequently activated in AML (acute myeloid leukemia) blasts and strongly contribute to their proliferation, survival, and drug resistance. Myelodysplastic syndromes (MDS) comprise a heterogeneous group of disorders characterized by ineffective hematopoiesis, with an increased propensity to develop AML. The molecular basis for MDS progression is unknown, but a key element in MDS disease progression is the genomic instability. NADPH oxidases are now recognized to have specific subcellular localizations, this targeting to specific compartments for localized ROS production. Local Nox-dependent ROS production in the nucleus may contribute to the regulation of redox-dependent cell growth, differentiation, senescence, DNA damage, and apoptosis. We observed that Nox1, 2, and 4 isoforms and p22phox and Rac1 subunits are expressed in MDS/AML cell lines and MDS samples, also in the nuclear fractions. Interestingly, Nox4 interacts with ERK and Akt1 within nuclear speckle domain, suggesting that Nox4 could be involved in regulating gene expression and splicing factor activity. These data contribute to the elucidation of the molecular mechanisms used by nuclear ROS to drive MDS evolution to AML.
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Inhibition of nuclear Nox4 activity by plumbagin: effect on proliferative capacity in human amniotic stem cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:680816. [PMID: 24489986 PMCID: PMC3893878 DOI: 10.1155/2013/680816] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 01/03/2023]
Abstract
Human amniotic fluid stem cells (AFSC) with multilineage differentiation potential are novel source for cell therapy. However, in vitro expansion leads to senescence affecting differentiation and proliferative capacities. Reactive oxygen species (ROS) have been involved in the regulation of stem cell pluripotency, proliferation, and differentiation. Redox-regulated signal transduction is coordinated by spatially controlled production of ROS within subcellular compartments. NAD(P)H oxidase family, in particular Nox4, has been known to produce ROS in the nucleus; however, the mechanisms and the meaning of this function remain largely unknown. In the present study, we show that Nox4 nuclear expression (nNox4) increases during culture passages up to cell cycle arrest and the serum starvation causes the same effect. With the decrease of Nox4 activity, obtained with plumbagin, a decline of nuclear ROS production and of DNA damage occurs. Moreover, plumbagin exposure reduces the binding between nNox4 and nucleoskeleton components, as Matrin 3. The same effect was observed also for the binding with phospho-ERK, although nuclear ERK and P-ERK are unchanged. Taken together, we suggest that nNox4 regulation may have important pathophysiologic effects in stem cell proliferation through modulation of nuclear signaling and DNA damage.
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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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Mendonça DMF, Pizzati L, Mostacada K, de S Martins SC, Higashi R, Ayres Sá L, Moura Neto V, Chimelli L, Martinez AMB. Neuroproteomics: an insight into ALS. Neurol Res 2013; 34:937-43. [PMID: 23146297 DOI: 10.1179/1743132812y.0000000092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease of unknown aetiology. Diagnosis is made through physical examination, electrophysiological findings, and by excluding other conditions. There is not a single biomarker that concludes the diagnosis. The aim of this study was to investigate differentially expressed proteins in cerebrospinal fluid (CSF) of ALS patients compared to control subjects, with the purpose to identify a panel of possible biomarkers for the disease. The differentially expressed spots/proteins were submitted to two-dimensional (2D) electrophoresis and recognized with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. Parkin-like and many iron and zinc binding were some of the proteins found in ALS CSF. Parkin is a ligase involved in ubiquitin-proteasome pathway and mutations in the parkin gene are the most common cause of recessive familial Parkinson's disease. Iron and zinc are involved with many important metabolic processes and are related to neurodegenerative disease. Common features of ALS comprise failure of the ubiquitin-proteasome system and increased levels of metal ions in the brain. Therefore, the identification of these proteins can be a significant step in ALS research. These and other identified proteins are discussed in this study.
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Affiliation(s)
- D M F Mendonça
- Departamento de Biociências, Universidade Federal de Sergipe, Sergipe, Brazil.
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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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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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