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Brusati A, Ratti A, Pensato V, Peverelli S, Gentilini D, Dalla Bella E, Sorce MN, Meneri M, Gagliardi D, Corti S, Gellera C, Lauria Pinter G, Ticozzi N, Silani V. Analysis of miRNA rare variants in amyotrophic lateral sclerosis and in silico prediction of their biological effects. Front Genet 2022; 13:1055313. [PMID: 36568378 PMCID: PMC9768194 DOI: 10.3389/fgene.2022.1055313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting upper and/or lower motor neurons and characterized by complex etiology. Familial cases show high genetic heterogeneity and sporadic cases (90%) are associated with several genetic and environmental risk factors. Among the genetic risk factors, the contribution of non-coding elements, such as microRNAs (miRNAs), to ALS disease susceptibility remains largely unexplored. Aim: This work aims to identify rare variants in miRNA genes in sporadic ALS (sALS) patients which may cause a defective miRNA maturation or altered target gene recognition by changing miRNA secondary structure or seed sequence, respectively. Methods: Rare variants located in miRNA loci with a minor allele frequency (MAF) < 0.01 were extracted from whole genome sequencing (WGS) data of 100 sALS patients. The secondary pre-miRNA structures were predicted using MiRVas to evaluate the impact of the variants on RNA folding process. Human TargetScan was used to retrieve all the potential target genes of miRNAs with variants in the seed region. Over Representation Analysis (ORA) was conducted to compare the lists of target genes for the reference and mutated miRNAs in the seed sequence. Results: Our analysis identified 86 rare variants in 77 distinct miRNAs and distributed in different parts of the miRNA precursors. The presence of these variants changed miRNA secondary structures in ∼70% of MiRVas predictions. By focusing on the 6 rare variants mapping within the seed sequence, the predicted target genes increased in number compared to the reference miRNA and included novel targets in a proportion ranging from 30 to 82%. Interestingly, ORA revealed significant changes in gene set enrichment only for mutated miR-509-1 and miR-941-3 for which the Gene Ontology term related to "nervous system development" was absent and present, respectively, compared to target lists of the reference miRNA. Conclusion: We here developed a workflow to study miRNA rare variants from WGS data and to predict their biological effects on miRNA folding, maturation and target gene recognition. Although this in silico approach certainly needs functional validation in vitro and in vivo, it may help define the role of miRNA variability in ALS and complex diseases.
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Affiliation(s)
- Alberto Brusati
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy,*Correspondence: Antonia Ratti,
| | - Viviana Pensato
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Silvia Peverelli
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Davide Gentilini
- Department Brain and Behavioral Sciences, University of Pavia, Pavia, Italy,Bioinformatics and Statistical Genomics Unit,IRCCS Istituto Auxologico Italiano,Milan,Italy
| | | | - Marta Nice Sorce
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Megi Meneri
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy,Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Delia Gagliardi
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Stefania Corti
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy,Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Cinzia Gellera
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Giuseppe Lauria Pinter
- Department Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy,Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
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2
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Luo B, Zhou K, Liufu Y, Huang X, Zeng H, Zhang Z. Novel insight into miRNA biology and its role in the pathogenesis of systemic lupus erythematosus. Front Immunol 2022; 13:1059887. [PMID: 36532020 PMCID: PMC9756849 DOI: 10.3389/fimmu.2022.1059887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022] Open
Abstract
MicroRNAs(miRNAs) have emerged as key regulators that control and influence gene expression as well as multiple biological processes depending on their potential binding sites in human-protein coding genes and other unconventional patterns, including coding for peptides, activating Toll-like receptors as a ligand, and other manners. Accumulating evidence has demonstrated that microRNA expression is tightly regulated during phases of development, differentiation, and effector functions of immune cells, immunological disorders of systemic lupus erythematosus (SLE). This review outlines the biogenesis of miRNAs and their unconventional functions as well as underlying cellular and molecular mechanisms. It then summarizes our current knowledge about how the biogenesis of miRNAs is regulated. Moreover, an overview was provided concerning the role of abnormal expression of miRNAs in lupus immune cells. In particular, we will shed some light on the recent advances in the role of miRNAs and exosome-derived miRNAs in immunological and epigenetic pathways in the pathogenesis of SLE.
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Affiliation(s)
- Baiwei Luo
- Department of Rheumatology and Immunology, Yuebei People’s Hospital Affifiliated to Shantou University Medical College, Shaoguan, Guangdong, China
| | - Kaixia Zhou
- Department of Rheumatology, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, Guangdong, China
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, China
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingcong Liufu
- Department of Anorectal, Shenzhen TCM Anorectal Hospital (Futian), Shenzhen, China
| | - Xia Huang
- Department of Xi Yuan Community Health Service Center, The Eighth Affifiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Huiqiong Zeng
- Department of Rheumatology, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, Guangdong, China
| | - Zhaoyang Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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3
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Shortridge MD, Olsen GL, Yang W, Walker MJ, Varani G. A Slow Dynamic RNA Switch Regulates Processing of microRNA-21. J Mol Biol 2022; 434:167694. [PMID: 35752213 PMCID: PMC10593484 DOI: 10.1016/j.jmb.2022.167694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 11/25/2022]
Abstract
The microRNAs are non-coding RNAs which post-transcriptionally regulate the expression of many eukaryotic genes, and whose dysregulation is a driver of human disease. Here we report the discovery of a very slow (0.1 s-1) conformational rearrangement at the Dicer cleavage site of pre-miR-21, which regulates the relative concentration of readily- and inefficiently-processed RNA structural states. We show that this dynamic switch is affected by single nucleotide mutations and can be biased by small molecule and peptide ligands, which can direct the microRNA to occupy the inefficiently processed state and reduce processing efficiency. This result reveals a new mechanism of RNA regulation and suggests a chemical approach to suppressing or activating pathogenic microRNAs by selective stabilization of their unprocessed or processed states.
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Affiliation(s)
| | - Greg L Olsen
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, Guangdong Province 518036, China
| | - Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA; Neoleukin Therapeutics, 188 East Blaine St, Suite 450, Seattle, WA 98102, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA.
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4
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Gonella-Diaza AM, Lopes E, Ribeiro da Silva K, Perecin Nociti R, Mamede Andrade G, Atuesta-Bustos JE, Coelho da Silveira J, Vieira Meirelles F, Binelli M. Steroidal Regulation of Oviductal microRNAs Is Associated with microRNA-Processing in Beef Cows. Int J Mol Sci 2021; 22:953. [PMID: 33477993 PMCID: PMC7835783 DOI: 10.3390/ijms22020953] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/21/2022] Open
Abstract
Information on molecular mechanisms through which sex-steroids regulate oviductal function to support early embryo development is lacking. Here, we hypothesized that the periovulatory endocrine milieu affects the miRNA processing machinery and miRNA expression in bovine oviductal tissues. Growth of the preovulatory follicle was controlled to obtain cows that ovulated a small follicle (SF) and subsequently bore a small corpus luteum (CL; SF-SCL) or a large follicle (LF) and large CL (LF-LCL). These groups differed in the periovulatory plasmatic sex-steroid's concentrations. Ampulla and isthmus samples were collected on day four of the estrous cycle. Abundance of DROSHA, DICER1, and AGO4 transcripts was greater in the ampulla than the isthmus. In the ampulla, transcription of these genes was greater for the SF-SCL group, while the opposite was observed in the isthmus. The expression of the 88 most abundant miRNAs and 14 miRNAs in the ampulla and 34 miRNAs in isthmus were differentially expressed between LF-LCL and SF-SCL groups. Integration of transcriptomic and miRNA data and molecular pathways enrichment showed that important pathways were inhibited in the SF-SCL group due to miRNA control. In conclusion, the endocrine milieu affects the miRNA expression in the bovine oviduct in a region-specific manner.
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Affiliation(s)
- Angela Maria Gonella-Diaza
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Marianna, FL 32446, USA;
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, 225, Avenida Duque de Caxias, Norte, Jardim, Elite, Pirassununga, SP 13635-900, Brazil; (E.L.); (K.R.d.S.)
| | - Everton Lopes
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, 225, Avenida Duque de Caxias, Norte, Jardim, Elite, Pirassununga, SP 13635-900, Brazil; (E.L.); (K.R.d.S.)
- Unianchieta, Av. Doutor Adoniro Ladeira, 94, (Km 55, 5 Rodovia Anhanguera), Jundiaí, SP 13210-795, Brazil
| | - Kauê Ribeiro da Silva
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, 225, Avenida Duque de Caxias, Norte, Jardim, Elite, Pirassununga, SP 13635-900, Brazil; (E.L.); (K.R.d.S.)
| | - Ricardo Perecin Nociti
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil; (R.P.N.); (G.M.A.); (J.C.d.S.); (F.V.M.)
| | - Gabriella Mamede Andrade
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil; (R.P.N.); (G.M.A.); (J.C.d.S.); (F.V.M.)
| | - Jorge Eduardo Atuesta-Bustos
- College of Agricultural Science—Agrarian University Foundation of Colombia-UNIAGRARIA, Calle 170 No 54a-10, Bogotá 111166, Colombia;
| | - Juliano Coelho da Silveira
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil; (R.P.N.); (G.M.A.); (J.C.d.S.); (F.V.M.)
| | - Flávio Vieira Meirelles
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil; (R.P.N.); (G.M.A.); (J.C.d.S.); (F.V.M.)
| | - Mario Binelli
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, 225, Avenida Duque de Caxias, Norte, Jardim, Elite, Pirassununga, SP 13635-900, Brazil; (E.L.); (K.R.d.S.)
- Department of Animal Sciences, University of Florida, PO Box 110910, Gainesville, FL 32611, USA
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5
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Behrens F, Holle J, Kuebler WM, Simmons S. Extracellular vesicles as regulators of kidney function and disease. Intensive Care Med Exp 2020; 8:22. [PMID: 33336297 PMCID: PMC7746786 DOI: 10.1186/s40635-020-00306-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 12/16/2022] Open
Abstract
Extracellular vesicles (EVs) are small, lipid bilayer-delimited particles of cellular origin that recently gained increasing attention for their potential use as diagnostic biomarkers, and beyond that for their role in intercellular communication and as regulators of homeostatic and disease processes. In acute kidney injury (AKI) and chronic kidney disease (CKD), the potential use of EVs as diagnostic and prognostic markers has been evaluated in a series of clinical studies and contributions to pathophysiologic pathways have been investigated in experimental models. While EV concentrations in biofluids could not distinguish renal patients from healthy subjects or determine disease progression, specific EV subpopulations have been identified that may provide useful diagnostic and prognostic tools in AKI. Specific EV subpopulations are also associated with clinical complications in sepsis-induced AKI and in CKD. Beyond their role as biomarkers, pathophysiologic involvement of EVs has been shown in hemolytic uremic syndrome- and sepsis-induced AKI as well as in cardiovascular complications of CKD. On the other hand, some endogenously formed or therapeutically applied EVs demonstrate protective effects pointing toward their usefulness as emerging treatment strategy in kidney disease.
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Affiliation(s)
- Felix Behrens
- Institute of Physiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.,Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Johannes Holle
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Wolfgang M Kuebler
- Institute of Physiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10117, Berlin, Germany. .,The Keenan Research Centre for Biomedical Science at St. Michael's, Toronto, Canada. .,Departments of Surgery and Physiology, University of Toronto, Toronto, Canada.
| | - Szandor Simmons
- Institute of Physiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10117, Berlin, Germany
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Dexheimer PJ, Cochella L. MicroRNAs: From Mechanism to Organism. Front Cell Dev Biol 2020; 8:409. [PMID: 32582699 PMCID: PMC7283388 DOI: 10.3389/fcell.2020.00409] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.
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Affiliation(s)
- Philipp J Dexheimer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
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Abstract
Myocardial infarction and post-infarction left ventricular remodelling involve a high risk of morbidity and mortality. For this reason, ongoing research is being conducted in order to learn the mechanisms of unfavourable left ventricular remodelling following a myocardial infarction. New biomarkers are also being sought that would allow for early identification of patients with a high risk of post-infarction remodelling and dysfunction of the left ventricle. In recent years, there has been ever more experimental data that confirms the significance of microRNA in cardiovascular diseases. It has been confirmed that microRNAs are stable in systemic circulation, and can be directly measured in patients’ blood. It has been found that significant changes occur in the concentrations of various types of microRNA in myocardial infarction and heart failure patients. Various types of microRNA are also currently being intensively researched in terms of their usefulness as markers of cardiomyocyte necrosis, and predictors of the post-infarction heart failure development. This paper is a summary of the current knowledge on the significance of microRNA in post-infarction left ventricular remodelling and heart failure.
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8
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Peng J, Liu F, Zheng H, Wu Q, Liu S. Long noncoding RNA ZFAS1 promotes tumorigenesis and metastasis in nasopharyngeal carcinoma by sponging miR-892b to up-regulate LPAR1 expression. J Cell Mol Med 2019; 24:1437-1450. [PMID: 31851778 PMCID: PMC6991699 DOI: 10.1111/jcmm.14823] [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: 06/02/2019] [Revised: 09/30/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE In this study, we explored the NPC-specific expression of ZFAS1 and the mechanism of ZFAS1-mediated growth, aggressiveness and tumorigenesis in NPC. METHODS The expression profile of lncRNAs was detected in NPC tissues and matching para-carcinoma tissues using microarray analysis. LncRNA-miRNA and miRNA-mRNA interaction networks were constructed using the miRcode v11 and TargetScanHuman v7.2 web server and then validated using dual-luciferase assay. Western blot and RT-qPCR were performed to detect protein and RNA expression. The effects of ZFAS1, miR-892b and LPAR1 dysregulation on the proliferative, migratory and invasive abilities of NPC cells were observed using colony formation, cell counting kit-8 (CCK-8) and transwell assays in vitro. In vivo, a xenograft nude mouse model was established to detect the impact of ZFAS1 dysregulation on the tumorigenicity of NPC cells. RESULTS The expression of multiple lncRNAs, of which ZFAS1 was up-regulated, was dysregulated in NPC tissues. ZFAS1 directly targeted miR-892b, and miR-892b negatively regulated the expression of downstream LPAR1. The proliferation, migration and invasion of NPC cells could be largely enhanced by the downregulation of miR-892b as well as the up-regulation of ZFAS1 and LPAR1, while the overexpression of miR-892b and the downregulation of ZFAS1 and LPAR1 decreased these abilities. In nude mice, the growth of tumour xenografts formed by HONE1 cells was significantly suppressed when ZFAS1 was silenced. CONCLUSION The study demonstrated that lncRNA ZFAS1 may act as a promoter of tumorigenesis and metastasis in nasopharyngeal carcinoma, by up-regulating the expression of LPAR1 in a miR-892b-dependent manner.
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Affiliation(s)
- Jiaojiao Peng
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Feng Liu
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Zheng
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Qi Wu
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Shixi Liu
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
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9
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Lin Y, Zhu S, Hu C, Wang J, Jiang P, Zhu L, Li Z, Wang S, Zhang Y, Xu X, Pan W. Cross-Species Suppression of Hepatoma Cell Growth and Migration by a Schistosoma japonicum MicroRNA. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:400-412. [PMID: 31655260 PMCID: PMC6831938 DOI: 10.1016/j.omtn.2019.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/12/2019] [Accepted: 09/08/2019] [Indexed: 12/22/2022]
Abstract
Schistosoma japonicum eggs trapped in host liver secretes microRNA (miRNA)-containing extracellular vesicles (EVs) that can be transferred to host cells. Recent studies demonstrated that miRNAs derived from plants can modulate gene expression and phenotype of mammalian cells in a cross-kingdom manner. In this study, we identified a Schistosoma japonicum miRNA (e.g., Sja-miR-3096) that is present in the hepatocytes of mice infected with the parasite and has notable antitumor effects in both in vitro and in vivo models. The Sja-miR-3096 mimics suppressed cell proliferation and migration of both murine and human hepatoma cell lines by targeting phosphoinositide 3-kinase class II alpha (PIK3C2A). We generated a murine hepatoma cell line that stably expressed the pri-Sja-miR-3096 gene and demonstrated cross-species processing of the schistosome pri-miRNA to the mature Sja-miR-3096 in the mammalian cell. Importantly, inoculation of this cell line into the scapula and livers of mice led to a complete suppression of tumorigenesis of the hepatoma cells. Moreover, tumor weight was significantly reduced on intravenous administration of Sja-miR-3096 mimics. Thus, the schistosome miRNA-mediated antitumor activity occurs in host liver cells during schistosome infection, which may strengthen resistance of host to liver cancer, and discovery and development of such miRNAs may present promising interventions for cancer therapy.
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Affiliation(s)
- Yu Lin
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Shanli Zhu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Chao Hu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Jing Wang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Pengyue Jiang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Liufang Zhu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Zhengli Li
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Sai Wang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Yuanbin Zhang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xindong Xu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Weiqing Pan
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China; Department of Tropical Diseases, Second Military Medical University, Shanghai, China.
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10
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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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11
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Evolutionary Divergence of Brain-specific Precursor miRNAs Drives Efficient Processing and Production of Mature miRNAs in Human. Neuroscience 2018; 392:141-159. [PMID: 30273624 DOI: 10.1016/j.neuroscience.2018.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022]
Abstract
The hallmark of human evolution encompasses the dramatic increase in brain size and complexity. The intricate interplays of micro-RNAs (miRNAs) and their target genes are indispensable in brain development. Sequence divergence in distinct structural regions of Brain-specific precursor miRNAs (pre-miRNAs) and its consequence in the production of corresponding mature miRNAs in human are unknown. To address these questions, first we classified miRNAs into three categories based on tissue expression: Brain-specific (expressed exclusively in brain), Non-brain (expressed in Non-brain tissues) and Common (expressed in all tissues) and compared the sequence divergence of different structural regions (basal segment, lower and upper stem, internal and terminal loop) of categorized pre-miRNAs across human, non-human primates and rodents. Our analysis revealed that unpaired regions of Brain-specific pre-miRNAs in human bear traces of relatively high rate of evolutionary divergence compared to those in other species. Cross-tissue expression analysis unveiled the higher expression of the Brain-specific miRNAs in human compared to other species. Intriguingly, in human brain, expression levels of these miRNAs superseded the levels of the ubiquitously expressed "Common-miRNAs". Further analysis revealed that presence of certain motif and nucleotide preference in the Brain-specific pre-miRNAs may favor DROSHA and DICER to ameliorate miRNA processing. The higher processing efficiency of human Brain-specific miRNAs was reflected as an elevated production of corresponding mature miRNAs in the human brain. Finally, re-construction of gene-regulatory network uncovers different pathways driven by Brain-specific miRNAs that may contribute to the development of brain in human.
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12
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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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13
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Kim B, Jeong K, Kim VN. Genome-wide Mapping of DROSHA Cleavage Sites on Primary MicroRNAs and Noncanonical Substrates. Mol Cell 2017; 66:258-269.e5. [DOI: 10.1016/j.molcel.2017.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/24/2017] [Accepted: 03/17/2017] [Indexed: 02/08/2023]
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14
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Malekpour Afshar R, Mollaei HR, Shokrizadeh M, Iranpour M. Evaluation Expression of Microrna-93 and Integrin Β8 in Different Types of Glioma Tumors. Asian Pac J Cancer Prev 2017; 18:603-608. [PMID: 28440610 PMCID: PMC5464472 DOI: 10.22034/apjcp.2017.18.3.603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
MicroRNAs (miRNAs), are a type of small non-coding RNAs, that induce mRNA degradation or repress translation by binding to the 3′-untranslated region (UTR) of its target mRNA. Some specific miRNAs, e.g. miR-93, have been discovered to be involved in pathological procedures by targeting some oncogenes or tumor suppressors in glioma. In the present study, real-time RT-PCR data was indicated the expression pattern and prognostic value of miR-93 in patients with types of Glioma. MiR-93 expression was significantly decreased in tumor tissue compared with normal group brain tissues (P<0.001). Low miR-93 expression was significantly correlated with progressive tumor grade (P=0.02). Moreover, multivariate analysis showed that miR-93 decreased expression (HR, 4.3; 95% CI, 0.8–17.2, P=0.02), advanced tumor grade (HR, 3.1; 95% CI, 0.2–13.9, P=0.04), for integrinβ8, level expression was inverse. Our data was shown that the down regulation of miR-93 was significantly correlated with unfavorable pathological features in patients with Glioma. Suggesting that decreased expression of miR-93can be used as a novel prognostic factor for this disease.
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Affiliation(s)
- Reza Malekpour Afshar
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Iran.
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15
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Chen Y, Zubovic L, Yang F, Godin K, Pavelitz T, Castellanos J, Macchi P, Varani G. Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer. Nucleic Acids Res 2016; 44:4381-95. [PMID: 27001519 PMCID: PMC4872098 DOI: 10.1093/nar/gkw177] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/26/2016] [Accepted: 03/07/2016] [Indexed: 12/26/2022] Open
Abstract
Rbfox proteins regulate tissue-specific splicing by targeting a conserved GCAUG sequence within pre-mRNAs. We report here that sequence-specific binding of the conserved Rbfox RRM to miRNA precursors containing the same sequence motif in their terminal loops, including miR-20b and miR-107, suppresses their nuclear processing. The structure of the complex between precursor miR-20b and Rbfox RRM shows the molecular basis for recognition, and reveals changes in the stem-loop upon protein binding. In mammalian cells, Rbfox2 downregulates mature miR-20b and miR-107 levels and increases the expression of their downstream targets PTEN and Dicer, respectively, suggesting that Rbfox2 indirectly regulates many more cellular miRNAs. Thus, some of the widespread cellular functions of Rbfox2 protein are attributable to regulation of miRNA biogenesis, and might include the mis-regulation of miR-20b and miR-107 in cancer and neurodegeneration.
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Affiliation(s)
- Yu Chen
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Lorena Zubovic
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Fan Yang
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Katherine Godin
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Tom Pavelitz
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Javier Castellanos
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Paolo Macchi
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Gabriele Varani
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
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16
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Lim MYT, Ng AWT, Chou Y, Lim TP, Simcox A, Tucker-Kellogg G, Okamura K. The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site. Cell Rep 2016; 15:1795-808. [PMID: 27184838 DOI: 10.1016/j.celrep.2016.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/03/2016] [Accepted: 04/15/2016] [Indexed: 12/24/2022] Open
Abstract
In Drosophila, Dicer-1 binds Loquacious-PB (Loqs-PB) as its major co-factor. Previous analyses indicated that loqs mutants only partially impede miRNA processing, but the activity of minor isoforms or maternally deposited Loqs was not eliminated in these studies. We addressed this by generating a cell line from loqs-null embryos and found that only ∼40% of miRNAs showed clear Loqs dependence. Genome-wide comparison of the hairpin structure and Loqs dependence suggested that Loqs substrates are influenced by base-pairing status at the dicing site. Artificial alteration of base-pairing stability at this position in model miRNA hairpins resulted in predicted changes in Loqs dependence, providing evidence for this hypothesis. Finally, we found that evolutionarily young miRNA genes tended to be Loqs dependent. We propose that Loqs may have roles in assisting the de novo emergence of miRNA genes by facilitating dicing of suboptimal hairpin substrates.
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Affiliation(s)
- Mandy Yu Theng Lim
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore
| | - Alvin Wei Tian Ng
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - Yuting Chou
- Sloan-Kettering Institute, Department of Developmental Biology, New York, NY 10065, USA
| | - Teck Por Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - Amanda Simcox
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Greg Tucker-Kellogg
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore.
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17
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Galka-Marciniak P, Olejniczak M, Starega-Roslan J, Szczesniak MW, Makalowska I, Krzyzosiak WJ. siRNA release from pri-miRNA scaffolds is controlled by the sequence and structure of RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:639-49. [DOI: 10.1016/j.bbagrm.2016.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/17/2023]
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18
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Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, Margaretha L, Robitaille AM, Margineantu D, Fiehn O, Hockenbery D, Blau CA, Raftery D, Margolin A, Hawkins RD, Moon RT, Ware CB, Ruohola-Baker H. The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Nat Cell Biol 2015; 17:1523-35. [PMID: 26571212 PMCID: PMC4662931 DOI: 10.1038/ncb3264] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/01/2015] [Indexed: 02/07/2023]
Abstract
For nearly a century developmental biologists have recognized that cells from embryos can differ in their potential to differentiate into distinct cell types. Recently, it has been recognized that embryonic stem cells derived from both mice and humans exhibit two stable yet epigenetically distinct states of pluripotency: naive and primed. We now show that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs). Specifically, in naive hESCs, NNMT and its enzymatic product 1-methylnicotinamide are highly upregulated, and NNMT is required for low S-adenosyl methionine (SAM) levels and the H3K27me3 repressive state. NNMT consumes SAM in naive cells, making it unavailable for histone methylation that represses Wnt and activates the HIF pathway in primed hESCs. These data support the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development.
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Affiliation(s)
- Henrik Sperber
- Department of Biochemistry, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
- Department of Chemistry, University of Washington, Seattle, WA
| | - Julie Mathieu
- Department of Biochemistry, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Yuliang Wang
- Sage Bionetworks, Seattle, WA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR
| | - Amy Ferreccio
- Department of Biochemistry, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Jennifer Hesson
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Zhuojin Xu
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Karin A. Fischer
- Department of Biochemistry, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Arikketh Devi
- Department of Biochemistry, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
- Department of Genetic Engineering, SRM University, Kattankulathur, India
| | - Damien Detraux
- Department of Biochemistry, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Haiwei Gu
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, CA
| | - Stephanie L. Battle
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
- Department of Medicine, Division of Medical Genetics and Department of Genome Sciences, University of Washington, CA
| | | | - Cristina Valensisi
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
- Department of Medicine, Division of Medical Genetics and Department of Genome Sciences, University of Washington, CA
| | - Jason H. Bielas
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | | | - Oliver Fiehn
- University of California Davis Genome Center, CA
| | | | - C. Anthony Blau
- Department of Biochemistry, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Daniel Raftery
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, CA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Adam Margolin
- Sage Bionetworks, Seattle, WA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR
| | - R. David Hawkins
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
- Department of Medicine, Division of Medical Genetics and Department of Genome Sciences, University of Washington, CA
| | - Randall T. Moon
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Carol B. Ware
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA
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Drosha inclusions are new components of dipeptide-repeat protein aggregates in FTLD-TDP and ALS C9orf72 expansion cases. J Neuropathol Exp Neurol 2015; 74:380-7. [PMID: 25756586 PMCID: PMC4362478 DOI: 10.1097/nen.0000000000000182] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Supplemental digital content is available in the text. Frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are 2 neurodegenerative disorders that share clinical, genetic, and neuropathologic features. The presence of abnormal expansions of GGGGCC repeats (G4C2 repeats) in a noncoding region of the Chromosome 9 open reading frame 72 (C9orf72) gene is the major genetic cause of both FTLD and ALS. Transcribed G4C2 repeats can form nuclear RNA foci and recruit RNA-binding proteins, thereby inhibiting their normal function. Moreover, through a repeat-associated non-ATG translation mechanism, G4C2 repeats translation leads to dipeptide-repeat protein aggregation in the cytoplasm of neurons. Here, we identify Drosha protein as a new component of these dipeptide-repeat aggregates. In C9orf72 mutation cases of FTLD-TDP (c9FTLD-TDP) and ALS (c9ALS), but not in FTLD or ALS cases without C9orf72 mutation, Drosha is mislocalized to form neuronal cytoplasmic inclusions in the hippocampus, frontal cortex, and cerebellum. Further characterization of Drosha-positive neuronal cytoplasmic inclusions in the hippocampus, frontal cortex, and cerebellum revealed colocalization with p62 and ubiquilin-2, 2 pathognomonic signatures of c9FTLD-TDP and c9ALS cases; however, Drosha inclusions rarely colocalized with TDP-43 pathology. We conclude that Drosha may play a unique pathogenic role in the onset or progression of FTLD-TDP/ALS in patients with the C9orf72 mutation.
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20
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Quarles KA, Chadalavada D, Showalter SA. Deformability in the cleavage site of primary microRNA is not sensed by the double-stranded RNA binding domains in the microprocessor component DGCR8. Proteins 2015; 83:1165-79. [PMID: 25851436 DOI: 10.1002/prot.24810] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 03/10/2015] [Accepted: 03/25/2015] [Indexed: 01/01/2023]
Abstract
The prevalence of double-stranded RNA (dsRNA) in eukaryotic cells has only recently been appreciated. Of interest here, RNA silencing begins with dsRNA substrates that are bound by the dsRNA-binding domains (dsRBDs) of their processing proteins. Specifically, processing of microRNA (miRNA) in the nucleus minimally requires the enzyme Drosha and its dsRBD-containing cofactor protein, DGCR8. The smallest recombinant construct of DGCR8 that is sufficient for in vitro dsRNA binding, referred to as DGCR8-Core, consists of its two dsRBDs and a C-terminal tail. As dsRBDs rarely recognize the nucleotide sequence of dsRNA, it is reasonable to hypothesize that DGCR8 function is dependent on the recognition of specific structural features in the miRNA precursor. Previously, we demonstrated that noncanonical structural elements that promote RNA flexibility within the stem of miRNA precursors are necessary for efficient in vitro cleavage by reconstituted Microprocessor complexes. Here, we combine gel shift assays with in vitro processing assays to demonstrate that neither the N-terminal dsRBD of DGCR8 in isolation nor the DGCR8-Core construct is sensitive to the presence of noncanonical structural elements within the stem of miRNA precursors, or to single-stranded segments flanking the stem. Extending DGCR8-Core to include an N-terminal heme-binding region does not change our conclusions. Thus, our data suggest that although the DGCR8-Core region is necessary for dsRNA binding and recruitment to the Microprocessor, it is not sufficient to establish the previously observed connection between RNA flexibility and processing efficiency.
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Affiliation(s)
- Kaycee A Quarles
- Department of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvannia, 16802
| | - Durga Chadalavada
- Department of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvannia, 16802
| | - Scott A Showalter
- Department of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvannia, 16802
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21
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Dhir A, Dhir S, Proudfoot NJ, Jopling CL. Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs. Nat Struct Mol Biol 2015; 22:319-27. [PMID: 25730776 PMCID: PMC4492989 DOI: 10.1038/nsmb.2982] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/05/2015] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) play a major part in the post-transcriptional regulation of gene expression. Mammalian miRNA biogenesis begins with cotranscriptional cleavage of RNA polymerase II (Pol II) transcripts by the Microprocessor complex. Although most miRNAs are located within introns of protein-coding transcripts, a substantial minority of miRNAs originate from long noncoding (lnc) RNAs, for which transcript processing is largely uncharacterized. We show, by detailed characterization of liver-specific lnc-pri-miR-122 and genome-wide analysis in human cell lines, that most lncRNA transcripts containing miRNAs (lnc-pri-miRNAs) do not use the canonical cleavage-and-polyadenylation pathway but instead use Microprocessor cleavage to terminate transcription. Microprocessor inactivation leads to extensive transcriptional readthrough of lnc-pri-miRNA and transcriptional interference with downstream genes. Consequently we define a new RNase III-mediated, polyadenylation-independent mechanism of Pol II transcription termination in mammalian cells.
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Affiliation(s)
- Ashish Dhir
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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