1
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Stocks J, Gilbert N. Nuclear RNA: a transcription-dependent regulator of chromatin structure. Biochem Soc Trans 2024; 52:1605-1615. [PMID: 39082979 DOI: 10.1042/bst20230787] [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: 05/14/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/29/2024]
Abstract
Although the majority of RNAs are retained in the nucleus, their significance is often overlooked. However, it is now becoming clear that nuclear RNA forms a dynamic structure through interacting with various proteins that can influence the three-dimensional structure of chromatin. We review the emerging evidence for a nuclear RNA mesh or gel, highlighting the interplay between DNA, RNA and RNA-binding proteins (RBPs), and assessing the critical role of protein and RNA in governing chromatin architecture. We also discuss a proposed role for the formation and regulation of the nuclear gel in transcriptional control. We suggest that it may concentrate the transcriptional machinery either by direct binding or inducing RBPs to form microphase condensates, nanometre sized membraneless structures with distinct properties to the surrounding medium and an enrichment of particular macromolecules.
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Affiliation(s)
- Jon Stocks
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, U.K
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, U.K
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2
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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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3
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Abstract
The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.
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Affiliation(s)
- Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Hector Romero
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany,CONTACT M. Cristina Cardoso Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287Darmstadt, Germany
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4
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Taliani V, Buonaiuto G, Desideri F, Setti A, Santini T, Galfrè S, Schirone L, Mariani D, Frati G, Valenti V, Sciarretta S, Perlas E, Nicoletti C, Musarò A, Ballarino M. The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart. eLife 2023; 12:81360. [PMID: 36877136 PMCID: PMC10023161 DOI: 10.7554/elife.81360] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/03/2023] [Indexed: 03/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of heart physiology and disease, although the studies unveiling their modes of action are still limited to few examples. We recently identified pCharme, a chromatin-associated lncRNA whose functional knockout in mice results in defective myogenesis and morphological remodeling of the cardiac muscle. Here, we combined Cap-Analysis of Gene Expression (CAGE), single-cell (sc)RNA sequencing, and whole-mount in situ hybridization analyses to study pCharme cardiac expression. Since the early steps of cardiomyogenesis, we found the lncRNA being specifically restricted to cardiomyocytes, where it assists the formation of specific nuclear condensates containing MATR3, as well as important RNAs for cardiac development. In line with the functional significance of these activities, pCharme ablation in mice results in a delayed maturation of cardiomyocytes, which ultimately leads to morphological alterations of the ventricular myocardium. Since congenital anomalies in myocardium are clinically relevant in humans and predispose patients to major complications, the identification of novel genes controlling cardiac morphology becomes crucial. Our study offers unique insights into a novel lncRNA-mediated regulatory mechanism promoting cardiomyocyte maturation and bears relevance to Charme locus for future theranostic applications.
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Affiliation(s)
- Valeria Taliani
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Giulia Buonaiuto
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Fabio Desideri
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT)RomeItaly
| | - Adriano Setti
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Tiziana Santini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Silvia Galfrè
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT)RomeItaly
| | - Leonardo Schirone
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Davide Mariani
- Center for Human Technologies, Istituto Italiano di TecnologiaGenovaItaly
| | - Giacomo Frati
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Valentina Valenti
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Sebastiano Sciarretta
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Emerald Perlas
- Epigenetics and Neurobiology Unit, EMBL-RomeMonterotondoItaly
| | - Carmine Nicoletti
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of RomeRomeItaly
| | - Antonio Musarò
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of RomeRomeItaly
| | - Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
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5
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Xue C, Liu C, Yun X, Zou X, Li X, Wang P, Li F, Ge Y, Zhang Q, Xie X, Li X, Luo B. Knockdown of hsa_circ_0008922 inhibits the progression of glioma. PeerJ 2022; 10:e14552. [PMID: 36570001 PMCID: PMC9784332 DOI: 10.7717/peerj.14552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background A glioma is a tumor originating from glial cells in the central nervous system. Although significant progress has been made in diagnosis and treatment, most high-grade glioma patients are prone to recurrence. Therefore, molecular targeted therapy may become a new direction for adjuvant therapy in glioma. In recent years, many studies have revealed that circular RNA (circRNA) may play an important role in the occurrence and development of many tumors including gliomas. Our previous study found that the expression of hsa_circ_0008922 was up-regulated in glioma tissues upon RNA sequencing. The biological mechanism of circ_0008922 is still unreported in gliomas. Therefore, in this study, we preliminarily outlined the expression of hsa_circ_0008922 in glioma and explored its biological functions. Methods The expression of hsa_circ_0008922 in forty glioma tissues and four glioma cell lines (A172, U251, SF763 and U87) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). The correlation between hsa_circ_0008922 expression and clinicopathological features of glioma patients was evaluated by Fisher's exact test. To understand the potential function of hsa_circ_0008922 in glioma, we constructed small interfering RNA (siRNA) to hsa_circ_0008922 to downregulate its expression in glioma cell lines A172 and U251. With these hsa_circ_0008922 downregulated cells, a series of assays were carried out as follows. Cell proliferation was detected by CCK8 assay, migration and invasion were determined by wound healing assay and transwell assay, respectively. Colony formation ability was evaluated by plate clonogenic assay. Moreover, flow cytometry combined with Western blot was performed to analyze apoptosis status and the expression of apoptotic related proteins (caspase 3 and caspase 9). Finally, the possible biological pathways and potential miRNA targets of hsa_circ_0008922 were predicted by bioinformatics. Results We found that the expression of hsa_circ_0008922 in glioma tissues was 3.4 times higher than that in normal tissues. The expression of has_circ_0008922 was correlated with WHO tumor grade. After down-regulating the expression of hsa_circ_0008922, malignant biological behavior of glioma cells was inhibited, such as cell proliferation, colony formation, migration, and invasion. At the same time, it also induced apoptosis of glioma cells. Predicted analysis by bioinformatics demonstrated that hsa_circ_0008922 may be involved in tumor-related pathways by acting as a molecular sponge for multiple miRNAs (hsa-let-7e-5p, hsa-miR-506-5p, hsa-let-7b-5p, hsa-let-7c-5p and hsa-let-7a-5p). Finally, we integrated our observation to build a circRNA-miRNA-mRNA predictive network.
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Affiliation(s)
- Chunhong Xue
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China
| | - Chang Liu
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,Postdoctoral Research Station, School of Basic Medicine Science, Guangxi Medical University, Nanning, China
| | - Xiang Yun
- Department of International Cooperation and External Exchange, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaoqiong Zou
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China
| | - Xin Li
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China
| | - Ping Wang
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China
| | - Feng Li
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China
| | - Yingying Ge
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China,Key Laboratory of Preclinical Medicine (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qingmei Zhang
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China,Key Laboratory of Preclinical Medicine (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiaoxun Xie
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China,Key Laboratory of Preclinical Medicine (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China,Key Laboratory of Early Prevention and Treatment of Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Xisheng Li
- Department of Neurosurgery, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
| | - Bin Luo
- Department of Histology and Embryology, School of Basic Medicine Science, Guangxi Medical University, Nanning, China,Key Laboratory of Preclinical Medicine (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
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6
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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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7
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Kinoshita C, Kubota N, Aoyama K. Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22105292. [PMID: 34069857 PMCID: PMC8157344 DOI: 10.3390/ijms22105292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/07/2023] Open
Abstract
The number of patients with neurodegenerative diseases (NDs) is increasing, along with the growing number of older adults. This escalation threatens to create a medical and social crisis. NDs include a large spectrum of heterogeneous and multifactorial pathologies, such as amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and multiple system atrophy, and the formation of inclusion bodies resulting from protein misfolding and aggregation is a hallmark of these disorders. The proteinaceous components of the pathological inclusions include several RNA-binding proteins (RBPs), which play important roles in splicing, stability, transcription and translation. In addition, RBPs were shown to play a critical role in regulating miRNA biogenesis and metabolism. The dysfunction of both RBPs and miRNAs is often observed in several NDs. Thus, the data about the interplay among RBPs and miRNAs and their cooperation in brain functions would be important to know for better understanding NDs and the development of effective therapeutics. In this review, we focused on the connection between miRNAs, RBPs and neurodegenerative diseases.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
| | - Noriko Kubota
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
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8
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Desideri F, Cipriano A, Petrezselyova S, Buonaiuto G, Santini T, Kasparek P, Prochazka J, Janson G, Paiardini A, Calicchio A, Colantoni A, Sedlacek R, Bozzoni I, Ballarino M. Intronic Determinants Coordinate Charme lncRNA Nuclear Activity through the Interaction with MATR3 and PTBP1. Cell Rep 2020; 33:108548. [PMID: 33357424 PMCID: PMC7773549 DOI: 10.1016/j.celrep.2020.108548] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
Chromatin architect of muscle expression (Charme) is a muscle-restricted long noncoding RNA (lncRNA) that plays an important role in myogenesis. Earlier evidence indicates that the nuclear Charme isoform, named pCharme, acts on the chromatin by assisting the formation of chromatin domains where myogenic transcription occurs. By combining RNA antisense purification (RAP) with mass spectrometry and loss-of-function analyses, we have now identified the proteins that assist these chromatin activities. These proteins—which include a sub-set of splicing regulators, principally PTBP1 and the multifunctional RNA/DNA binding protein MATR3—bind to sequences located within the alternatively spliced intron-1 to form nuclear aggregates. Consistent with the functional importance of pCharme interactome in vivo, a targeted deletion of the intron-1 by a CRISPR-Cas9 approach in mouse causes the release of pCharme from the chromatin and results in cardiac defects similar to what was observed upon knockout of the full-length transcript. pCharme is the chromatin-retained isoform of the muscle-specific Charme lncRNA Intronic signals coordinate the association of pCharme with MATR3 and PTBP1 The particle assembly prompts pCharme intron-1 chromatin retention Deletion of the intron-1 by CRISPR-Cas9 leads to heart defects in mouse
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Affiliation(s)
- Fabio Desideri
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Andrea Cipriano
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Silvia Petrezselyova
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Giulia Buonaiuto
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Petr Kasparek
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Giacomo Janson
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Calicchio
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Irene Bozzoni
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy.
| | - Monica Ballarino
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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9
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Ramesh N, Daley EL, Gleixner AM, Mann JR, Kour S, Mawrie D, Anderson EN, Kofler J, Donnelly CJ, Kiskinis E, Pandey UB. RNA dependent suppression of C9orf72 ALS/FTD associated neurodegeneration by Matrin-3. Acta Neuropathol Commun 2020; 8:177. [PMID: 33129345 PMCID: PMC7603783 DOI: 10.1186/s40478-020-01060-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022] Open
Abstract
The most common genetic cause of amyotrophic lateral sclerosis (ALS) is a GGGGCC (G4C2) hexanucleotide repeat expansions in first intron of the C9orf72 gene. The accumulation of repetitive RNA sequences can mediate toxicity potentially through the formation of intranuclear RNA foci that sequester key RNA-binding proteins (RBPs), and non-ATG mediated translation into toxic dipeptide protein repeats. However, the contribution of RBP sequestration to the mechanisms underlying RNA-mediated toxicity remain unknown. Here we show that the ALS-associated RNA-binding protein, Matrin-3 (MATR3), colocalizes with G4C2 RNA foci in patient tissues as well as iPSC-derived motor neurons harboring the C9orf72 mutation. Hyperexpansion of C9 repeats perturbed subcellular distribution and levels of endogenous MATR3 in C9-ALS patient-derived motor neurons. Interestingly, we observed that ectopic expression of human MATR3 strongly mitigates G4C2-mediated neurodegeneration in vivo. MATR3-mediated suppression of C9 toxicity was dependent on the RNA-binding domain of MATR3. Importantly, we found that expression of MATR3 reduced the levels of RAN-translation products in mammalian cells in an RNA-dependent manner. Finally, we have shown that knocking down endogenous MATR3 in C9-ALS patient-derived iPSC neurons decreased the presence of G4C2 RNA foci in the nucleus. Overall, these studies suggest that MATR3 genetically modifies the neuropathological and the pathobiology of C9orf72 ALS through modulating the RNA foci and RAN translation.
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Affiliation(s)
- Nandini Ramesh
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Human Genetics, School of Public Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elizabeth L Daley
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Amanda M Gleixner
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh Brain Institute, Pittsburgh, PA, USA
| | - Jacob R Mann
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Darilang Mawrie
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christopher J Donnelly
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh Brain Institute, Pittsburgh, PA, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Human Genetics, School of Public Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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10
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Ihara K, Sasano T, Hiraoka Y, Togo-Ohno M, Soejima Y, Sawabe M, Tsuchiya M, Ogawa H, Furukawa T, Kuroyanagi H. A missense mutation in the RSRSP stretch of Rbm20 causes dilated cardiomyopathy and atrial fibrillation in mice. Sci Rep 2020; 10:17894. [PMID: 33110103 PMCID: PMC7591520 DOI: 10.1038/s41598-020-74800-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is a fatal heart disease characterized by left ventricular dilatation and cardiac dysfunction. Recent genetic studies on DCM have identified causative mutations in over 60 genes, including RBM20, which encodes a regulator of heart-specific splicing. DCM patients with RBM20 mutations have been reported to present with more severe cardiac phenotypes, including impaired cardiac function, atrial fibrillation (AF), and ventricular arrhythmias leading to sudden cardiac death, compared to those with mutations in the other genes. An RSRSP stretch of RBM20, a hotspot of missense mutations found in patients with idiopathic DCM, functions as a crucial part of its nuclear localization signals. However, the relationship between mutations in the RSRSP stretch and cardiac phenotypes has never been assessed in an animal model. Here, we show that Rbm20 mutant mice harboring a missense mutation S637A in the RSRSP stretch, mimicking that in a DCM patient, demonstrated severe cardiac dysfunction and spontaneous AF and ventricular arrhythmias mimicking the clinical state in patients. In contrast, Rbm20 mutant mice with frame-shifting deletion demonstrated less severe phenotypes, although loss of RBM20-dependent alternative splicing was indistinguishable. RBM20S637A protein cannot be localized to the nuclear speckles, but accumulated in cytoplasmic, perinuclear granule-like structures in cardiomyocytes, which might contribute to the more severe cardiac phenotypes.
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Affiliation(s)
- Kensuke Ihara
- Department of Bio-informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan. .,Department of Cardiovascular Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
| | - Tetsuo Sasano
- Department of Cardiovascular Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Yuichi Hiraoka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Marina Togo-Ohno
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Yurie Soejima
- Department of Molecular Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Motoji Sawabe
- Department of Molecular Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Megumi Tsuchiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hidesato Ogawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tetsushi Furukawa
- Department of Bio-informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
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11
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A protein assembly mediates Xist localization and gene silencing. Nature 2020; 587:145-151. [PMID: 32908311 PMCID: PMC7644664 DOI: 10.1038/s41586-020-2703-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 06/17/2020] [Indexed: 12/22/2022]
Abstract
Nuclear compartments play diverse roles in regulating gene expression, yet the molecular forces and components driving compartment formation remain largely unclear1. The long non-coding RNA Xist establishes an intra-chromosomal compartment by localizing at a high concentration in a territory spatially close to its transcription locus2 and binding diverse proteins3–5 to achieve X-chromosome inactivation (XCI)6,7. The XCI-process therefore serves as paradigm for understanding how RNA-mediated recruitment of diffusible proteins induces a functional compartment. Interestingly, the properties of the inactive X (Xi)-compartment change over time because upon initial Xist spreading and transcriptional shutoff a state is reached where gene silencing remains stable even if Xist is turned off8. Here, we show that the Xist RNA-binding-proteins (RBPs) PTBP19, MATR310, TDP4311, and CELF112 assemble on the multivalent E-repeat-element of Xist7 and, via self-aggregation and heterotypic protein-protein interactions, form a condensate1 in the Xi. This condensate is required for gene silencing and anchoring of Xist to the Xi-territory and can be sustained in the absence of Xist. Notably, these E-repeat-binding RBPs become essential coincident with transition to the Xist-independent XCI-phase8, indicating that the condensate seeded by the E-repeat underlies the developmental switch from Xist-dependence to Xist-independence. Taken together, our data reveal that Xist forms the Xi-compartment by seeding a heteromeric condensate consisting of ubiquitous RBPs and uncover an unanticipated mechanism for heritable gene silencing.
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12
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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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13
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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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14
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Phillips BT, Williams JG, Atchley DT, Xu X, Li JL, Adams AL, Johnson KL, Hall TMT. Mass spectrometric identification of candidate RNA-binding proteins associated with Transition Nuclear Protein mRNA in the mouse testis. Sci Rep 2019; 9:13618. [PMID: 31541158 PMCID: PMC6754440 DOI: 10.1038/s41598-019-50052-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 11/23/2022] Open
Abstract
Spermatogenesis is a differentiation process that requires dramatic changes to DNA architecture, a process governed in part by Transition Nuclear Proteins 1 and 2 (TNP1 and TNP2). Translation of Tnp1 and Tnp2 mRNAs is temporally disengaged from their transcription. We hypothesized that RNA regulatory proteins associate specifically with Tnp mRNAs to control the delayed timing of their translation. To identify potential regulatory proteins, we isolated endogenous mRNA/protein complexes from testis extract and identified by mass spectrometry proteins that associated with one or both Tnp transcripts. Five proteins showed strong association with Tnp transcripts but had low signal when Actin mRNA was isolated. We visualized the expression patterns in testis sections of the five proteins and found that each of the proteins was detected in germ cells at the appropriate stages to regulate Tnp RNA expression.
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Affiliation(s)
- Bart T Phillips
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Dustin T Atchley
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Xiaojiang Xu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Jian-Liang Li
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Andrea L Adams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Katina L Johnson
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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15
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Watanabe T, Kimura A, Kuroyanagi H. Alternative Splicing Regulator RBM20 and Cardiomyopathy. Front Mol Biosci 2018; 5:105. [PMID: 30547036 PMCID: PMC6279932 DOI: 10.3389/fmolb.2018.00105] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/09/2018] [Indexed: 12/17/2022] Open
Abstract
RBM20 is a vertebrate-specific RNA-binding protein with two zinc finger (ZnF) domains, one RNA-recognition motif (RRM)-type RNA-binding domain and an arginine/serine (RS)-rich region. RBM20 has initially been identified as one of dilated cardiomyopathy (DCM)-linked genes. RBM20 is a regulator of heart-specific alternative splicing and Rbm20ΔRRM mice lacking the RRM domain are defective in the splicing regulation. The Rbm20ΔRRM mice, however, do not exhibit a characteristic DCM-like phenotype such as dilatation of left ventricles or systolic dysfunction. Considering that most of the RBM20 mutations identified in familial DCM cases were heterozygous missense mutations in an arginine-serine-arginine-serine-proline (RSRSP) stretch whose phosphorylation is crucial for nuclear localization of RBM20, characterization of a knock-in animal model is awaited. One of the major targets for RBM20 is the TTN gene, which is comprised of the largest number of exons in mammals. Alternative splicing of the TTN gene is exceptionally complicated and RBM20 represses >160 of its consecutive exons, yet detailed mechanisms for such extraordinary regulation are to be elucidated. The TTN gene encodes the largest known protein titin, a multi-functional sarcomeric structural protein specific to striated muscles. As titin is the most important factor for passive tension of cardiomyocytes, extensive heart-specific and developmentally regulated alternative splicing of the TTN pre-mRNA by RBM20 plays a critical role in passive stiffness and diastolic function of the heart. In disease models with diastolic dysfunctions, the phenotypes were rescued by increasing titin compliance through manipulation of the Ttn pre-mRNA splicing, raising RBM20 as a potential therapeutic target.
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Affiliation(s)
- Takeshi Watanabe
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Psychosomatic Dentistry, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akinori Kimura
- Division of Pathology, Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Laboratory for Integrated Research Projects on Intractable Diseases Advanced Technology Laboratories, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Laboratory for Integrated Research Projects on Intractable Diseases Advanced Technology Laboratories, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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16
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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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17
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Fenelon KD, Hopyan S. Structural components of nuclear integrity with gene regulatory potential. Curr Opin Cell Biol 2017. [PMID: 28641117 DOI: 10.1016/j.ceb.2017.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The nucleus is a mechanosensitive and load-bearing structure. Structural components of the nucleus interact to maintain nuclear integrity and have become subjects of exciting research that is relevant to cell and developmental biology. Here we outline the boundaries of what is known about key architectural elements within the nucleus and highlight their potential structural and transcriptional regulatory functions.
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Affiliation(s)
- Kelli D Fenelon
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, M5S 1A8, Canada
| | - Sevan Hopyan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, M5S 1A8, Canada; Division of Orthopaedic Surgery, Hospital for Sick Children and University of Toronto, M5G 1X8, Canada.
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