101
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Zhang B, Tian L, Xie J, Chen G, Wang F. Targeting miRNAs by natural products: A new way for cancer therapy. Biomed Pharmacother 2020; 130:110546. [PMID: 32721631 DOI: 10.1016/j.biopha.2020.110546] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/13/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression through mRNA degradation or translation inhibition. MiRNAs play important roles in a variety of biological processes, and dysregulation of miRNA expression is highly associated with cancer development. Individual miRNA regulates multiple gene expressions, enabling them to regulate multiple cellular signaling pathways simultaneously. Hence, miRNAs could be served as cancer biomarkers for diagnosis and prognosis, and also therapeutic targets. Recently, more and more evidences showed that natural products such as paclitaxel, curcumin, resveratrol, genistein or epigallocatechin-3-gallate exert their anti-proliferative and/or pro-apoptotic effects through regulating one or more miRNAs, leading to the inhibition of cancer cell growth, induction of apoptosis or enhancement of conventional cancer therapeutic efficacy. Herein, we outlined the recent advances in the regulation of miRNAs expression by the natural products and highlight the importance of these natural drugs as a potential strategy in cancer treatment. This review will help us better understand how natural products modulate miRNAs and contribute to the development of effective and safe natural drugs for therapeutic purposes.
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Affiliation(s)
- Beilei Zhang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China; Department of Gynecology and Obstetrics, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710038, China
| | - Ling Tian
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, 510632, Guangzhou, Guangdong, China
| | - Jinrong Xie
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Guo Chen
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, 510632, Guangzhou, Guangdong, China.
| | - Fu Wang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China.
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102
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Chen ZH, Chen TQ, Zeng ZC, Wang D, Han C, Sun YM, Huang W, Sun LY, Fang K, Chen YQ, Luo XQ, Wang WT. Nuclear export of chimeric mRNAs depends on an lncRNA-triggered autoregulatory loop in blood malignancies. Cell Death Dis 2020; 11:566. [PMID: 32703936 PMCID: PMC7378249 DOI: 10.1038/s41419-020-02795-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/05/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022]
Abstract
Aberrant chromosomal translocations leading to tumorigenesis have been ascribed to the heterogeneously oncogenic functions. However, how fusion transcripts exporting remains to be declared. Here, we showed that the nuclear speckle-specific long noncoding RNA MALAT1 controls chimeric mRNA export processes and regulates myeloid progenitor cell differentiation in malignant hematopoiesis. We demonstrated that MALAT1 regulates chimeric mRNAs export in an m6A-dependent manner and thus controls hematopoietic cell differentiation. Specifically, reducing MALAT1 or m6A methyltransferases and the 'reader' YTHDC1 result in the universal retention of distinct oncogenic gene mRNAs in nucleus. Mechanically, MALAT1 hijacks both the chimeric mRNAs and fusion proteins in nuclear speckles during chromosomal translocations and mediates the colocalization of oncogenic fusion proteins with METTL14. MALAT1 and fusion protein complexes serve as a functional loading bridge for the interaction of chimeric mRNA and METTL14. This study demonstrated a universal mechanism of chimeric mRNA transport that involves lncRNA-fusion protein-m6A autoregulatory loop for controlling myeloid cell differentiation. Targeting the lncRNA-triggered autoregulatory loop to disrupt chimeric mRNA transport might represent a new common paradigm for treating blood malignancies.
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Affiliation(s)
- Zhen-Hua Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Tian-Qi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Zhan-Cheng Zeng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Dan Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, 510060, Guangzhou, Guangdong, China
| | - Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Wei Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Ke Fang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Xue-Qun Luo
- The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China.
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103
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He B, Zhao Z, Cai Q, Zhang Y, Zhang P, Shi S, Xie H, Peng X, Yin W, Tao Y, Wang X. miRNA-based biomarkers, therapies, and resistance in Cancer. Int J Biol Sci 2020; 16:2628-2647. [PMID: 32792861 PMCID: PMC7415433 DOI: 10.7150/ijbs.47203] [Citation(s) in RCA: 262] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/04/2020] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs), small non-coding RNAs (ncRNAs) of about 22 nucleotides in size, play important roles in gene regulation, and their dysregulation is implicated in human diseases including cancer. A variety of miRNAs could take roles in the cancer progression, participate in the process of tumor immune, and function with miRNA sponges. During the last two decades, the connection between miRNAs and various cancers has been widely researched. Based on evidence about miRNA, numerous potential cancer biomarkers for the diagnosis and prognosis have been put forward, providing a new perspective on cancer screening. Besides, there are several miRNA-based therapies among different cancers being conducted, advanced treatments such as the combination of synergistic strategies and the use of complementary miRNAs provide significant clinical benefits to cancer patients potentially. Furthermore, it is demonstrated that many miRNAs are engaged in the resistance of cancer therapies with their complex underlying regulatory mechanisms, whose comprehensive cognition can help clinicians and improve patient prognosis. With the belief that studies about miRNAs in human cancer would have great clinical implications, we attempt to summarize the current situation and potential development prospects in this review.
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Affiliation(s)
- Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yuqian Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Shuai Shi
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hui Xie
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Wei Yin
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yongguang Tao
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078 China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, 410078 China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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104
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Taiana E, Ronchetti D, Todoerti K, Nobili L, Tassone P, Amodio N, Neri A. LncRNA NEAT1 in Paraspeckles: A Structural Scaffold for Cellular DNA Damage Response Systems? Noncoding RNA 2020; 6:ncrna6030026. [PMID: 32630183 PMCID: PMC7549348 DOI: 10.3390/ncrna6030026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/25/2020] [Accepted: 06/28/2020] [Indexed: 12/13/2022] Open
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect different cellular functions, including stress response. Furthermore, increasing evidence supports the crucial role of NEAT1 and essential structural proteins of PSs (PSPs) in the regulation of the DNA damage repair (DDR) system. This review aims to provide an overview of the current knowledge on the involvement of NEAT1 and PSPs in DDR, which might strengthen the rationale underlying future NEAT1-based therapeutic options in tumor and neurodegenerative diseases.
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Affiliation(s)
- Elisa Taiana
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
- Correspondence: (E.T.); (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.)
| | - Domenica Ronchetti
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
| | - Katia Todoerti
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
| | - Lucia Nobili
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (P.T.); (N.A.)
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (P.T.); (N.A.)
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
- Correspondence: (E.T.); (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.)
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105
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Liu S, Li B, Liang Q, Liu A, Qu L, Yang J. Classification and function of RNA-protein interactions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1601. [PMID: 32488992 DOI: 10.1002/wrna.1601] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 12/11/2022]
Abstract
Almost all RNAs need to interact with proteins to fully exert their functions, and proteins also bind to RNAs to act as regulators. It has now become clear that RNA-protein interactions play important roles in many biological processes among organisms. Despite the great progress that has been made in the field, there is still no precise classification system for RNA-protein interactions, which makes it challenging to further decipher the functions and mechanisms of these interactions. In this review, we propose four different categories of RNA-protein interactions according to their basic characteristics: RNA motif-dependent RNA-protein interactions, RNA structure-dependent RNA-protein interactions, RNA modification-dependent RNA-protein interactions, and RNA guide-based RNA-protein interactions. Moreover, the integration of different types of RNA-protein interactions and the regulatory factors implicated in these interactions are discussed. Furthermore, we emphasize the functional diversity of these four types of interactions in biological processes and disease development and assess emerging trends in this exciting research field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiaoxia Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anrui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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106
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Pham J, Keon M, Brennan S, Saksena N. Connecting RNA-Modifying Similarities of TDP-43, FUS, and SOD1 with MicroRNA Dysregulation Amidst A Renewed Network Perspective of Amyotrophic Lateral Sclerosis Proteinopathy. Int J Mol Sci 2020; 21:ijms21103464. [PMID: 32422969 PMCID: PMC7278980 DOI: 10.3390/ijms21103464] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
Beyond traditional approaches in understanding amyotrophic lateral sclerosis (ALS), multiple recent studies in RNA-binding proteins (RBPs)-including transactive response DNA-binding protein (TDP-43) and fused in sarcoma (FUS)-have instigated an interest in their function and prion-like properties. Given their prominence as hallmarks of a highly heterogeneous disease, this prompts a re-examination of the specific functional interrelationships between these proteins, especially as pathological SOD1-a non-RBP commonly associated with familial ALS (fALS)-exhibits similar properties to these RBPs including potential RNA-regulatory capabilities. Moreover, the cytoplasmic mislocalization, aggregation, and co-aggregation of TDP-43, FUS, and SOD1 can be identified as proteinopathies akin to other neurodegenerative diseases (NDs), eliciting strong ties to disrupted RNA splicing, transport, and stability. In recent years, microRNAs (miRNAs) have also been increasingly implicated in the disease, and are of greater significance as they are the master regulators of RNA metabolism in disease pathology. However, little is known about the role of these proteins and how they are regulated by miRNA, which would provide mechanistic insights into ALS pathogenesis. This review seeks to discuss current developments across TDP-43, FUS, and SOD1 to build a detailed snapshot of the network pathophysiology underlying ALS while aiming to highlight possible novel therapeutic targets to guide future research.
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Affiliation(s)
- Jade Pham
- Faculty of Medicine, The University of New South Wales, Kensington, Sydney, NSW 2033, Australia;
| | - Matt Keon
- Iggy Get Out, Neurodegenerative Disease Section, Darlinghurst, Sydney, NSW 2010, Australia; (M.K.); (S.B.)
| | - Samuel Brennan
- Iggy Get Out, Neurodegenerative Disease Section, Darlinghurst, Sydney, NSW 2010, Australia; (M.K.); (S.B.)
| | - Nitin Saksena
- Iggy Get Out, Neurodegenerative Disease Section, Darlinghurst, Sydney, NSW 2010, Australia; (M.K.); (S.B.)
- Correspondence:
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107
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Gast M, Rauch BH, Nakagawa S, Haghikia A, Jasina A, Haas J, Nath N, Jensen L, Stroux A, Böhm A, Friebel J, Rauch U, Skurk C, Blankenberg S, Zeller T, Prasanth KV, Meder B, Kuss A, Landmesser U, Poller W. Immune system-mediated atherosclerosis caused by deficiency of long non-coding RNA MALAT1 in ApoE-/-mice. Cardiovasc Res 2020; 115:302-314. [PMID: 30101304 DOI: 10.1093/cvr/cvy202] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Aims The immune system is considered a key driver of atherosclerosis, and beyond proteins and microRNAs (miRs), long non-coding RNAs (lncRNAs) are implicated in immune control. We previously described that lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is involved in cardiac innate immunity in a myocarditis model. Here, we investigated the impact of MALAT1 deficiency upon atherosclerosis development. Methods and results Heterozygous MALAT1-deficient ApoE-/- mice displayed massive immune system dysregulation and atherosclerosis within 2 months even when kept on normal diet. Aortic plaque area (P < 0.05) and aortic root plaque size (P < 0.001) were increased in MALAT1-deficient vs. MALAT1-wildtype ApoE-/- mice. Serum levels of interferon-γ (IFN-γ), tumour necrosis factor (TNF), and interleukin 6 (IL6) were elevated (P < 0.001) in MALAT1-deficient animals. MALAT1-deficient bone marrow-derived macrophages showed enhanced expression of TNF (P = 0.001) and inducible NO synthase (NOS2) (P = 0.002), suppressed MMP9 (P < 0.001), and impaired phagocytic activity (P < 0.001) upon lipopolysaccharide stimulation. RNA-sequencing revealed grossly altered transcriptomes of MALAT1-deficient splenocytes already at baseline, with massive induction of IFN- γ, TNF, NOS2, and granzyme B; CC and CXC chemokines and CCR8; and innate immunity genes interferon-induced protein with tetratricopeptide repeats (IFIT)1/3, interferon-induced transmembrane protein (IFITM)1/3, ISG15. Multiple miRs were up to 45-fold upregulated. Further, selective ablation of the cytosolic part of the MALAT1 system only, the enzymatically MALAT1-derived mascRNA, resulted in massive induction of TNF (P = 0.004) and IL6 (P = 0.028) in macrophages. Northern analysis of post-myocardial infarction patient vs. control peripheral blood mononuclear cells showed reduced (P = 0.005) mascRNA in the patients. CHART-enriched RNA-sequencing reads at the genomic loci of MALAT1 and neighbouring nuclear enriched abundant transcript (NEAT1) documented direct interaction between these lncRNA transcripts. Conclusion The data suggest a molecular circuit involving the MALAT1-mascRNA system, interactions between MALAT1 and NEAT1, and key immune effector molecules, cumulatively impacting upon the development of atherosclerosis. It appears reasonable to look for therapeutic targets in this circuit and to screen for anomalies in the NEAT1-MALAT1 region in humans, too, as possible novel disease risk factors.
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Affiliation(s)
- Martina Gast
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Bernhard H Rauch
- Institute for Pharmacology, Universitätsmedizin Greifswald, Felix-Hausdorff-Strasse 3, Greifswald, Germany.,German Center for Cardiovascular Research (DZHK), Felix-Hausdorff-Strasse 3, Greifswald, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan.,Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 jo, Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Arash Haghikia
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Hindenburgdamm 30, Berlin, Germany
| | - Andrzej Jasina
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Jan Haas
- Institute for Cardiomyopathies, Department of Cardiology, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Im Neuenheimer Feld 669, Heidelberg, Germany
| | - Neetika Nath
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany.,Institute for Bioinformatics, Universitätsmedizin Greifswald, Walther-Rathenau-Strasse 48, Greifswald, Germany
| | - Lars Jensen
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany.,Institute for Bioinformatics, Universitätsmedizin Greifswald, Walther-Rathenau-Strasse 48, Greifswald, Germany
| | - Andrea Stroux
- Institute for Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Chariteplatz 1, Berlin, Germany
| | - Andreas Böhm
- Institute for Pharmacology, Universitätsmedizin Greifswald, Felix-Hausdorff-Strasse 3, Greifswald, Germany
| | - Julian Friebel
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Ursula Rauch
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Carsten Skurk
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Chemical and Life Sciences Laboratory, 601 S. Goodwin Avenue, Urbana, IL, USA
| | - Benjamin Meder
- Institute for Cardiomyopathies, Department of Cardiology, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Im Neuenheimer Feld 669, Heidelberg, Germany
| | - Andreas Kuss
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany.,Institute for Bioinformatics, Universitätsmedizin Greifswald, Walther-Rathenau-Strasse 48, Greifswald, Germany
| | - Ulf Landmesser
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Hindenburgdamm 30, Berlin, Germany.,Berlin Institute of Health, Anna-Louisa-Karsch-Strasse 2, Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Hindenburgdamm 30, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, Germany
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108
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Yamazaki T, Nakagawa S, Hirose T. Architectural RNAs for Membraneless Nuclear Body Formation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:227-237. [PMID: 32019862 DOI: 10.1101/sqb.2019.84.039404] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) are fundamental regulators of various cellular processes. A subset of lncRNAs, termed architectural RNAs (arcRNAs), function in the formation and maintenance of phase-separated membraneless organelles in multiple eukaryotic species. These membraneless organelles represent an important type of compartmentalization in the crowded cellular environment and have several distinct features. The NEAT1_2 lncRNA is a well-characterized arcRNA that functions as an essential scaffold of paraspeckle nuclear bodies. Here, we describe the biogenesis of paraspeckles on arcRNAs through phase separation, focusing on the specific functions of multiple NEAT1_2 RNA domains and their partner RNA-binding proteins. Finally, we present an updated model of paraspeckle formation and discuss future perspectives of research into arcRNA-instructed architectures of phase-separated nuclear bodies.
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Affiliation(s)
- Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815 Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812 Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815 Japan
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109
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Chen L, Zhang J, Chen Q, Ge W, Meng L, Huang X, Shen P, Yuan H, Shi G, Miao Y, Jiang K. Long noncoding RNA SOX2OT promotes the proliferation of pancreatic cancer by binding to FUS. Int J Cancer 2020; 147:175-188. [PMID: 31837005 DOI: 10.1002/ijc.32827] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/03/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors has one of the worst prognoses, and the role of long noncoding RNAs (lncRNAs) in the biological and pathological processes of pancreatic cancer, including tumor cell proliferation, is a popular topic in tumor research. Our previous study revealed the correlation between high levels of the lncRNA-SOX2OT (SOX2OT) with poor survival outcomes. Cell Counting Kit-8, EdU, Flow cytometry and Colony formation assays as well as Xenograft growth of PDAC cells in mice were used for the detection of PDAC cells proliferation progression. Fluorescence in situ hybridization, RNA-binding protein pulldown and RNA immunoprecipitation assays were also used to identify the putative mechanisms of SOX2OT participating in the tumor progression. SOX2OT and its potential downstream targets were verified by Western blot and quantitative real-time polymerase chain reaction (qRT-PCR). SOX2OT was confirmed to promote the proliferation of PDAC cells. It was found to directly physically bind to FUS and we also demonstrated that FUS protein stability was affected by binding with SOX2OT and FUS could suppressed PDAC tumor by regulating cell cycle-associated factors CCND1 and p27. Our findings suggest that SOX2OT may act as a tumor promoter in PDAC through physically binding FUS and regulating its downstream cell cycle-associated factors CCND1 and p27. It may serve as an effective target for antitumor treatment for pancreatic cancer.
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Affiliation(s)
- Lei Chen
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Jingjing Zhang
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Qun Chen
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Wanli Ge
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Lingdong Meng
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Xumin Huang
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Peng Shen
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Hao Yuan
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Guodong Shi
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Yi Miao
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Kuirong Jiang
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Pancreas Institute of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
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110
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Silla T, Karadoulama E, Mąkosa D, Lubas M, Jensen TH. The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts. Cell Rep 2019; 23:2199-2210. [PMID: 29768216 PMCID: PMC5972229 DOI: 10.1016/j.celrep.2018.04.061] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Accepted: 04/15/2018] [Indexed: 12/31/2022] Open
Abstract
Mammalian genomes are promiscuously transcribed, yielding protein-coding and non-coding products. Many transcripts are short lived due to their nuclear degradation by the ribonucleolytic RNA exosome. Here, we show that abolished nuclear exosome function causes the formation of distinct nuclear foci, containing polyadenylated (pA+) RNA secluded from nucleocytoplasmic export. We asked whether exosome co-factors could serve such nuclear retention. Co-localization studies revealed the enrichment of pA+ RNA foci with “pA-tail exosome targeting (PAXT) connection” components MTR4, ZFC3H1, and PABPN1 but no overlap with known nuclear structures such as Cajal bodies, speckles, paraspeckles, or nucleoli. Interestingly, ZFC3H1 is required for foci formation, and in its absence, selected pA+ RNAs, including coding and non-coding transcripts, are exported to the cytoplasm in a process dependent on the mRNA export factor AlyREF. Our results establish ZFC3H1 as a central nuclear pA+ RNA retention factor, counteracting nuclear export activity. Abolished RNA exosome function leads to pA+ RNA accumulation in nuclear foci pA+ RNA foci are enriched with various transcripts and exosome adaptor proteins The exosome adaptor protein ZFC3H1 is required for pA+ RNA foci formation ZFC3H1 functionally counteracts the mRNA export factor AlyREF
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Affiliation(s)
- Toomas Silla
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Evdoxia Karadoulama
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark; The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloesvej 5, 2200 Copenhagen, Denmark
| | - Dawid Mąkosa
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Michal Lubas
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark.
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111
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Pisani G, Baron B. Nuclear paraspeckles function in mediating gene regulatory and apoptotic pathways. Noncoding RNA Res 2019; 4:128-134. [PMID: 32072080 PMCID: PMC7012776 DOI: 10.1016/j.ncrna.2019.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 12/26/2022] Open
Abstract
The nucleus is an essential hub for the regulation of gene expression in both spatial and temporal contexts. The complexity required to manage such a feat has resulted in the evolution of multiple sub-structures in the nucleus such as the nucleolus, small cajal bodies and nuclear stress bodies. The paraspeckle is another membraneless structure composed of RNA elements, primarily the long non-coding RNA (lncRNA) Nuclear Enriched Abundant Transcript 1 (NEAT1), associated with RNA binding proteins (RBPs). The paraspeckle is showing signs of being involved in various aspects of gene regulation and its role in many pathologies from cancer to viral infection is beginning to be addressed. Research into paraspeckle-directed gene regulation highlights the increase in the appreciation of the biological significance of non-coding RNA (ncRNA). This review will thus cover the basis of how a structure as large as a paraspeckle forms along with its functions. It will also explore how it effects pathological conditions and can be used in clinical intervention, with special emphasis on the multitude of methods utilised by paraspeckles for apoptotic regulation.
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Affiliation(s)
| | - Byron Baron
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, MSD2080, Malta
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112
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Adriaens C, Rambow F, Bervoets G, Silla T, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S, Jensen TH, Marine JC. The long noncoding RNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth. RNA (NEW YORK, N.Y.) 2019; 25:1681-1695. [PMID: 31551298 PMCID: PMC6859857 DOI: 10.1261/rna.071456.119] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/30/2019] [Indexed: 05/27/2023]
Abstract
NEAT1 is one of the most studied lncRNAs, in part because its silencing in mice causes defects in mammary gland development and corpus luteum formation and protects them from skin cancer development. Moreover, depleting NEAT1 in established cancer cell lines reduces growth and sensitizes cells to DNA damaging agents. However, NEAT1 produces two isoforms and because the short isoform, NEAT1_1, completely overlaps the 5' part of the long NEAT1_2 isoform; the respective contributions of each of the isoforms to these phenotypes has remained unclear. Whereas NEAT1_1 is highly expressed in most tissues, NEAT1_2 is the central architectural component of paraspeckles, which are nuclear bodies that assemble in specific tissues and cells exposed to various forms of stress. Using dual RNA-FISH to detect both NEAT1_1 outside of the paraspeckles and NEAT1_2/NEAT1 inside this nuclear body, we report herein that NEAT1_1 levels are dynamically regulated during the cell cycle and targeted for degradation by the nuclear RNA exosome. Unexpectedly, however, cancer cells engineered to lack NEAT1_1, but not NEAT1_2, do not exhibit cell cycle defects. Moreover, Neat1_1-specific knockout mice do not exhibit the phenotypes observed in Neat1-deficient mice. We propose that NEAT1 functions are mainly, if not exclusively, attributable to NEAT1_2 and, by extension, to paraspeckles.
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Affiliation(s)
- Carmen Adriaens
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Toomas Silla
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, 351-0198 Saitama, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 113-8510 Tokyo, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 113-8510 Tokyo, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, 060-0808 Sapporo, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, 060-0812 Sapporo, Japan
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
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113
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Dong M, Dong Z, Zhu X, Zhang Y, Song L. Long non-coding RNA MIR205HG regulates KRT17 and tumor processes in cervical cancer via interaction with SRSF1. Exp Mol Pathol 2019; 111:104322. [PMID: 31655037 DOI: 10.1016/j.yexmp.2019.104322] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/09/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022]
Abstract
Abnormal expression of long non-coding RNAs (lncRNAs) has been demonstrated to be a vital regulatory factor in a large number of malignancies. The investigation in cervical cancer and the associated modulation mechanisms are yet to be probed. The aim of this study is to specifically investigate the expression pattern and modulatory mechanism of MIR205HG in cervical cancer. Our paper firstly revealed the up-regulation of KRT17 in cervical cancer. Function assays further displayed that KRT17 silencing impaired the proliferation and migration, and activated the apoptosis of cervical cancer cells. Based on the finding that MIR205HG could regulate KRT17 expression, we further probed the detailed mechanism between MIR205HG and KRT17. It was observed from mechanism experiments that MIR205HG depleted SRSF1 to increase KRT17 expression. The whole mechanism of MIR205HG/SRSF1/KRT17 axis affecting cell proliferation, apoptosis and migration in cervical cancer was validated using rescue assays. In conclusion, MIR205HG modulated the biological activities of cervical cancer cells via targeting SRSF1 and regulating KRT17, which better understood the pathogenesis of cervical carcinoma and excavated a novel therapeutic target.
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Affiliation(s)
- Mingli Dong
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhennan Dong
- Department of Medical Laboratory, Chinese PLA General Hospital, Beijing 100853, China
| | - Xinyu Zhu
- Department of Obstetrics and Gynecology, Beijing Corps Hospital of Chinese People's Armed Police Force, Beijing 100027, China
| | - Yunhe Zhang
- Department of Obstetrics and Gynecology, China Mei-tan General Hospital, Beijing 100028, China
| | - Lei Song
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing 100853, China..
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114
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C9-ALS/FTD-linked proline-arginine dipeptide repeat protein associates with paraspeckle components and increases paraspeckle formation. Cell Death Dis 2019; 10:746. [PMID: 31582731 PMCID: PMC6776546 DOI: 10.1038/s41419-019-1983-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/29/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
A GGGGCC hexanucleotide repeat expansion in the C9ORF72 gene has been identified as the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. The repeat expansion undergoes unconventional translation to produce five dipeptide repeat proteins (DPRs). Although DPRs are thought to be neurotoxic, the molecular mechanism underlying the DPR-caused neurotoxicity has not been fully elucidated. The current study shows that poly-proline-arginine (poly-PR), the most toxic DPR in vitro, binds to and up-regulates nuclear paraspeckle assembly transcript 1 (NEAT1) that plays an essential role as a scaffold non-coding RNA during the paraspeckle formation. The CRISPR-assisted up-regulation of endogenous NEAT1 causes neurotoxicity. We also show that the poly-PR modulates the function of several paraspeckle-localizing heterogeneous nuclear ribonucleoproteins. Furthermore, dysregulated expression of TAR DNA-binding protein 43 (TDP-43) up-regulates NEAT1 expression and induces neurotoxicity. These results suggest that the increase in the paraspeckle formation may be involved in the poly-PR- and TDP-43-mediated neurotoxicity.
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115
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Das S, Zhang E, Senapati P, Amaram V, Reddy MA, Stapleton K, Leung A, Lanting L, Wang M, Chen Z, Kato M, Oh HJ, Guo Q, Zhang X, Zhang B, Zhang H, Zhao Q, Wang W, Wu Y, Natarajan R. A Novel Angiotensin II-Induced Long Noncoding RNA Giver Regulates Oxidative Stress, Inflammation, and Proliferation in Vascular Smooth Muscle Cells. Circ Res 2019; 123:1298-1312. [PMID: 30566058 DOI: 10.1161/circresaha.118.313207] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RATIONALE AngII (angiotensin II)-mediated vascular smooth muscle cell (VSMC) dysfunction plays a major role in hypertension. Long noncoding RNAs have elicited much interest, but their molecular roles in AngII actions and hypertension are unclear. OBJECTIVE To investigate the regulation and functions of a novel long noncoding RNA growth factor- and proinflammatory cytokine-induced vascular cell-expressed RNA ( Giver), in AngII-mediated VSMC dysfunction. METHODS AND RESULTS RNA-sequencing and real-time quantitative polymerase chain reactions revealed that treatment of rat VSMC with AngII increased the expression of Giver and Nr4a3, an adjacent gene encoding a nuclear receptor. Similar changes were observed in rat and mouse aortas treated ex vivo with AngII. RNA-FISH (fluorescence in situ hybridization) and subcellular fractionation showed predominantly nuclear localization of Giver. AngII increased Giver expression via recruitment of Nr4a3 to Giver promoter. Microarray profiling and real-time quantitative polymerase chain reaction validation in VSMC showed that Giver knockdown attenuated the expression of genes involved in oxidative stress ( Nox1) and inflammation ( Il6, Ccl2, Tnf) but increased Nr4a3. Conversely, endogenous Giver overexpression showed opposite effects supporting its role in oxidative stress and inflammation. Chromatin immunoprecipitation assays showed Giver overexpression also increased Pol II (RNA polymerase II) enrichment and decreased repressive histone modification histone H3 trimethylation on lysine 27 at Nox1 and inflammatory gene promoters. Accordingly, Giver knockdown inhibited AngII-induced oxidative stress and proliferation in rat VSMC. RNA-pulldown combined with mass spectrometry showed Giver interacts with nuclear and chromatin remodeling proteins and corepressors, including NONO (non-pou domain-containing octamer-binding protein). Moreover, NONO knockdown elicited similar effects as Giver knockdown on the expression of key Giver-regulated genes. Notably, GIVER and NR4A3 were increased in AngII-treated human VSMC and in arteries from hypertensive patients but attenuated in hypertensive patients treated with ACE (angiotensin-converting enzyme) inhibitors or angiotensin receptor blockers. Furthermore, human GIVER also exhibits partial functional conservation with rat Giver. CONCLUSIONS Giver and its regulator Nr4a3 are important players in AngII-mediated VSMC dysfunction and could be novel targets for antihypertensive therapy.
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Affiliation(s)
- Sadhan Das
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Erli Zhang
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA.,Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Center for Structural Heart Diseases (E.Z., W.W., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Parijat Senapati
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Vishnu Amaram
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (V.A., K.S., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Marpadga A Reddy
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Kenneth Stapleton
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (V.A., K.S., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Amy Leung
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Linda Lanting
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Mei Wang
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhuo Chen
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Mitsuo Kato
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Hyung Jung Oh
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Qianyun Guo
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyue Zhang
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Zhang
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haitong Zhang
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qinghao Zhao
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Wang
- Center for Structural Heart Diseases (E.Z., W.W., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongjian Wu
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Center for Structural Heart Diseases (E.Z., W.W., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rama Natarajan
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (V.A., K.S., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
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116
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Abstract
Mammalian genomes are extensively transcribed, which produces a large number of both coding and non-coding transcripts. Various RNAs are physically associated with chromatin, through being either retained in cis at their site of transcription or recruited in trans to other genomic regions. Driven by recent technological innovations for detecting chromatin-associated RNAs, diverse roles are being revealed for these RNAs and associated RNA-binding proteins (RBPs) in gene regulation and genome function. Such functions include locus-specific roles in gene activation and silencing, as well as emerging roles in higher-order genome organization, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions.
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Affiliation(s)
- Xiao Li
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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Simchovitz A, Hanan M, Niederhoffer N, Madrer N, Yayon N, Bennett ER, Greenberg DS, Kadener S, Soreq H. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. FASEB J 2019; 33:11223-11234. [PMID: 31311324 PMCID: PMC6766647 DOI: 10.1096/fj.201900830r] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent reports attribute numerous regulatory functions to the nuclear paraspeckle-forming long noncoding RNA, nuclear enriched assembly transcript 1 (NEAT1), but the implications of its involvement in Parkinson’s disease (PD) remain controversial. To address this issue, we assessed NEAT1 expression levels and cell type patterns in the substantia nigra (SN) from 53 donors with and without PD, as well as in interference tissue culture tests followed by multiple in-house and web-available models of PD. PCR quantification identified elevated levels of NEAT1 expression in the PD SN compared with control brains, an elevation that was reproducible across a multitude of disease models. In situ RNA hybridization supported neuron-specific formation of NEAT1-based paraspeckles at the SN and demonstrated coincreases of NEAT1 and paraspeckles in cultured cells under paraquat (PQ)-induced oxidative stress. Furthermore, neuroprotective agents, including fenofibrate and simvastatin, induced NEAT1 up-regulation, whereas RNA interference–mediated depletion of NEAT1 exacerbated death of PQ-exposed cells in a leucine-rich repeat kinase 2–mediated manner. Our findings highlight a novel protective role for NEAT1 in PD and suggest a previously unknown mechanism for the neuroprotective traits of widely used preventive therapeutics.—Simchovitz, A., Hanan, M., Niederhoffer, N., Madrer, N., Yayon, N., Bennett, E. R., Greenberg, D. S., Kadener, S., Soreq, H. NEAT1 is overexpressed in Parkinson’s disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress.
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Affiliation(s)
- Alon Simchovitz
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mor Hanan
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Naomi Niederhoffer
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nimrod Madrer
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nadav Yayon
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Estelle R Bennett
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David S Greenberg
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sebastian Kadener
- Biology Department, Brandeis University, Waltham, Massachusetts, USA
| | - Hermona Soreq
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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118
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Long noncoding RNA SNHG14 facilitates colorectal cancer metastasis through targeting EZH2-regulated EPHA7. Cell Death Dis 2019; 10:514. [PMID: 31273190 PMCID: PMC6609685 DOI: 10.1038/s41419-019-1707-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/28/2019] [Indexed: 12/24/2022]
Abstract
Accumulating evidence suggested the participation of long noncoding RNAs (lncRNAs) in regulating various biological processes so as to affecting cancer progression. However, the functional role of most lncRNAs in colorectal carcer (CRC) is still largely covered. In the present study, we disclosed SNHG14 as a carcinogene in CRC development, as it was low-expressed in normal colon tissues but markedly upregulated in CRC cell lines. Besides, SNHG14 contributed to CRC cell proliferation, motility and EMT in vitro, and inhibition of it confined CRC tumor growth and liver metastasis in vivo. Next, the mechanistic investigations confirmed that SNHG14-promoted CRC progression was mediated by EPHA7, which was negatively regulated by SNHG14 in CRC via an EZH2-dependent way. Importantly, EZH2 was proved as a transcription factor of EPHA7 and functioned as a repressor in EPHA7 transcription by enhancing methylation on EPHA7 promoter. Meanwhile, SNHG14 increased EZH2 expression in CRC via stabilizing its mRNA by interacting with FUS, and via freeing its mRNA from miR-186-5p-induced silence. All in all, our observations demonstrated that SNHG14 serves as a facilitator in CRC through targeting EZH2-repressed EPHA7 by enhancing EZH2 via recruiting FUS and absorbing miR-186-5p, indicating a promising new road for CRC diagnosis and treatment.
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119
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Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, Drukker M. Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition. Mol Cell 2019; 74:951-965.e13. [PMID: 31047794 PMCID: PMC6561722 DOI: 10.1016/j.molcel.2019.03.041] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 02/12/2019] [Accepted: 03/28/2019] [Indexed: 01/22/2023]
Abstract
RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation.
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Affiliation(s)
- Miha Modic
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Markus Grosch
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Gregor Rot
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Silvia Schirge
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tjasa Lepko
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Flora C Y Lee
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ejona Rusha
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Michael Palo
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| | - Davide Cacchiarelli
- Broad Institute of Harvard University/MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Telethon Institute of Genetics and Medicine (TIGEM), NA 80078 Pozzuoli, Italy
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia; Biomedical Research Institute BRIS, 1000 Ljubljana, Slovenia
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Alexander Meissner
- Broad Institute of Harvard University/MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Heiko Lickert
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK.
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Comprehensive Pneumology Center (CPC-M), Ludwig-Maximilians-Universität München, Asklepios Fachkliniken München-Gauting und Helmholtz Zentrum München, Max-Lebsche-Platz 31, 81377 Munich, Germany.
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120
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Fu K, Tian S, Tan H, Wang C, Wang H, Wang M, Wang Y, Chen Z, Wang Y, Yue Q, Xu Q, Zhang S, Li H, Xie J, Lin M, Luo M, Chen F, Ye L, Zheng K. Biological and RNA regulatory function of MOV10 in mammalian germ cells. BMC Biol 2019; 17:39. [PMID: 31088452 PMCID: PMC6515687 DOI: 10.1186/s12915-019-0659-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
Background RNA regulation by RNA-binding proteins (RBPs) involve extremely complicated mechanisms. MOV10 and MOV10L1 are two homologous RNA helicases implicated in distinct intracellular pathways. MOV10L1 participates specifically in Piwi-interacting RNA (piRNA) biogenesis and protects mouse male fertility. In contrast, the functional complexity of MOV10 remains incompletely understood, and its role in the mammalian germline is unknown. Here, we report a study of the biological and molecular functions of the RNA helicase MOV10 in mammalian male germ cells. Results MOV10 is a nucleocytoplasmic protein mainly expressed in spermatogonia. Knockdown and transplantation experiments show that MOV10 deficiency has a negative effect on spermatogonial progenitor cells (SPCs), limiting proliferation and in vivo repopulation capacity. This effect is concurrent with a global disturbance of RNA homeostasis and downregulation of factors critical for SPC proliferation and/or self-renewal. Unexpectedly, microRNA (miRNA) biogenesis is impaired due partially to decrease of miRNA primary transcript levels and/or retention of miRNA via splicing control. Genome-wide analysis of RNA targetome reveals that MOV10 binds preferentially to mRNAs with long 3′-UTR and also interacts with various non-coding RNA species including those in the nucleus. Intriguingly, nuclear MOV10 associates with an array of splicing factors, particularly with SRSF1, and its intronic binding sites tend to reside in proximity to splice sites. Conclusions These data expand the landscape of MOV10 function and highlight a previously unidentified role initiated from the nucleus, suggesting that MOV10 is a versatile RBP involved in a broader RNA regulatory network. Electronic supplementary material The online version of this article (10.1186/s12915-019-0659-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaiqiang Fu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Suwen Tian
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.,Department of Preventive Medicine, Heze Medical College, Heze, 274000, China
| | - Huanhuan Tan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Caifeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hanben Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Min Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yuanyuan Wang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Zhen Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanfeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Qiushi Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Shuya Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Haixin Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Jie Xie
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Mingyan Lin
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Mengcheng Luo
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
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121
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Abstract
A diverse catalog of long noncoding RNAs (lncRNAs), which lack protein-coding potential, are transcribed from the mammalian genome. They are emerging as important regulators in gene expression networks by controlling nuclear architecture and transcription in the nucleus and by modulating mRNA stability, translation and post-translational modifications in the cytoplasm. In this Review, we highlight recent progress in cellular functions of lncRNAs at the molecular level in mammalian cells.
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122
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Vaschetto LM, Beccacece HM. The emerging importance of noncoding RNAs in the insecticide tolerance, with special emphasis on Plutella xylostella (Lepidoptera: Plutellidae). WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1539. [PMID: 31045325 DOI: 10.1002/wrna.1539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/20/2019] [Accepted: 04/02/2019] [Indexed: 01/11/2023]
Abstract
Recently generated high-throughput sequencing data sets have shed light on the important regulatory roles of noncoding RNA (ncRNA) molecules in the development of higher organisms. Nowadays it is well-known that regulatory ncRNAs can bind complementary RNA or DNA sequences and recruit chromatin remodelers to selectively modulate gene expression. Consequently, genome sequencing and transcriptomics technologies are now being used to reveal hidden associations among ncRNAs and distinct biological mechanisms. This is the case for the diamondback moth Plutella xylostella, a worldwide pest known to infest cruciferous crops and to display resistance to most insecticides, including Bacillus thuringiensis (Bt) based biopesticides. In P. xylostella, it is thought that ncRNAs could play important roles in both development and insecticide resistance. This review will highlight recent insights into the roles of ncRNAs in P. xylostella and related lepidopterans, and will outline genetic engineering technologies which might be used to design efficient ncRNA-based pest control strategies. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Luis María Vaschetto
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Córdoba, Argentina.,Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba (FCEFyN, UNC), Córdoba, Argentina
| | - Hernán Mario Beccacece
- Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba (FCEFyN, UNC), Córdoba, Argentina.,Instituto de Investigaciones Biológicas y Tecnológicas Consejo Nacional de Investigaciones Científicas y Técnicas (IIByT, CONICET), Córdoba, Argentina
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123
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NEAT1-TFE3 and KAT6A-TFE3 renal cell carcinomas, new members of MiT family translocation renal cell carcinoma. Mod Pathol 2019; 32:710-716. [PMID: 30622287 PMCID: PMC6486435 DOI: 10.1038/s41379-018-0191-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 12/31/2022]
Abstract
Microphthalmia-associated transcription factor (MiT) family translocation renal cell carcinoma harbors variable gene fusions involving either TFE3 or TFEB genes. Multiple 5' fusion partners for TFE3 have been reported, including ASPSCR1, CLTC, DVL2, LUC7L3, KHSRP, PRCC, PARP14, NONO, SFPQ1, MED15, and RBM10. Each of these fusion genes activates TFE3 transcription which can be detected by immunostaining. Using targeted RNA-sequencing, TFE3 fusion gene partners were identified in 5 cases of TFE3 immunohistochemistry positive translocation renal cell carcinoma. Three cases demonstrated known fusions: ASPSCR1-TFE3, MED15-TFE3 and RBM10-TFE3. However, two cases showed unreported NEAT1-TFE3 and KAT6A-TFE3 fusion transcripts. The NEAT1-TFE3 RCC arose in a 59-year-old male; which demonstrated overlapping morphological features seen in NEAT2(MALAT1)-TFEB t(6;11) renal cell carcinoma, including biphasic alveolar/nested tumor cells with eosinophilic cytoplasm. The KAT6A-TFE3 renal cell carcinoma demonstrated typical morphological features of TFE3/Xp11 renal cell carcinoma including papillae, eosinophilic cytoplasm with focal clearing and abundant psammoma bodies. KAT6A gene fusion was reported in some cases of acute myeloid leukemia, which has not been previously reported in solid tumors. This report highlights the genetic complexity of TFE3 translocation renal cell carcinoma; and RNA-sequencing is a powerful approach for elucidating the underlying genetic alterations.
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124
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Hirose T, Yamazaki T, Nakagawa S. Molecular anatomy of the architectural NEAT1 noncoding RNA: The domains, interactors, and biogenesis pathway required to build phase-separated nuclear paraspeckles. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1545. [PMID: 31044562 DOI: 10.1002/wrna.1545] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) are extremely diverse and have various significant physiological functions. lncRNAs generally associate with specific sets of RNA-binding proteins (RBPs) to form functional ribonucleoprotein (RNP) complexes. NEAT1 is a highly abundant lncRNA in the mammalian cell nucleus that associates with specific RBPs to form NEAT1 RNPs. Intriguingly, cellular NEAT1 RNPs are extraordinarily large and can be detected using an optical microscope. These gigantic RNPs, so-called paraspeckles, are a type of membraneless nuclear body. Paraspeckles contain approximately 50 NEAT1 RNA molecules together with characteristic RBPs possessing aggregation-prone prion-like domains. Paraspeckle formation proceeds on the nascent NEAT1 transcript in conjunction with NEAT1 biogenesis, which exhibits various features that differ from those exhibited by mRNA biogenesis, including a lack of introns, noncanonical 3' end formation, and nuclear retention. These unique features may be required for the mechanism of paraspeckle formation. NEAT1 possesses three distinct RNA domains (A, B, and C), which function in stabilization (A), isoform switching (B), and paraspeckle assembly (C). In particular, the central C domain contains smaller subdomains that are high-affinity binding sites for the essential paraspeckle proteins (NONO and SFPQ) that subsequently polymerize along NEAT1. Subsequent recruitment of additional essential PSPs (FUS and RBM14) induces liquid-liquid phase separation to build a massive paraspeckle structure. Thus, the molecular anatomy of the NEAT1 arcRNA provides an ideal model to understand how lncRNAs form the functional RNP machinery. This article is characterized under: RNA Export and Localization > Nuclear Export/Import RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Tetsuro Hirose
- Laboratory of RNA Biofucntion, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tomohiro Yamazaki
- Laboratory of RNA Biofucntion, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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125
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Shields EJ, Petracovici AF, Bonasio R. lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. Biochem J 2019; 476:1083-1104. [PMID: 30971458 PMCID: PMC6745715 DOI: 10.1042/bcj20180440] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/28/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts that do not code for proteins, but nevertheless exert regulatory effects on various biochemical pathways, in part via interactions with proteins, DNA, and other RNAs. LncRNAs are thought to regulate transcription and other biological processes by acting, for example, as guides that target proteins to chromatin, scaffolds that facilitate protein-protein interactions and complex formation, and orchestrators of phase-separated compartments. The study of lncRNAs has reached an exciting time, as recent advances in experimental and computational methods allow for genome-wide interrogation of biochemical and biological mechanisms of these enigmatic transcripts. A better appreciation for the biochemical versatility of lncRNAs has allowed us to begin closing gaps in our knowledge of how they act in diverse cellular and organismal contexts, including development and disease.
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Affiliation(s)
- Emily J Shields
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Ana F Petracovici
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A.
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
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126
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Harries LW. RNA Biology Provides New Therapeutic Targets for Human Disease. Front Genet 2019; 10:205. [PMID: 30906315 PMCID: PMC6418379 DOI: 10.3389/fgene.2019.00205] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
RNA is the messenger molecule that conveys information from the genome and allows the production of biomolecules required for life in a responsive and regulated way. Most genes are able to produce multiple mRNA products in response to different internal or external environmental signals, in different tissues and organs, and at specific times in development or later life. This fine tuning of gene expression is dependent on the coordinated effects of a large and intricate set of regulatory machinery, which together orchestrate the genomic output at each locus and ensure that each gene is expressed at the right amount, at the right time and in the correct location. This complexity of control, and the requirement for both sequence elements and the entities that bind them, results in multiple points at which errors may occur. Errors of RNA biology are common and found in association with both rare, single gene disorders, but also more common, chronic diseases. Fortunately, complexity also brings opportunity. The existence of many regulatory steps also offers multiple levels of potential therapeutic intervention which can be exploited. In this review, I will outline the specific points at which coding RNAs may be regulated, indicate potential means of intervention at each stage, and outline with examples some of the progress that has been made in this area. Finally, I will outline some of the remaining challenges with the delivery of RNA-based therapeutics but indicate why there are reasons for optimism.
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Affiliation(s)
- Lorna W. Harries
- RNA-Mediated Mechanisms of Disease, College of Medicine and Health, The Institute of Biomedical and Clinical Science, Medical School, University of Exeter, Exeter, United Kingdom
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127
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Bajc Česnik A, Darovic S, Prpar Mihevc S, Štalekar M, Malnar M, Motaln H, Lee YB, Mazej J, Pohleven J, Grosch M, Modic M, Fonovič M, Turk B, Drukker M, Shaw CE, Rogelj B. Nuclear RNA foci from C9ORF72 expansion mutation form paraspeckle-like bodies. J Cell Sci 2019; 132:jcs.224303. [PMID: 30745340 DOI: 10.1242/jcs.224303] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/31/2019] [Indexed: 12/12/2022] Open
Abstract
The GGGGCC (G4C2) repeat expansion mutation in the C9ORF72 gene is the most common genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Transcription of the repeat and formation of nuclear RNA foci, which sequester specific RNA-binding proteins, is one of the possible pathological mechanisms. Here, we show that (G4C2) n repeat RNA predominantly associates with essential paraspeckle proteins SFPQ, NONO, RBM14, FUS and hnRNPH and colocalizes with known paraspeckle-associated RNA hLinc-p21. As formation of paraspeckles in motor neurons has been associated with early phases of ALS, we investigated the extent of similarity between paraspeckles and (G4C2) n RNA foci. Overexpression of (G4C2)72 RNA results in their increased number and colocalization with SFPQ-stained nuclear bodies. These paraspeckle-like (G4C2)72 RNA foci form independently of the known paraspeckle scaffold, the long non-coding RNA NEAT1 Moreover, the knockdown of SFPQ protein in C9ORF72 expansion mutation-positive fibroblasts significantly reduces the number of (G4C2) n RNA foci. In conclusion, (G4C2) n RNA foci have characteristics of paraspeckles, which suggests that both RNA foci and paraspeckles play roles in FTD and ALS, and implies approaches for regulation of their formation.
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Affiliation(s)
- Ana Bajc Česnik
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia.,Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Simona Darovic
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia.,Biomedical Research Institute BRIS, Ljubljana 1000, Slovenia
| | - Sonja Prpar Mihevc
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia
| | - Maja Štalekar
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia.,Biomedical Research Institute BRIS, Ljubljana 1000, Slovenia
| | - Mirjana Malnar
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia.,Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Helena Motaln
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia
| | - Youn-Bok Lee
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 9RT, UK
| | - Julija Mazej
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Jure Pohleven
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia
| | - Markus Grosch
- Helmholtz Center Munich, Institute of Stem Cell Research, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Miha Modic
- Helmholtz Center Munich, Institute of Stem Cell Research, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Marko Fonovič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana 1000, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana 1000, Slovenia
| | - Micha Drukker
- Helmholtz Center Munich, Institute of Stem Cell Research, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 9RT, UK
| | - Boris Rogelj
- Department of Biotechnology, Jozef Stefan Institute, Ljubljana 1000, Slovenia .,Biomedical Research Institute BRIS, Ljubljana 1000, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia
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128
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Pyfrom SC, Luo H, Payton JE. PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities. BMC Genomics 2019; 20:137. [PMID: 30767760 PMCID: PMC6377765 DOI: 10.1186/s12864-019-5497-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/29/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA's functional versatility includes epigenetic modification, nuclear domain organization, transcriptional control, regulation of RNA splicing and translation, and modulation of protein activity. However, most lncRNAs remain uncharacterized due to a shortage of predictive tools available to guide functional experiments. RESULTS To address this gap for lymphoma-associated lncRNAs identified in our studies, we developed a new computational method, Predicting LncRNA Activity through Integrative Data-driven 'Omics and Heuristics (PLAIDOH), which has several unique features not found in other methods. PLAIDOH integrates transcriptome, subcellular localization, enhancer landscape, genome architecture, chromatin interaction, and RNA-binding (eCLIP) data and generates statistically defined output scores. PLAIDOH's approach identifies and ranks functional connections between individual lncRNA, coding gene, and protein pairs using enhancer, transcript cis-regulatory, and RNA-binding protein interactome scores that predict the relative likelihood of these different lncRNA functions. When applied to 'omics datasets that we collected from lymphoma patients, or to publicly available cancer (TCGA) or ENCODE datasets, PLAIDOH identified and prioritized well-known lncRNA-target gene regulatory pairs (e.g., HOTAIR and HOX genes, PVT1 and MYC), validated hits in multiple lncRNA-targeted CRISPR screens, and lncRNA-protein binding partners (e.g., NEAT1 and NONO). Importantly, PLAIDOH also identified novel putative functional interactions, including one lymphoma-associated lncRNA based on analysis of data from our human lymphoma study. We validated PLAIDOH's predictions for this lncRNA using knock-down and knock-out experiments in lymphoma cell models. CONCLUSIONS Our study demonstrates that we have developed a new method for the prediction and ranking of functional connections between individual lncRNA, coding gene, and protein pairs, which were validated by genetic experiments and comparison to published CRISPR screens. PLAIDOH expedites validation and follow-on mechanistic studies of lncRNAs in any biological system. It is available at https://github.com/sarahpyfrom/PLAIDOH .
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Affiliation(s)
- Sarah C. Pyfrom
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Hong Luo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Jacqueline E. Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
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129
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Prinz F, Kapeller A, Pichler M, Klec C. The Implications of the Long Non-Coding RNA NEAT1 in Non-Cancerous Diseases. Int J Mol Sci 2019; 20:ijms20030627. [PMID: 30717168 PMCID: PMC6387324 DOI: 10.3390/ijms20030627] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/10/2019] [Accepted: 01/29/2019] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in a variety of biological and cellular processes as well as in physiologic and pathophysiologic events. This review summarizes recent literature about the role of the lncRNA nuclear enriched abundant transcript 1 (NEAT1) in non-cancerous diseases with a special focus on viral infections and neurodegenerative diseases. In contrast to its role as competing endogenous RNA (ceRNA) in carcinogenesis, NEAT1's function in non-cancerous diseases predominantly focuses on paraspeckle-mediated effects on gene expression. This involves processes such as nuclear retention of mRNAs or sequestration of paraspeckle proteins from specific promoters, resulting in transcriptional induction or repression of genes involved in regulating the immune system or neurodegenerative processes. NEAT1 expression is aberrantly-mostly upregulated-in non-cancerous pathological conditions, indicating that it could serve as potential prognostic biomarker. Additional studies are needed to elucidate NEAT1's capability to be a therapeutic target for non-cancerous diseases.
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Affiliation(s)
- Felix Prinz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Medical University of Graz, 8010 Graz, Austria.
| | - Anita Kapeller
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Medical University of Graz, 8010 Graz, Austria.
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Medical University of Graz, 8010 Graz, Austria.
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
| | - Christiane Klec
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Medical University of Graz, 8010 Graz, Austria.
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130
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Zhou B, Wu F, Han J, Qi F, Ni T, Qian F. Exploitation of nuclear protein SFPQ by the encephalomyocarditis virus to facilitate its replication. Biochem Biophys Res Commun 2019; 510:65-71. [PMID: 30661786 DOI: 10.1016/j.bbrc.2019.01.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 01/07/2019] [Indexed: 11/25/2022]
Abstract
The encephalomyocarditis virus (EMCV) is a single-stranded RNA virus that induces sudden death, diabetes, myocarditis and nervous disorders in non-human primates. The rapid development of xenografts such as heart transplantation from pig to human raises the issue of EMCV safety in human cells. SFPQ, a proline and glutamine rich splicing factor that participates in diverse molecular functions including paraspeckle formation, microRNA synthesis and transcription regulation, is known to regulate host innate immune response to viruses. However, the role of SFPQ in EMCV infection remains unclear. Here we reported that the SFPQ was essential for EMCV replication. Depletion of SFPQ impaired EMCV production, while forced expression of SFPQ promoted viral replication. Mechanistically, loss of SFPQ affected the transcription profile of host mitochondria pathway related genes. In addition, cellular SFPQ was exploited by EMCV and accumulated in cytoplasm and it interacted with eukaryotic initiation factors and ribosomal proteins to facilitate internal ribosome entry site (IRES)-dependent translation of EMCV protein. Altogether, our work discovered host SFPQ as a new target to inhibit EMCV replication and infection.
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Affiliation(s)
- Bin Zhou
- Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China; State Key Laboratory of Genetic Engineering & MOE Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, PR China
| | - Fangyi Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Jingxuan Han
- Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Fei Qi
- Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering & MOE Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, PR China.
| | - Feng Qian
- Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China.
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131
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An H, Skelt L, Notaro A, Highley JR, Fox AH, La Bella V, Buchman VL, Shelkovnikova TA. ALS-linked FUS mutations confer loss and gain of function in the nucleus by promoting excessive formation of dysfunctional paraspeckles. Acta Neuropathol Commun 2019; 7:7. [PMID: 30642400 PMCID: PMC6330737 DOI: 10.1186/s40478-019-0658-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/07/2019] [Indexed: 12/13/2022] Open
Abstract
Mutations in the FUS gene cause amyotrophic lateral sclerosis (ALS-FUS). Mutant FUS is known to confer cytoplasmic gain of function but its effects in the nucleus are less understood. FUS is an essential component of paraspeckles, subnuclear bodies assembled on a lncRNA NEAT1. Paraspeckles may play a protective role specifically in degenerating spinal motor neurons. However it is still unknown how endogenous levels of mutant FUS would affect NEAT1/paraspeckles. Using novel cell lines with the FUS gene modified by CRISPR/Cas9 and human patient fibroblasts, we found that endogenous levels of mutant FUS cause accumulation of NEAT1 isoforms and paraspeckles. However, despite only mild cytoplasmic mislocalisation of FUS, paraspeckle integrity is compromised in these cells, as confirmed by reduced interaction of mutant FUS with core paraspeckle proteins NONO and SFPQ and increased NEAT1 extractability. This results in NEAT1 localisation outside paraspeckles, especially prominent under conditions of paraspeckle-inducing stress. Consistently, paraspeckle-dependent microRNA production, a readout for functionality of paraspeckles, is impaired in cells expressing mutant FUS. In line with the cellular data, we observed paraspeckle hyper-assembly in spinal neurons of ALS-FUS patients. Therefore, despite largely preserving its nuclear localisation, mutant FUS leads to loss (dysfunctional paraspeckles) and gain (excess of free NEAT1) of function in the nucleus. Perturbed fine structure and functionality of paraspeckles accompanied by accumulation of non-paraspeckle NEAT1 may contribute to the disease severity in ALS-FUS.
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Affiliation(s)
- Haiyan An
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX UK
| | - Lucy Skelt
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX UK
| | - Antonietta Notaro
- ALS Clinical Research Center and Laboratory of Neurochemistry, Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - J. Robin Highley
- The Sheffield Institute for Translational Neuroscience, Sheffield, S10 2HQ UK
| | - Archa H. Fox
- School of Human Sciences, School of Molecular Sciences and Harry Perkins Institute of Medical Research, University of Western Australia, Crawley, 6009 Australia
| | - Vincenzo La Bella
- ALS Clinical Research Center and Laboratory of Neurochemistry, Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - Vladimir L. Buchman
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX UK
- Institute of Physiologically Active Compounds RAS, Chernogolovka, Russian Federation 142432
| | - Tatyana A. Shelkovnikova
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX UK
- Institute of Physiologically Active Compounds RAS, Chernogolovka, Russian Federation 142432
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT UK
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132
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Bofill-De Ros X, Kasprzak WK, Bhandari Y, Fan L, Cavanaugh Q, Jiang M, Dai L, Yang A, Shao TJ, Shapiro BA, Wang YX, Gu S. Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires. Cell Rep 2019; 26:447-459.e4. [PMID: 30625327 PMCID: PMC6369706 DOI: 10.1016/j.celrep.2018.12.054] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/11/2018] [Accepted: 12/11/2018] [Indexed: 12/16/2022] Open
Abstract
MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low-grade glioma patient samples indicate that the alternative-miR-9 has a potential role in tumor progression. Furthermore, we provide evidence that distortion of pri-miRNA stems induced by asymmetric internal loops correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing.
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Affiliation(s)
- Xavier Bofill-De Ros
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wojciech K Kasprzak
- Basic Science Program, RNA Biology Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Yuba Bhandari
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Lixin Fan
- Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Quinn Cavanaugh
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Minjie Jiang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisheng Dai
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Acong Yang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Tie-Juan Shao
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Bruce A Shapiro
- RNA Structure and Design Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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133
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression. Precursor miRNA molecules undergo nuclear and cytoplasmic processing events, carried out by the endoribonucleases DROSHA and DICER, respectively, to produce mature miRNAs that are loaded onto the RISC (RNA-induced silencing complex) to exert their biological function. Regulation of mature miRNA levels is critical in development, differentiation, and disease, as demonstrated by multiple levels of control during their biogenesis cascade. Here, we will focus on post-transcriptional mechanisms and will discuss the impact of cis-acting sequences in precursor miRNAs, as well as trans-acting factors that bind to these precursors and influence their processing. In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and function.
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Affiliation(s)
- Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Zhejiang 314400, P.R. China
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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134
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Cheng C, Spengler RM, Keiser MS, Monteys AM, Rieders JM, Ramachandran S, Davidson BL. The long non-coding RNA NEAT1 is elevated in polyglutamine repeat expansion diseases and protects from disease gene-dependent toxicities. Hum Mol Genet 2018; 27:4303-4314. [PMID: 30239724 PMCID: PMC6276831 DOI: 10.1093/hmg/ddy331] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 12/28/2022] Open
Abstract
Polyglutamine (polyQ) repeat diseases are a class of neurodegenerative disorders caused by CAG-repeat expansion. There are diverse cellular mechanisms behind the pathogenesis of polyQ disorders, including transcriptional dysregulation. Interestingly, we find that levels of the long isoform of nuclear paraspeckle assembly transcript 1 (Neat1L) are elevated in the brains of mouse models of spinocerebellar ataxia types 1, 2, 7 and Huntington's disease (HD). Neat1L was also elevated in differentiated striatal neurons derived from HD knock-in mice and in HD patient brains. The elevation was mutant Huntingtin (mHTT) dependent, as knockdown of mHTT in vitro and in vivo restored Neat1L to normal levels. In additional studies, we found that Neat1L is repressed by methyl CpG binding protein 2 (MeCP2) by RNA-protein interaction but not by occupancy of MeCP2 at its promoter. We also found that NEAT1L overexpression protects from mHTT-induced cytotoxicity, while reducing it enhanced mHTT-dependent toxicity. Gene set enrichment analysis of previously published RNA sequencing data from mouse embryonic fibroblasts and cells derived from HD patients shows that loss of NEAT1L impairs multiple cellular functions, including pathways involved in cell proliferation and development. Intriguingly, the genes dysregulated in HD human brain samples overlap with pathways affected by a reduction in NEAT1, confirming the correlation of NEAT1L and HD-induced perturbations. Cumulatively, the role of NEAT1L in polyQ disease model systems and human tissues suggests that it may play a protective role in CAG-repeat expansion diseases.
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Affiliation(s)
- Congsheng Cheng
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ryan M Spengler
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Megan S Keiser
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alejandro Mas Monteys
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julianne M Rieders
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shyam Ramachandran
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA, USA
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135
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Vito D, Smales CM. Engineering of the cellular translational machinery and non-coding RNAs to enhance CHO cell growth, recombinant product yields and quality. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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136
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Trabucchi M, Mategot R. Subcellular Heterogeneity of the microRNA Machinery. Trends Genet 2018; 35:15-28. [PMID: 30503571 DOI: 10.1016/j.tig.2018.10.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/20/2018] [Accepted: 10/26/2018] [Indexed: 01/09/2023]
Abstract
Different methods have recently been developed to understand the subcellular localization and role of microRNAs (miRNAs) as well as small RNAs associated with Argonaute (AGO) proteins. The heterogeneity of the protein complexes associated with miRNAs, along with their subcellular localization, provides clues into their biochemical mechanism of function. Subcellular diversity indicates that miRNAs localized to different cellular regions could have different functions, including transcriptional regulation on chromatin or post-transcriptional control, providing global regulation of gene expression by miRNAs. Herein, I review the current knowledge and most recent discoveries relating to the subcellular function of miRNAs and other AGO-associated small RNAs, revealing the emergence of a multitude of functions of the miRNA pathway to control different steps of the gene expression program(s).
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Affiliation(s)
- Michele Trabucchi
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France.
| | - Raphael Mategot
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France
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137
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An H, Williams NG, Shelkovnikova TA. NEAT1 and paraspeckles in neurodegenerative diseases: A missing lnc found? Noncoding RNA Res 2018; 3:243-252. [PMID: 30533572 PMCID: PMC6257911 DOI: 10.1016/j.ncrna.2018.11.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases are among the most common causes of disability worldwide. Although neurodegenerative diseases are heterogeneous in both their clinical features and the underlying physiology, they are all characterised by progressive loss of specific neuronal populations. Recent experimental evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the CNS in health and disease. Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) is an abundant, ubiquitously expressed lncRNA, which forms a scaffold for a specific RNA granule in the nucleus, or nuclear body, the paraspeckle. Paraspeckles act as molecular hubs for cellular processes commonly affected by neurodegeneration. Transcriptomic analyses of the diseased human tissue have revealed altered NEAT1 levels in the CNS in major neurodegenerative disorders as well as in some disease models. Although it is clear that changes in NEAT1 expression (and in some cases, paraspeckle assembly) accompany neuronal damage, our understanding of NEAT1 contribution to the disease pathogenesis is still rudimentary. In this review, we have summarised the available knowledge on NEAT1 involvement in the molecular processes linked to neurodegeneration and on NEAT1 dysregulation in this type of disease, with a special focus on amyotrophic lateral sclerosis. The goal of this review is to attract the attention of researchers in the field of neurodegeneration to NEAT1 and paraspeckles.
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Affiliation(s)
- Haiyan An
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Non G Williams
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Tatyana A Shelkovnikova
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
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138
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Sawyer IA, Sturgill D, Dundr M. Membraneless nuclear organelles and the search for phases within phases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1514. [DOI: 10.1002/wrna.1514] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/20/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Iain A. Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School Rosalind Franklin University of Medicine and Science North Chicago Illinois
- Laboratory of Receptor Biology and Gene Expression National Cancer Institute, National Institutes of Health Bethesda Maryland
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression National Cancer Institute, National Institutes of Health Bethesda Maryland
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School Rosalind Franklin University of Medicine and Science North Chicago Illinois
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139
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Nakagawa S, Yamazaki T, Hirose T. Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu. Open Biol 2018; 8:rsob.180150. [PMID: 30355755 PMCID: PMC6223218 DOI: 10.1098/rsob.180150] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/27/2018] [Indexed: 02/06/2023] Open
Abstract
Paraspeckles are nuclear bodies built on an architectural long noncoding RNA, NEAT1, and a series of studies have revealed their molecular components, fine internal structures and cellular and physiological functions. Emerging lines of evidence suggest that paraspeckle formation is elicited by phase separation of associating RNA-binding proteins containing intrinsically disordered regions, which induce ordered arrangement of paraspeckle components along NEAT1. In this review, we will summarize the history of paraspeckle research over the last couple of decades, especially focusing on the function and structure of the nuclear bodies. We also discuss the future directions of research on long noncoding RNAs that form ‘RNP milieux’, large and flexible phase-separated ribonucleoprotein complexes.
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Affiliation(s)
- Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
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140
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Li BJ, Jiang DL, Meng ZN, Zhang Y, Zhu ZX, Lin HR, Xia JH. Genome-wide identification and differentially expression analysis of lncRNAs in tilapia. BMC Genomics 2018; 19:729. [PMID: 30286721 PMCID: PMC6172845 DOI: 10.1186/s12864-018-5115-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022] Open
Abstract
Background Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited. Results Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs. Conclusions This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia. Electronic supplementary material The online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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141
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Treiber T, Treiber N, Meister G. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Nat Rev Mol Cell Biol 2018; 20:5-20. [DOI: 10.1038/s41580-018-0059-1] [Citation(s) in RCA: 628] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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142
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Yong W, Yu D, Jun Z, Yachen D, Weiwei W, Midie X, Xingzhu J, Xiaohua W. Long noncoding RNA NEAT1, regulated by LIN28B, promotes cell proliferation and migration through sponging miR-506 in high-grade serous ovarian cancer. Cell Death Dis 2018; 9:861. [PMID: 30154460 PMCID: PMC6113267 DOI: 10.1038/s41419-018-0908-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/06/2018] [Accepted: 07/22/2018] [Indexed: 02/07/2023]
Abstract
The aberrant expression of long noncoding RNAs (lncRNAs) has been reported frequently in specific cancers, including high-grade serous ovarian cancer (HGSOC). The purpose of the present study was to explore the clinical significance and underlying mechanisms of a significantly dysregulated lncRNA (NEAT1) in HGSOC. Our results showed that elevated NEAT1 expression in human HGSOC specimens correlated with a poor prognosis. Functional experiments demonstrated that knockdown of NEAT1 significantly prohibited ovarian cancer cell proliferation and invasion in vitro and restrained tumor growth in vivo. LIN28B was identified by bioinformatics analysis along with experimental evidence as a direct actor that enhanced NEAT1 stability. A rescue functional assay confirmed that the LIN28B/NEAT1 axis contributed to oncogenic functions in ovarian cancer cells. Moreover, gene expression profile data and dual luciferase reporter assay results demonstrated that NEAT1 functioned as a competing endogenous RNA (ceRNA) for miR-506 to promote cell proliferation and migration. Taken together, our results showed that NEAT1, stabilized by LIN28B, promoted HGSOC progression by sponging miR-506. Thus, NEAT1 can be regarded as a vital diagnostic biomarker for HGSOC and a therapeutic target.
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Affiliation(s)
- Wu Yong
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Deng Yu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhu Jun
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Duan Yachen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weng Weiwei
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xu Midie
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ju Xingzhu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wu Xiaohua
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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143
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Wang S, Zhang Q, Wang Q, Shen Q, Chen X, Li Z, Zhou Y, Hou J, Xu B, Li N, Cao X. NEAT1 paraspeckle promotes human hepatocellular carcinoma progression by strengthening IL-6/STAT3 signaling. Oncoimmunology 2018; 7:e1503913. [PMID: 30377567 DOI: 10.1080/2162402x.2018.1503913] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
The formation of paraspeckle, a stress-induced nuclear body, increases in response to viral infection or proinflammatory stimuli. Paraspeckle consists of lncRNA (nuclear paraspeckle assembly transcript 1, NEAT1) and protein components including NONO, SFPQ, PSPC1, etc., which are shown to be involved in viral infection and cancer. Both NEAT1 and NONO expression increase in human hepatocellular carcinoma (HCC) samples according to TCGA data. However, the role of paraspeckle in HCC progression needs further identification. IL-6 signaling is well known to contribute to HCC progression. Here we reported that IL-6 signaling increased paraspeckle formation in HCC cells. Destruction of paraspeckle formation by silencing the paraspeckle essential components NEAT1_2 or NONO could suppress IL-6-induced STAT3 phosphorylation in HCC cells, and consequently repressed IL-6-promoted in vitro HCC cell invasion, cell cycle progression and survival. Mechanistically, paraspeckle promotes IL-6-induced STAT3 phosphorylation by binding and trapping peroxiredoxin-5 (PRDX5) mRNA in nucleus, decreasing protein level of PRDX5 which can directly interact with STAT3 and inhibit STAT3 phosphorylation. Besides, glutathione S-transferase P (GSTP1) protein, which inhibits DNA damage and apoptosis through its detoxification and anti-oxidation function, was also trapped within paraspeckles under IL-6 stimulation. Paraspeckle-trapping of both PRDX5 mRNA and GSTP1 protein contributes to IL-6-increased DNA damage in HCC cells. Our results demonstrate that paraspeckle can nuclear entrap the inhibitors of IL-6/STAT3 signaling as well as DNA damage, and then strengthen the promoting effect on HCC progression by IL-6. Therefore, paraspeckle contributes to the inflammation-related HCC progression and might be a potential therapeutic target for HCC.
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Affiliation(s)
- Shuai Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Zhang
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Qinlan Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Qicong Shen
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Xiang Chen
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Zhenyang Li
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Ye Zhou
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Jin Hou
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Bowen Xu
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Nan Li
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China.,National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
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144
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Mello SS, Attardi LD. Neat-en-ing up our understanding of p53 pathways in tumor suppression. Cell Cycle 2018; 17:1527-1535. [PMID: 29895201 DOI: 10.1080/15384101.2018.1464835] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
Although the p53 transcription factor has a well-established role in tumor suppression, little is known about how the non-coding targets of p53 mediate its tumor suppression function. Analysis of ncRNAs regulated by p53 revealed Neat1 as a direct p53 target gene. Neat1 has physiological roles in the development and differentiation of the mammary gland and corpus luteum, but its roles in cancer have been conflicting. To unequivocally understand Neat1 function in cancer, we used Neat1 null mice. Interestingly, we found that Neat1 deficiency promotes transformation both in oncogene-expressing fibroblasts and in a mouse model for pancreatic cancer. Specifically, Neat1 loss in the pancreas results in the enhanced development of preneoplastic lesions associated with dampened expression of differentiation genes. While the exact mechanisms underlying tumor suppression are unknown, there are several described mechanisms that may be responsible for Neat1-mediated tumor suppression. Collectively, these findings suggest that Neat1 enforces differentiation to suppress pancreatic cancer.
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Affiliation(s)
- Stephano Spano Mello
- a Department of Radiation Oncology , Stanford University School of Medicine , Stanford , CA , USA
| | - Laura Donatella Attardi
- a Department of Radiation Oncology , Stanford University School of Medicine , Stanford , CA , USA.,b Stanford Cancer Institute , Stanford University School of Medicine , Stanford , CA , USA.,c Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
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145
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Yang S, Sun Z, Zhou Q, Wang W, Wang G, Song J, Li Z, Zhang Z, Chang Y, Xia K, Liu J, Yuan W. MicroRNAs, long noncoding RNAs, and circular RNAs: potential tumor biomarkers and targets for colorectal cancer. Cancer Manag Res 2018; 10:2249-2257. [PMID: 30100756 PMCID: PMC6065600 DOI: 10.2147/cmar.s166308] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Noncoding RNAs (ncRNAs) can be divided into microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), pRNAs, and tRNAs. Traditionally, miRNAs exert their biological function mainly through the inhibition of translation via the induction of target RNA transcript degradation. lncRNAs and circRNAs were once considered to have no potential to code proteins. Here, we will review the current knowledge on ncRNAs in relation to their origins, characteristics, and functions. We will also review how ncRNAs work as competitive endogenous RNA, gene transcription and expression regulators, and RNA-binding protein sponges in colorectal cancer (CRC). Notably, except for the abovementioned mechanisms, recent advances revealed that lncRNAs can also act as the precursor of miRNAs, and a small portion of lncRNAs and circRNAs was verified to have the potential to code proteins, providing new evidence for the significance of ncRNAs in CRC tumorigenesis and development.
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Affiliation(s)
- Shuaixi Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Quanbo Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China.,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan 450002, People's Republic of China
| | - Guixian Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Junmin Song
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhen Li
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhiyong Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Yuan Chang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Kunkun Xia
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
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146
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Prospects of Noncoding RNAs in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6579436. [PMID: 30148169 PMCID: PMC6083484 DOI: 10.1155/2018/6579436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/16/2018] [Accepted: 06/06/2018] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a global health problem and one of the most common malignant tumors. Recent studies have shown that noncoding RNAs (ncRNAs) contribute to the pathogenesis of hepatocellular carcinoma (HCC). These RNAs may be involved in a variety of pathological processes such as cell proliferation, apoptosis, angiogenesis, invasion, and metastasis. In addition, abnormal expression of ncRNAs in HCC may provide potential prognostic or diagnostic biomarkers. This review provides an overview of the role and potential applications of ncRNAs, miRNAs, lncRNAs, circRNAs, and snoRNAs in liver cancer.
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147
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Spreafico M, Grillo B, Rusconi F, Battaglioli E, Venturin M. Multiple Layers of CDK5R1 Regulation in Alzheimer's Disease Implicate Long Non-Coding RNAs. Int J Mol Sci 2018; 19:ijms19072022. [PMID: 29997370 PMCID: PMC6073344 DOI: 10.3390/ijms19072022] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 11/16/2022] Open
Abstract
Cyclin-dependent kinase 5 regulatory subunit 1 (CDK5R1) gene encodes for p35, the main activator of Cyclin-dependent kinase 5 (CDK5). The active p35/CDK5 complex is involved in numerous aspects of brain development and function, and its deregulation is closely associated to Alzheimer's disease (AD) onset and progression. We recently showed that miR-15/107 family can negatively regulate CDK5R1 expression modifying mRNA stability. Interestingly, miRNAs belonging to miR-15/107 family are downregulated in AD brain while CDK5R1 is upregulated. Long non-coding RNAs (lncRNAs) are emerging as master regulators of gene expression, including miRNAs, and their dysregulation has been implicated in the pathogenesis of AD. Here, we evaluated the existence of an additional layer of CDK5R1 expression regulation provided by lncRNAs. In particular, we focused on three lncRNAs potentially regulating CDK5R1 expression levels, based on existing data: NEAT1, HOTAIR, and MALAT1. We demonstrated that NEAT1 and HOTAIR negatively regulate CDK5R1 mRNA levels, while MALAT1 has a positive effect. We also showed that all three lncRNAs positively control miR-15/107 family of miRNAs. Moreover, we evaluated the expression of NEAT1, HOTAIR, and MALAT1 in AD and control brain tissues. Interestingly, NEAT1 displayed increased expression levels in temporal cortex and hippocampus of AD patients. Interestingly, we observed a strong positive correlation between CDK5R1 and NEAT1 expression levels in brain tissues, suggesting a possible neuroprotective role of NEAT1 in AD to compensate for increased CDK5R1 levels. Overall, our work provides evidence of another level of CDK5R1 expression regulation mediated by lncRNAs and points to NEAT1 as a biomarker, as well as a potential pharmacological target for AD therapy.
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Affiliation(s)
- Marco Spreafico
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
| | - Barbara Grillo
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
| | - Francesco Rusconi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
| | - Elena Battaglioli
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
- Istituto di Neuroscienze, CNR, Via Vanvitelli 32, 20129 Milano, Italy.
| | - Marco Venturin
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
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148
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Shelkovnikova TA, Kukharsky MS, An H, Dimasi P, Alexeeva S, Shabir O, Heath PR, Buchman VL. Protective paraspeckle hyper-assembly downstream of TDP-43 loss of function in amyotrophic lateral sclerosis. Mol Neurodegener 2018; 13:30. [PMID: 29859124 PMCID: PMC5984788 DOI: 10.1186/s13024-018-0263-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/25/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Paraspeckles are subnuclear bodies assembled on a long non-coding RNA (lncRNA) NEAT1. Their enhanced formation in spinal neurons of sporadic amyotrophic lateral sclerosis (ALS) patients has been reported but underlying mechanisms are unknown. The majority of ALS cases are characterized by TDP-43 proteinopathy. In current study we aimed to establish whether and how TDP-43 pathology may augment paraspeckle assembly. METHODS Paraspeckle formation in human samples was analysed by RNA-FISH and laser capture microdissection followed by qRT-PCR. Mechanistic studies were performed in stable cell lines, mouse primary neurons and human embryonic stem cell-derived neurons. Loss and gain of function for TDP-43 and other microRNA pathway factors were modelled by siRNA-mediated knockdown and protein overexpression. RESULTS We show that de novo paraspeckle assembly in spinal neurons and glial cells is a hallmark of both sporadic and familial ALS with TDP-43 pathology. Mechanistically, loss of TDP-43 but not its cytoplasmic accumulation or aggregation augments paraspeckle assembly in cultured cells. TDP-43 is a component of the microRNA machinery, and recently, paraspeckles have been shown to regulate pri-miRNA processing. Consistently, downregulation of core protein components of the miRNA pathway also promotes paraspeckle assembly. In addition, depletion of these proteins or TDP-43 results in accumulation of endogenous dsRNA and activation of type I interferon response which also stimulates paraspeckle formation. We demonstrate that human or mouse neurons in vitro lack paraspeckles, but a synthetic dsRNA is able to trigger their de novo formation. Finally, paraspeckles are protective in cells with compromised microRNA/dsRNA metabolism, and their assembly can be promoted by a small-molecule microRNA enhancer. CONCLUSIONS Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.
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Affiliation(s)
| | - Michail S Kukharsky
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
| | - Haiyan An
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Pasquale Dimasi
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Svetlana Alexeeva
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Osman Shabir
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Paul R Heath
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Vladimir L Buchman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
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149
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Creugny A, Fender A, Pfeffer S. Regulation of primary microRNA processing. FEBS Lett 2018; 592:1980-1996. [PMID: 29683487 DOI: 10.1002/1873-3468.13067] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNAs) are evolutionarily conserved small regulatory RNAs that participate in the adjustment of many, if not all, fundamental biological processes. Molecular mechanisms involved in miRNA biogenesis and mode of action have been elucidated in the past two decades. Similar to many cellular pathways, miRNA processing and function can be globally or specifically regulated at several levels and by numerous proteins and RNAs. Given their role as fine-tuning molecules, it is essential for miRNA expression to be tightly regulated in order to maintain cellular homeostasis. Here, we review our current knowledge of the first step of their maturation occurring in the nucleus and how it can be specifically and dynamically modulated.
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Affiliation(s)
- Antoine Creugny
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
| | - Aurélie Fender
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
| | - Sébastien Pfeffer
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
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150
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Paraspeckles: Where Long Noncoding RNA Meets Phase Separation. Trends Biochem Sci 2018; 43:124-135. [DOI: 10.1016/j.tibs.2017.12.001] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 12/26/2022]
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