1
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Velázquez-Flores MÁ, Ruiz Esparza-Garrido R. Fragments derived from non-coding RNAs: how complex is genome regulation? Genome 2024. [PMID: 38684113 DOI: 10.1139/gen-2023-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.
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Affiliation(s)
- Miguel Ángel Velázquez-Flores
- Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
| | - Ruth Ruiz Esparza-Garrido
- Investigadora por México, Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
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2
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Szakats S, McAtamney A, Wilson MJ. Identification of novel microRNAs in the embryonic mouse brain using deep sequencing. Mol Cell Biochem 2024; 479:297-311. [PMID: 37059894 PMCID: PMC10890980 DOI: 10.1007/s11010-023-04730-2] [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: 02/04/2023] [Accepted: 04/04/2023] [Indexed: 04/16/2023]
Abstract
Many advances in small RNA-seq technology and bioinformatics pipelines have been made recently, permitting the discovery of novel miRNAs in the embryonic day 15.5 (E15.5) mouse brain. We aimed to improve miRNA discovery in this tissue to expand our knowledge of the regulatory networks that underpin normal neurodevelopment, find new candidates for neurodevelopmental disorder aetiology, and deepen our understanding of non-coding RNA evolution. A high-quality small RNA-seq dataset of 458 M reads was generated. An unbiased miRNA discovery pipeline identified fifty putative novel miRNAs, six of which were selected for further validation. A combination of conservation analysis and target functional prediction was used to determine the authenticity of novel miRNA candidates. These findings demonstrate that miRNAs remain to be discovered, particularly if they have the features of other small RNA species.
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Affiliation(s)
- Susanna Szakats
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Alice McAtamney
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Megan J Wilson
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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3
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Olliff NS, Hunt MA, Paudel SS, Nguyen KN, Delcher HA, DeMeis JD, Roberts JT, Fouty BW, Audia JP, Kim JH, Borchert GM. Human YRNA 4 (HY4) plasma levels are a prognostic indicator of SARS-CoV-2 infection clinical severity. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000925. [PMID: 37662051 PMCID: PMC10474479 DOI: 10.17912/micropub.biology.000925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
SARS-CoV-2 infection can result in a range of outcomes from asymptomatic/mild disease to severe COVID-19/fatality. In this study, we investigated the differential expression of small noncoding RNAs (sncRNAs) between patient cohorts defined by disease severity. We collected plasma samples, stratified these based on clinical outcomes, and sequenced their circulating sncRNAs. Excitingly, we found YRNA HY4 displays significant differential expression (p=0.025) between patients experiencing mild and severe disease. In agreement with recent reports identifying plasma YRNAs as indicators of influenza infection severity, our results strongly suggest that circulating HY4 levels represent a powerful prognostic indicator of likely SARS-CoV-2 patient infection outcome.
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Affiliation(s)
| | - Miles A. Hunt
- Biology, Howard University, Washington, Washington, D.C., United States
| | - Sunita S. Paudel
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Kevin N. Nguyen
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Haley A. Delcher
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Jeffrey D. DeMeis
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Justin T. Roberts
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
| | - Brian W. Fouty
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
- Internal Medicine, University of South Alabama, Mobile, Alabama, United States
| | - Jonathon P. Audia
- Microbiology & Immunology, University of South Alabama, Mobile, Alabama, United States
| | - Jin H. Kim
- Microbiology & Immunology, University of South Alabama, Mobile, Alabama, United States
| | - Glen M. Borchert
- Pharmacology, University of South Alabama, Mobile, Alabama, United States
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4
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Piselli A, Pishvaian MJ, Noel MS. Anti-Ro60 Antibodies Utility as a Diagnostic Indicator of Pancreatic Cancer: A Case Report. Pancreas 2022; 51:e121-e122. [PMID: 37099798 DOI: 10.1097/mpa.0000000000002202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
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5
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Chen W, Li L, Wang J, Li Q, Zhang R, Wang S, Wu Y, Xing D. Extracellular vesicle YRNA in atherosclerosis. Clin Chim Acta 2021; 517:15-22. [DOI: 10.1016/j.cca.2021.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 02/08/2023]
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6
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Valkov N, Das S. Y RNAs: Biogenesis, Function and Implications for the Cardiovascular System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:327-342. [PMID: 32285422 DOI: 10.1007/978-981-15-1671-9_20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In recent years, progress in the field of high-throughput sequencing technology and its application to a wide variety of biological specimens has greatly advanced the discovery and cataloging of a diverse set of non-coding RNAs (ncRNAs) that have been found to have unexpected biological functions. Y RNAs are an emerging class of highly conserved, small ncRNAs. There is a growing number of reports in the literature demonstrating that Y RNAs and their fragments are not just random degradation products but are themselves bioactive molecules. This review will outline what is currently known about Y RNA including biogenesis, structure and functional roles. In addition, we will provide an overview of studies reporting the presence and functions attributed to Y RNAs in the cardiovascular system.
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Affiliation(s)
- Nedyalka Valkov
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Saumya Das
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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7
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Lovisa F, Di Battista P, Gaffo E, Damanti CC, Garbin A, Gallingani I, Carraro E, Pillon M, Biffi A, Bortoluzzi S, Mussolin L. RNY4 in Circulating Exosomes of Patients With Pediatric Anaplastic Large Cell Lymphoma: An Active Player? Front Oncol 2020; 10:238. [PMID: 32175280 PMCID: PMC7056873 DOI: 10.3389/fonc.2020.00238] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/12/2020] [Indexed: 12/20/2022] Open
Abstract
Emerging evidence indicates that extracellular vesicles, particularly exosomes, play a role in several biological processes and actively contribute to cancer development and progression, by carrying and delivering proteins, transcripts and small RNAs (sRNAs). There is high interest in studying exosomes of cancer patients both to develop non-invasive liquid biopsy tests for risk stratification and to elucidate their possible involvement in disease mechanisms. We profiled by RNA-seq the sRNA content of circulating exosomes of 20 pediatric patients with Anaplastic Large Cell Lymphoma (ALCL) and five healthy controls. Our analysis disclosed that non-miRNA derived sRNAs constitute the prominent fraction of sRNA loaded in exosomes and identified 180 sRNAs significantly more abundant in exosomes of ALCL patients compared to controls. YRNA fragments, accounting for most of exosomal content and being significantly increased in ALCL patients, were prioritized for further investigation by qRT-PCR. Quantification of RNY4 fragments and full-length sequences disclosed that the latter are massively loaded into exosomes of ALCL patients with more advanced and aggressive disease. These results are discussed in light of recent findings on the role of RNY4 in the modulation of tumor microenvironment.
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Affiliation(s)
- Federica Lovisa
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Piero Di Battista
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Carlotta C Damanti
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Anna Garbin
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Ilaria Gallingani
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Elisa Carraro
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Marta Pillon
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Alessandra Biffi
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy.,Gene Therapy Program, Dana Farber/Boston Children's Cancer and Blood Disorders Centers, Boston, MA, United States
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy.,CRIBI Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, Padova, Italy
| | - Lara Mussolin
- Clinic of Pediatric Onco-Hematology, Department of Women's and Children's Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
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8
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Isidoro-García M, García-Sánchez A, Sanz C, Estravís M, Marcos-Vadillo E, Pascual M, Roa S, Marques-García F, Triviño JC, Dávila I. YRNAs overexpression and potential implications in allergy. World Allergy Organ J 2019; 12:100047. [PMID: 31384359 PMCID: PMC6664241 DOI: 10.1016/j.waojou.2019.100047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 06/10/2019] [Accepted: 06/18/2019] [Indexed: 02/08/2023] Open
Abstract
Background Small non-coding RNAs (snRNAs) develop important functions related to epigenetic regulation. YRNAs are snRNAs involved in the initiation of DNA replication and RNA stability that regulate gene expression. They have been related to autoimmune, cancer and inflammatory diseases but never before to allergy. In this work we described for the first time in allergic patients the differential expression profile of YRNAs, their regulatory mechanisms and their potential as new diagnostic and therapeutic targets. Methods From a previous whole RNAseq study in B cells of allergic patients, differential expression profiles of coding and non-coding transcripts were obtained. To select the most differentially expressed non coding transcripts, fold change and p-values were analyzed. A validation of the expression differences detected was developed in an independent cohort of 304 individuals, 208 allergic patients and 96 controls by using qPCR. Potential binding and retrotransponibility capacity were characterized by in silico structural analysis. Using a novel bioinformatics approach, RNA targets identification, functional enrichment and network analyses were performed. Results We found that almost 70% of overexpressed non-coding transcripts in allergic patients corresponded to YRNAs. From the three more differentially overexpressed candidates, increased expression was independently confirmed in the peripheral blood of allergic patients. Structural analysis suggested a protein binding capacity decrease and an increase in retrotransponibility. Studies of RNA targets allowed the identification of sequences related to the immune mechanisms underlying allergy. Conclusions Overexpression of YRNAs is observed for the first time in allergic patients. Structural and functional information points to their implication on regulatory mechanisms of the disease.
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Affiliation(s)
- María Isidoro-García
- Department of Clinical Biochemistry, University Hospital of Salamanca, Spain.,Institute for Biomedical Research of Salamanca, Spain.,Department of Medicine, University of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
| | - Asunción García-Sánchez
- Institute for Biomedical Research of Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
| | - Catalina Sanz
- Institute for Biomedical Research of Salamanca, Spain.,Department of Microbiology and Genetics, University of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
| | - Miguel Estravís
- Institute for Biomedical Research of Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
| | - Elena Marcos-Vadillo
- Department of Clinical Biochemistry, University Hospital of Salamanca, Spain.,Institute for Biomedical Research of Salamanca, Spain
| | - Marien Pascual
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Sergio Roa
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Fernando Marques-García
- Department of Clinical Biochemistry, University Hospital of Salamanca, Spain.,Institute for Biomedical Research of Salamanca, Spain
| | | | - Ignacio Dávila
- Institute for Biomedical Research of Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Spain.,Department of Allergy, University Hospital of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
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9
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Driedonks TAP, Nolte-'t Hoen ENM. Circulating Y-RNAs in Extracellular Vesicles and Ribonucleoprotein Complexes; Implications for the Immune System. Front Immunol 2019; 9:3164. [PMID: 30697216 PMCID: PMC6340977 DOI: 10.3389/fimmu.2018.03164] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/21/2018] [Indexed: 12/25/2022] Open
Abstract
The exchange of extracellular vesicles (EV) between immune cells plays a role in various immune regulatory processes. EV are nano-sized lipid bilayer-enclosed structures that contain a multitude of proteins and small non-coding RNA molecules. Of the various RNA classes present in EV, miRNAs have been most intensively studied because of their known gene-regulatory functions. These miRNAs constitute only a minor part of all EV-enclosed RNA, whereas other 20–200 nt sized non-coding RNAs were shown to be abundantly present in EV. Several of these mid-sized RNAs perform basic functions in cells, but their function in EV remains elusive. One prominent class of mid-sized extracellular RNAs associated with EV are the Y-RNAs. This family of highly conserved non-coding RNAs was initially discovered as RNA component of circulating ribonucleoprotein autoantigens in serum from Systemic Lupus Erythematosus and Sjögren's Syndrome patients. Y-RNA has been implicated in cellular processes such as DNA replication and RNA quality control. In recent years, Y-RNA has been abundantly detected in EV from multiple different cell lines and biofluids, and also in murine and human retroviruses. Accumulating evidence suggests that EV-associated Y-RNA may be involved in a range of immune-related processes, including inflammation, immune suppression, and establishment of the tumor microenvironment. Moreover, changes in plasma levels of extracellular Y-RNA have been associated with various diseases. Recent studies have aimed to address the mechanisms underlying their release and function. We for example showed that the levels of EV-associated Y-RNA released by immune cells can be regulated by Toll-like receptor (TLR) signaling. Combined, these data have triggered increased interest in extracellular Y-RNAs. In this review, we provide an overview of studies reporting the occurrence of extracellular Y-RNAs, as well as signaling properties and immune-related functions attributed to these RNAs. We list RNA-binding proteins currently known to interact with Y-RNAs and evaluate their occurrence in EV. In parallel, we discuss technical challenges in assessing whether extracellular Y-RNAs are contained in ribonucleoprotein complexes or EV. By integrating the current knowledge on extracellular Y-RNA we further reflect on the biomarker potential of Y-RNA and their role in immune cell communication and immunopathology.
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Affiliation(s)
- Tom A P Driedonks
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Esther N M Nolte-'t Hoen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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10
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Sandhya P, Kurien BT, Danda D, Scofield RH. Update on Pathogenesis of Sjogren's Syndrome. Curr Rheumatol Rev 2018; 13:5-22. [PMID: 27412602 DOI: 10.2174/1573397112666160714164149] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 11/15/2015] [Accepted: 01/01/2016] [Indexed: 01/06/2023]
Abstract
Sjogren's syndrome is a common autoimmune disease that presents with sicca symptoms and extraglandular features. Sjogren's syndrome is presumably as common as RA; yet it is poorly understood, underdiagnosed and undertreated. From the usual identity as an autoimmune exocrinopathy to its most recent designate as an autoimmune epithelitis - the journey of SS is complex. We herein review some of the most important milestones that have shed light on different aspects of pathogenesis of this enigmatic disease. This includes role of salivary gland epithelial cells, and their interaction with cells of the innate and adaptive immune system. Non-immune factors acting in concert or in parallel with immune factors may also be important. The risk genes identified so far have only weak association, nevertheless advances in genetics have enhanced understanding of disease mechanisms. Role of epigenetic and environmental role factors is also being explored. SS has also some unique features such as congenital heart block and high incidence of lymphoma; disease mechanisms accounting for these manifestations are also reviewed.
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11
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Liu D, Qian W, Li D, Kong L. Ro60/SSA levels are increased and promote the progression of pancreatic ductal adenocarcinoma. Biochem Biophys Res Commun 2017; 495:2519-2524. [PMID: 29274781 DOI: 10.1016/j.bbrc.2017.12.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/22/2022]
Abstract
Ro60/SSA is a vital auto antigen that is targeted in Sjogren's syndrome and systemic lupus erythematosus (SLE). However, its role in solid cancers has rarely been reported. The present study investigated the expression and function of Ro60/SSA in the development of pancreatic ductal adenocarcinoma (PDAC) both in vitro and in vivo. Immunohistochemistry was used to examine the expression of Ro60/SSA in PDAC and normal pancreatic tissues by using tissue microarray chips. The results showed that Ro60/SSA expression was increased in PDAC tissues compared with normal pancreatic tissues. Knockdown of Ro60/SSA by siRNA transfection significantly decreased cell proliferation and invasion in vitro. Furthermore, knockdown of Ro60/SSA inhibited the growth of subcutaneous tumors in vivo. Taken together, the current study provides evidence of new function of Ro60/SSA in the development of cancer. It facilitates pancreatic cancer proliferation, migration and invasion. Therefore, it may represent a novel molecular target for the management of pancreatic cancer.
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Affiliation(s)
- Dan Liu
- Department of Gastroenteology and Hepatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Wenbiao Qian
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Deliang Li
- Department of Gastroenteology and Hepatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Lingjian Kong
- Department of Gastroenteology and Hepatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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12
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Kabeerdoss J, Sandhya P, Danda D. Y RNA derived small RNAs in Sjögren's syndrome: Candidate biomarkers? Int J Rheum Dis 2017; 20:1763-1766. [PMID: 29152879 DOI: 10.1111/1756-185x.13229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Anti-Ro and anti-La antibodies are important in pathogenesis and diagnosis of Sjögren's syndrome (SS). Ro60, Ro52 and La are RNA binding proteins of Y RNA, which were discovered more than three decades ago. Significance of Y RNA is not appreciated as much as Ro and La in SS. It can be hypothesised that 5'-YsRNA, short fragment derived from Y RNA may be recognized by TLR7 in pDC, which induces type I interferon signature in SS. New genomics tools, namely RNA seq, enables assay of 5'-YsRNA in blood. 5'-YsRNA has the potential to be a novel biomarker of SS.
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Affiliation(s)
- Jayakanthan Kabeerdoss
- Department of Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Pulukool Sandhya
- Department of Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Debashish Danda
- Department of Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
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13
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Rassi DM, De Paiva CS, Dias LC, Módulo CM, Adriano L, Fantucci MZ, Rocha EM. Review: MicroRNAS in ocular surface and dry eye diseases. Ocul Surf 2017; 15:660-669. [DOI: 10.1016/j.jtos.2017.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 04/15/2017] [Accepted: 05/04/2017] [Indexed: 12/21/2022]
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14
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RNY (YRNA)-derived small RNAs regulate cell death and inflammation in monocytes/macrophages. Cell Death Dis 2017; 8:e2530. [PMID: 28055017 PMCID: PMC5386355 DOI: 10.1038/cddis.2016.429] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/15/2016] [Accepted: 11/15/2016] [Indexed: 01/01/2023]
Abstract
The recent discovery of new classes of small RNAs has opened unknown territories to explore new regulations of physiopathological events. We have recently demonstrated that RNY (or Y RNA)-derived small RNAs (referred to as s-RNYs) are an independent class of clinical biomarkers to detect coronary artery lesions and are associated with atherosclerosis burden. Here, we have studied the role of s-RNYs in human and mouse monocytes/macrophages and have shown that in lipid-laden monocytes/macrophages s-RNY expression is timely correlated to the activation of both NF-κB and caspase 3-dependent cell death pathways. Loss- or gain-of-function experiments demonstrated that s-RNYs activate caspase 3 and NF-κB signaling pathways ultimately promoting cell death and inflammatory responses. As, in atherosclerosis, Ro60-associated s-RNYs generated by apoptotic macrophages are released in the blood of patients, we have investigated the extracellular function of the s-RNY/Ro60 complex. Our data demonstrated that s-RNY/Ro60 complex induces caspase 3-dependent cell death and NF-κB-dependent inflammation, when added to the medium of cultured monocytes/macrophages. Finally, we have shown that s-RNY function is mediated by Toll-like receptor 7 (TLR7). Indeed using chloroquine, which disrupts signaling of endosome-localized TLRs 3, 7, 8 and 9 or the more specific TLR7/9 antagonist, the phosphorothioated oligonucleotide IRS954, we blocked the effect of either intracellular or extracellular s-RNYs. These results position s-RNYs as relevant novel functional molecules that impacts on macrophage physiopathology, indicating their potential role as mediators of inflammatory diseases, such as atherosclerosis.
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15
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Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH. miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends Genet 2015; 31:613-626. [PMID: 26453491 DOI: 10.1016/j.tig.2015.09.002] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/10/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022]
Abstract
High-throughput sequencing of miRNAs has revealed the diversity and variability of mature and functional short noncoding RNAs, including their genomic origins, biogenesis pathways, sequence variability, and newly identified products such as miRNA-offset RNAs (moRs). Here we review known cases of alternative mature miRNA-like RNA fragments and propose a revised definition of miRNAs to encompass this diversity. We then review nomenclature guidelines for miRNAs and propose to extend nomenclature conventions to align with those for protein-coding genes established by international consortia. Finally, we suggest a system to encompass the full complexity of sequence variations (i.e., isomiRs) in the analysis of small RNA sequencing experiments.
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Affiliation(s)
- T Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - P Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - E Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - K Eilbeck
- Utah Science, Technology, and Research Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - J T Eppig
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - M S McAndrews
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - A Singer
- ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA
| | - J H Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
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16
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Repetto E, Lichtenstein L, Hizir Z, Tekaya N, Benahmed M, Ruidavets JB, Zaragosi LE, Perret B, Bouchareychas L, Genoux A, Lotte R, Ruimy R, Ferrières J, Barbry P, Martinez LO, Trabucchi M. RNY-derived small RNAs as a signature of coronary artery disease. BMC Med 2015; 13:259. [PMID: 26449324 PMCID: PMC4599655 DOI: 10.1186/s12916-015-0489-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/16/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Data from next generation sequencing technologies uncovered the existence of many classes of small RNAs. Recent studies reported that small RNAs are released by cells and can be detected in the blood. In this report, we aimed to discover the occurrence of novel circulating small RNAs in coronary artery disease (CAD). METHODS We used high-throughput sequencing of small RNAs from human and mouse apoptotic primary macrophages, and analyzed the data by empirical Bayes moderated t-statistics to assess differential expression and the Benjamini and Hochberg method to control the false discovery rate. Results were then confirmed by Northern blot and RT-qPCR in foam cells and in two animal models for atherosclerosis, namely ApoE(-/-) and Ldlr(-/-) mouse lines. Quantitative RT-PCR to detect identified small RNAs, the RNY-derived small RNAs, was performed using sera of 263 patients with CAD compared to 514 matched healthy controls; the Student t-test was applied to statistically assess differences. Associations of small RNAs with clinical characteristics and biological markers were tested using Spearman's rank correlations, while multivariate logistic regressions were performed to test the statistical association of small RNA levels with CAD. RESULTS Here, we report that, in macrophages stimulated with pro-apoptotic or pro-atherogenic stimuli, the Ro-associated non-coding RNAs, called RNYs or Y-RNAs, are processed into small RNAs (~24-34 nt) referred to as small-RNYs (s-RNYs), including s-RNY1-5p processed from RNY1. A significant upregulation of s-RNY expression was found in aortic arches and blood plasma from ApoE(-/-) and Ldlr(-/-) mice and in serum from CAD patients (P <0.001). Biostatistical analysis revealed a positive association of s-RNY1-5p with hs-CRP and ApoB levels; however, no statistical interaction was found between either of these two markers and s-RNY1-5p in relation to the CAD status. Levels of s-RNY1-5p were also independent from statin and fibrate therapies. CONCLUSION Our results position the s-RNY1-5p as a relevant novel independent diagnostic biomarker for atherosclerosis-related diseases. Measurement of circulating s-RNY expression would be a valuable companion diagnostic to monitor foam cell apoptosis during atherosclerosis pathogenesis and to evaluate patient's responsiveness to future therapeutic strategies aiming to attenuate apoptosis in foam cells in advanced atherosclerotic lesions.
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Affiliation(s)
- Emanuela Repetto
- INSERM U1065 and University of Nice Sophia Antipolis, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 10 "Control of Gene Expression", F-06204, Nice, France.
| | - Laeticia Lichtenstein
- INSERM UMR 1048, Toulouse, 31000, France.,Université de Toulouse III, UMR 1048, Toulouse, 31300, France
| | - Zoheir Hizir
- INSERM U1065 and University of Nice Sophia Antipolis, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 10 "Control of Gene Expression", F-06204, Nice, France
| | - Nedra Tekaya
- INSERM U1065 and University of Nice Sophia Antipolis, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 10 "Control of Gene Expression", F-06204, Nice, France
| | | | | | | | - Bertrand Perret
- INSERM UMR 1048, Toulouse, 31000, France.,Université de Toulouse III, UMR 1048, Toulouse, 31300, France.,CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Laura Bouchareychas
- Sorbonne Universités, UPMC Université Paris 06, UMR_S 1166, ICAN, Integrative Biology of Atherosclerosis Team, Paris, F-75005, France
| | - Annelise Genoux
- INSERM UMR 1048, Toulouse, 31000, France.,Université de Toulouse III, UMR 1048, Toulouse, 31300, France.,CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | | | | | - Jean Ferrières
- INSERM U1027, Faculté de Médecine, Toulouse, 31073, France.,CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Pascal Barbry
- CNRS and University of Nice Sophia Antipolis, IPMC, Sophia Antipolis, Nice, France
| | - Laurent O Martinez
- INSERM UMR 1048, Toulouse, 31000, France.,Université de Toulouse III, UMR 1048, Toulouse, 31300, France.,CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Michele Trabucchi
- INSERM U1065 and University of Nice Sophia Antipolis, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 10 "Control of Gene Expression", F-06204, Nice, France.
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17
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Kowalski MP, Krude T. Functional roles of non-coding Y RNAs. Int J Biochem Cell Biol 2015; 66:20-9. [PMID: 26159929 PMCID: PMC4726728 DOI: 10.1016/j.biocel.2015.07.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/03/2015] [Accepted: 07/04/2015] [Indexed: 12/20/2022]
Abstract
Non-coding RNAs are involved in a multitude of cellular processes but the biochemical function of many small non-coding RNAs remains unclear. The family of small non-coding Y RNAs is conserved in vertebrates and related RNAs are present in some prokaryotic species. Y RNAs are also homologous to the newly identified family of non-coding stem-bulge RNAs (sbRNAs) in nematodes, for which potential physiological functions are only now emerging. Y RNAs are essential for the initiation of chromosomal DNA replication in vertebrates and, when bound to the Ro60 protein, they are involved in RNA stability and cellular responses to stress in several eukaryotic and prokaryotic species. Additionally, short fragments of Y RNAs have recently been identified as abundant components in the blood and tissues of humans and other mammals, with potential diagnostic value. While the number of functional roles of Y RNAs is growing, it is becoming increasingly clear that the conserved structural domains of Y RNAs are essential for distinct cellular functions. Here, we review the biochemical functions associated with these structural RNA domains, as well as the functional conservation of Y RNAs in different species. The existing biochemical and structural evidence supports a domain model for these small non-coding RNAs that has direct implications for the modular evolution of functional non-coding RNAs.
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Affiliation(s)
- Madzia P Kowalski
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom.
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18
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van Balkom BWM, Eisele AS, Pegtel DM, Bervoets S, Verhaar MC. Quantitative and qualitative analysis of small RNAs in human endothelial cells and exosomes provides insights into localized RNA processing, degradation and sorting. J Extracell Vesicles 2015; 4:26760. [PMID: 26027894 PMCID: PMC4450249 DOI: 10.3402/jev.v4.26760] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 03/25/2015] [Accepted: 05/03/2015] [Indexed: 01/08/2023] Open
Abstract
Exosomes are small vesicles that mediate cell-cell communication. They contain proteins, lipids and RNA, and evidence is accumulating that these molecules are specifically sorted for release via exosomes. We recently showed that endothelial-cell-produced exosomes promote angiogenesis in vivo in a small RNA-dependent manner. Recent deep sequencing studies in exosomes from lymphocytic origin revealed a broad spectrum of small RNAs. However, selective depletion or incorporation of small RNA species into endothelial exosomes has not been studied extensively. With next generation sequencing, we identified all known non-coding RNA classes, including microRNAs (miRNAs), small nucleolar RNAs, yRNAs, vault RNAs, 5p and 3p fragments of miRNAs and miRNA-like fragments. In addition, we mapped many fragments of messenger RNAs (mRNAs) and mitochondrial RNAs (mtRNAs). The distribution of small RNAs in exosomes revealed a considerable overlap with the distribution in the producing cells. However, we identified a remarkable enrichment of yRNA fragments and mRNA degradation products in exosomes consistent with yRNAs having a role in degradation of structured and misfolded RNAs in close proximity to endosomes. We propose that endothelial endosomes selectively sequester cytoplasmic RNA-degrading machineries taking part in gene regulation. The release of these regulatory RNAs via exosomes may have implications for endothelial cell-cell communication.
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Affiliation(s)
- Bas W M van Balkom
- Department of Nephrology and Hypertension, UMC Utrecht, Utrecht, the Netherlands;
| | - Almut S Eisele
- Department of Nephrology and Hypertension, UMC Utrecht, Utrecht, the Netherlands
| | - D Michiel Pegtel
- Exosomes Research Group, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Marianne C Verhaar
- Department of Nephrology and Hypertension, UMC Utrecht, Utrecht, the Netherlands
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19
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Abstract
Cells have developed molecular machineries, which can chemically modify DNA and RNA nucleosides. One particular and chemically simple modification, (cytosine-5) methylation (m(5)C), has been detected both in RNA and DNA suggesting universal use of m(5)C for the function of these nucleotide polymers. m(5)C can be reproducibly mapped to abundant noncoding RNAs (transfer RNA, tRNA and ribosomal RNA, rRNA), and recently, also nonabundant RNAs (including mRNAs) have been reported to carry this modification. Quantification of m(5)C content in total RNA preparations indicates that a limited number of RNAs carry this modification and suggests specific functions for (cytosine-5) RNA methylation. What exactly is the biological function of m(5)C in RNA? Before attempting to address this question, m(5)C needs to be mapped specifically and reproducibly, preferably on a transcriptome-wide scale. To facilitate the detection of m(5)C in its sequence context, RNA bisulfite sequencing (RNA-BisSeq) has been developed. This method relies on the efficient chemical deamination of nonmethylated cytosine, which can be read out as single nucleotide polymorphism (nonmethylated cytosine as thymine vs. methylated cytosine as cytosine), when differentially comparing cDNA libraries to reference sequences after DNA sequencing. Here, the basic protocol of RNA-BisSeq, its current applications and limitations are described.
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Affiliation(s)
- Matthias Schaefer
- Vienna Biocenter, Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Universität Wien, Vienna, Austria.
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20
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Ninomiya S, Kawano M, Abe T, Ishikawa T, Takahashi M, Tamura M, Takahashi Y, Nashimoto M. Potential small guide RNAs for tRNase ZL from human plasma, peripheral blood mononuclear cells, and cultured cell lines. PLoS One 2015; 10:e0118631. [PMID: 25730316 PMCID: PMC4346264 DOI: 10.1371/journal.pone.0118631] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/09/2015] [Indexed: 11/18/2022] Open
Abstract
Several pieces of evidence suggest that small RNA degradation products together with tRNase ZL appear to form another layer of the whole gene regulatory network. The degraded RNA such as a 5'-half-tRNA and an rRNA fragment function as small guide RNA (sgRNA) to guide the enzyme to target RNA. We were curious whether there exist RNAs in plasma that can function as sgRNAs for tRNase ZL, whether these RNAs are working as signaling molecules between cells to fulfill physiological roles, and whether there are any differences in plasma sgRNA species and levels between normal and pathological conditions. Here, we analyzed small plasma RNAs from three healthy persons and three multiple myeloma patients for potential sgRNAs by deep sequencing. We also examined small RNAs from peripheral blood mononuclear cells (PBMC) of three healthy persons and three myeloma patients and from various cultured human cell lines for sgRNAs. We found that read-number distribution patterns of plasma and PBMC RNAs differ between persons in the range of 5-40 nt and that there are many RNA species that exist significantly more or less abundantly in the plasma or PBMC of the myeloma patients than those of the healthy persons. Furthermore, we found that there are many potential sgRNAs in the 5-40-nt RNAs and that, among them, a 31-nt RNA fragment derived from 94-nt Y4-RNA, which can function as a 5'-half-tRNA-type sgRNA, is overwhelmingly abundant in the plasma of 2/3 of the examinees. These observations suggest that the gene regulatory network via tRNase ZL and sgRNA may be extended intercellularly.
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Affiliation(s)
- Sho Ninomiya
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mitsuoki Kawano
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Takashi Abe
- Department of Information Engineering, Niigata University, Niigata, Japan
| | - Tatsuya Ishikawa
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masayuki Takahashi
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masato Tamura
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Yoshiaki Takahashi
- Laboratory of Biochemistry, Niigata University Graduate School of Health Sciences, Niigata, Japan
| | - Masayuki Nashimoto
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
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21
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Thomson DW, Pillman KA, Anderson ML, Lawrence DM, Toubia J, Goodall GJ, Bracken CP. Assessing the gene regulatory properties of Argonaute-bound small RNAs of diverse genomic origin. Nucleic Acids Res 2015; 43:470-81. [PMID: 25452337 PMCID: PMC4288155 DOI: 10.1093/nar/gku1242] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/23/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022] Open
Abstract
High-throughput sequencing reveals an abundance of microRNA-sized fragments derived from larger non-coding RNAs. Roles for these small RNAs in gene silencing are suggested by their co-precipitation with Argonaute, the microRNA effector protein, though the extent to which they suppress gene expression endogenously remains unclear. To address this, we used luciferase reporters to determine the endogenous functionality of small RNAs from a diverse range of sources. We demonstrate small RNAs derived from snoRNAs have the capacity to act in a microRNA-like manner, though we note the vast majority of these are bound to Argonaute at levels below that required for detectable silencing activity. We show Argonaute exhibits a high degree of selectivity for the small RNAs with which it interacts and note that measuring Argonaute-associated levels is a better indicator of function than measuring total expression. Although binding to Argonaute at sufficient levels is necessary for demonstrating microRNA functionality in our reporter assay, this alone is not enough as some small RNAs derived from other non-coding RNAs (tRNAs, rRNAs, Y-RNAs) are associated with Argonaute at very high levels yet do not serve microRNA-like roles.
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Affiliation(s)
- Daniel W Thomson
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Matthew L Anderson
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - David M Lawrence
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Adelaide, SA 5005, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA 5005, Australia School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA 5005, Australia School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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22
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Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY. Dissecting noncoding and pathogen RNA-protein interactomes. RNA (NEW YORK, N.Y.) 2015; 21:135-143. [PMID: 25411354 PMCID: PMC4274633 DOI: 10.1261/rna.047803.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/27/2014] [Indexed: 05/30/2023]
Abstract
RNA-protein interactions are central to biological regulation. Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA-protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and nonhuman RNAs. Here we present FAST-iCLIP, an integrated pipeline with improved CLIP biochemistry and an automated informatic pipeline for comprehensive analysis across protein coding, noncoding, repetitive, retroviral, and nonhuman transcriptomes. FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2-bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA-protein recognition across the diversity of human and pathogen RNAs.
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Affiliation(s)
- Ryan A Flynn
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lance Martin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Brian T Do
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Brian Zarnegar
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kun Qu
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA Department of Applied Physics, Stanford University, Stanford, California 94305, USA Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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23
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Duarte Junior FF, de Lima Neto QA, Rando FDS, de Freitas DVB, Pattaro Júnior JR, Polizelli LG, Munhoz REF, Seixas FAV, Fernandez MA. Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome. MOLECULAR BIOSYSTEMS 2014; 11:801-8. [PMID: 25521575 DOI: 10.1039/c4mb00595c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The small noncoding group of RNAs called stem-bulge RNAs (sbRNAs), first reported in Caenorhabditis elegans, is described as molecules homologous to the Y RNAs, a specific class of noncoding RNAs that is present in vertebrates. This homology indicates the possibility of the existence of sbRNAs in other invertebrate organisms. In this work, we used bioinformatic tools and conserved sequences of sbRNAs from C. Elegans and Y RNAs to search for homologous sbRNA sequences in the Bombyx mori genome. This analysis led to the discovery of one noncoding gene, which was translated into RNA segments and comparatively analysed with segments from human and hamster Y RNAs and C. elegans sbRNAs in molecular dynamic simulations. This gene represents the first evidence for a new sbRNA-like noncoding RNA, the BmsbRNA gene, in this Lepidoptera genome.
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Affiliation(s)
- Francisco Ferreira Duarte Junior
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo, 5790, 87020-900, Maringá, Paraná, Brasil.
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24
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Brenu EW, Ashton KJ, Batovska J, Staines DR, Marshall-Gradisnik SM. High-throughput sequencing of plasma microRNA in chronic fatigue syndrome/myalgic encephalomyelitis. PLoS One 2014; 9:e102783. [PMID: 25238588 PMCID: PMC4169517 DOI: 10.1371/journal.pone.0102783] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/29/2014] [Indexed: 12/17/2022] Open
Abstract
Background MicroRNAs (miRNAs) are known to regulate many biological processes and their dysregulation has been associated with a variety of diseases including Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME). The recent discovery of stable and reproducible miRNA in plasma has raised the possibility that circulating miRNAs may serve as novel diagnostic markers. The objective of this study was to determine the role of plasma miRNA in CFS/ME. Results Using Illumina high-throughput sequencing we identified 19 miRNAs that were differentially expressed in the plasma of CFS/ME patients in comparison to non-fatigued controls. Following RT-qPCR analysis, we were able to confirm the significant up-regulation of three miRNAs (hsa-miR-127-3p, hsa-miR-142-5p and hsa-miR-143-3p) in the CFS/ME patients. Conclusion Our study is the first to identify circulating miRNAs from CFS/ME patients and also to confirm three differentially expressed circulating miRNAs in CFS/ME patients, providing a basis for further study to find useful CFS/ME biomarkers.
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Affiliation(s)
- Ekua W. Brenu
- School of Medical Science, Griffith Health Centre, Griffith University, Gold Coast, Queensland, Australia
- The National Centre for Neuroimmunology and Emerging Diseases, Griffith University, Gold Coast, Queensland, Australia
- * E-mail:
| | - Kevin J. Ashton
- Faculty of Health Sciences and Medicine, Bond University, Robina, Queensland, Australia
| | - Jana Batovska
- Faculty of Health Sciences and Medicine, Bond University, Robina, Queensland, Australia
| | - Donald R. Staines
- The National Centre for Neuroimmunology and Emerging Diseases, Griffith University, Gold Coast, Queensland, Australia
- Queensland Health, Gold Coast Public Health Unit, Robina, Gold Coast, Queensland, Australia
| | - Sonya M. Marshall-Gradisnik
- School of Medical Science, Griffith Health Centre, Griffith University, Gold Coast, Queensland, Australia
- The National Centre for Neuroimmunology and Emerging Diseases, Griffith University, Gold Coast, Queensland, Australia
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25
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Wang I, Kowalski MP, Langley AR, Rodriguez R, Balasubramanian S, Hsu STD, Krude T. Nucleotide contributions to the structural integrity and DNA replication initiation activity of noncoding y RNA. Biochemistry 2014; 53:5848-63. [PMID: 25151917 DOI: 10.1021/bi500470b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Noncoding Y RNAs are small stem-loop RNAs that are involved in different cellular processes, including the regulation of DNA replication. An evolutionarily conserved small domain in the upper stem of vertebrate Y RNAs has an essential function for the initiation of chromosomal DNA replication. Here we provide a structure-function analysis of this essential RNA domain under physiological conditions. Solution state nuclear magnetic resonance and far-ultraviolet circular dichroism spectroscopy show that the upper stem domain of human Y1 RNA adopts a locally destabilized A-form helical structure involving eight Watson-Crick base pairs. Within this helix, two G:C base pairs are highly stable even at elevated temperatures and therefore may serve as clamps to maintain the local structure of the helix. These two stable G:C base pairs frame three unstable base pairs, which are located centrally between them. Systematic substitution mutagenesis results in a disruption of the ordered A-form helical structure and in the loss of DNA replication initiation activity, establishing a positive correlation between folding stability and function. Our data thus provide a structural basis for the evolutionary conservation of key nucleotides in this RNA domain that are essential for the functionality of noncoding Y RNAs during the initiation of DNA replication.
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Affiliation(s)
- Iren Wang
- Institute of Biological Chemistry, Academia Sinica , 128, Section 2, Academia Road, Taipei 11529, Taiwan
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26
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Dhahbi JM. Circulating small noncoding RNAs as biomarkers of aging. Ageing Res Rev 2014; 17:86-98. [PMID: 24607831 DOI: 10.1016/j.arr.2014.02.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 12/31/2022]
Abstract
Small noncoding RNAs (sncRNAs) mediate a variety of cellular functions in animals and plants. Deep sequencing has made it possible to obtain highly detailed information on the types and abundance of sncRNAs in biological specimens, leading to the discovery that sncRNAs circulate in the blood of humans and mammals. The most abundant types of circulating sncRNAs are microRNAs (miRNAs), 5' transfer RNA (tRNA) halves, and YRNA fragments, with minute amounts of other types that may nevertheless be significant. Of the more abundant circulating sncRNAs only miRNAs have well described functions, but characteristics of the others suggest specific processing and secretion as complexes that protect the RNA from degradation. The properties of circulating sncRNAs are consistent with their serving as signaling molecules, and investigations of circulating miRNAs support the view that they can enter cells and regulate cellular functions. The serum levels of specific sncRNAs change markedly with age, and these changes can be mitigated by calorie restriction (CR), indicating that levels are under physiologic control. The ability of circulating sncRNAs to transmit functions between cells and to regulate a broad spectrum of cellular functions, and the changes in their levels with age, implicate them in the manifestations of aging. Our understanding of the functions of circulating sncRNA, particularly in relation to aging, is currently at a very early stage; results to date suggest that more extensive investigation will yield important insights into mechanisms of aging.
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Affiliation(s)
- Joseph M Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA; Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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27
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Desvignes T, Beam MJ, Batzel P, Sydes J, Postlethwait JH. Expanding the annotation of zebrafish microRNAs based on small RNA sequencing. Gene 2014; 546:386-9. [PMID: 24835514 PMCID: PMC4130647 DOI: 10.1016/j.gene.2014.05.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/29/2014] [Accepted: 05/14/2014] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range of biological processes. Because of their role in the regulation of gene expression, miRs are essential players in development by acting on cell fate determination and progression towards cell differentiation and are increasingly relevant to human health and disease. Although the zebrafish Danio rerio is a major model for studies of development, genetics, physiology, evolution, and human biology, the annotation of zebrafish miR-producing genes remains limited. In the present work, we report deep sequencing data of zebrafish small RNAs from brain, heart, testis, and ovary. Results provide evidence for the expression of 56 un-annotated mir genes and 248 un-annotated mature strands, increasing the number of zebrafish mir genes over those already deposited in miRBase by 16% and the number of mature sequences by 63%. We also describe the existence of three pairs of mirror-mir genes and two mirtron genes, genetic features previously undescribed in non-mammalian vertebrates. This report provides information that substantially increases our knowledge of the zebrafish miRNome and will benefit the entire miR community.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
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28
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Abstract
The different RNA populations within the cell, or the 'RNAome', form a complex and integral layer of gene regulation. In particular, small non-coding RNAs such as microRNAs have been shown to regulate as much as half of all genes expressed in mammals. The recent discovery of novel small RNAs derived from tRNAs, snoRNAs and Y RNAs, as well as the development of techniques that can reduce sequencing bias of these molecules, is slowly helping us to unveil the secrets of the genome.
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Meredith BK, Berry DP, Kearney F, Finlay EK, Fahey AG, Bradley DG, Lynn DJ. A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility. Front Genet 2013; 4:229. [PMID: 24223582 PMCID: PMC3818585 DOI: 10.3389/fgene.2013.00229] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/17/2013] [Indexed: 12/19/2022] Open
Abstract
Mastitis is an inflammation-driven disease of the bovine mammary gland that occurs in response to physical damage or infection and is one of the most costly production-related diseases in the dairy industry worldwide. We performed a genome-wide association study (GWAS) to identify genetic loci associated with somatic cell score (SCS), an indicator trait of mammary gland inflammation. A total of 702 Holstein-Friesian bulls were genotyped for 777,962 single nucleotide polymorphisms (SNPs) and associated with SCS phenotypes. The SCS phenotypes were expressed as daughter yield deviations (DYD) based on a large number of progeny performance records. A total of 138 SNPs on 15 different chromosomes reached genome-wide significance (corrected p-value ≤ 0.05) for association with SCS (after correction for multiple testing). We defined 28 distinct QTL regions and a number of candidate genes located in these QTL regions were identified. The most significant association (p-value = 1.70 × 10−7) was observed on chromosome 6. This QTL had no known genes annotated within it, however, the Ensembl Genome Browser predicted the presence of a small non-coding RNA (a Y RNA gene) in this genomic region. This Y RNA gene was 99% identical to human RNY4. Y RNAs are a rare type of non-coding RNA that were originally discovered due to their association with the autoimmune disease, systemic lupus erythematosus. Examining small-RNA sequencing (RNAseq) data being generated by us in multiple different mastitis-pathogen challenged cell-types has revealed that this Y RNA is expressed (but not differentially expressed) in these cells. Other QTL regions identified in this study also encoded strong candidate genes for mastitis susceptibility. A QTL region on chromosome 13, for example, was found to contain a cluster of β-defensin genes, a gene family with known roles in innate immunity. Due to the increased SNP density, this study also refined the boundaries for several known QTL for SCS and mastitis.
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Affiliation(s)
- Brian K Meredith
- Animal and Bioscience Research Department, Teagasc, Animal and Grassland Research and Innovation Centre Grange, Dunsany, Co. Meath, Ireland ; School of Agriculture and Food Science, University College Dublin Dublin 4, Ireland
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30
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Miao CG, Yang YY, He X, Huang C, Huang Y, Zhang L, Lv XW, Jin Y, Li J. The emerging role of microRNAs in the pathogenesis of systemic lupus erythematosus. Cell Signal 2013; 25:1828-36. [DOI: 10.1016/j.cellsig.2013.05.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/06/2013] [Indexed: 12/31/2022]
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31
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Chen CJ, Heard E. Small RNAs derived from structural non-coding RNAs. Methods 2013; 63:76-84. [DOI: 10.1016/j.ymeth.2013.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 04/12/2013] [Accepted: 05/06/2013] [Indexed: 12/25/2022] Open
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32
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Perez P, Jang SI, Alevizos I. Emerging landscape of non-coding RNAs in oral health and disease. Oral Dis 2013; 20:226-35. [PMID: 23781896 DOI: 10.1111/odi.12142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022]
Abstract
The world of non-coding RNAs has only recently started being discovered. For the past 40 years, coding genes, mRNA, and proteins have been the center of cellular and molecular biology, and pathologic alterations were attributed to either the aberration of gene sequence or altered promoter activity. It was only after the completion of the human genome sequence that the scientific community started seriously wondering why only a very small portion of the genome corresponded to protein-coding genes. New technologies such as the whole-genome and whole-transcriptome sequencing demonstrated that at least 90% of the genome is actively transcribed. The identification and cataloguing of multiple kinds of non-coding RNA (ncRNA) have exponentially increased, and it is now widely accepted that ncRNAs play major biological roles in cellular physiology, development, metabolism, and are also implicated in a variety of diseases. The aim of this review is to describe the two major classes (long and short forms) of non-coding RNAs and describe their subclasses in terms of function and their relevance and potential in oral diseases.
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Affiliation(s)
- P Perez
- Sjögren's Clinic, Molecular Physiology & Therapeutics, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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33
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Leung YY, Ryvkin P, Ungar LH, Gregory BD, Wang LS. CoRAL: predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Res 2013; 41:e137. [PMID: 23700308 PMCID: PMC3737537 DOI: 10.1093/nar/gkt426] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The surprising observation that virtually the entire human genome is transcribed means we know little about the function of many emerging classes of RNAs, except their astounding diversities. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their abilities to classify the various collections of non-coding RNAs (ncRNAs). To address this, we developed Classification of RNAs by Analysis of Length (CoRAL), a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length and cleavage specificity to distinguish between different ncRNA populations. We evaluated CoRAL using genome-wide small RNA sequencing data sets from four human tissue types and were able to classify six different types of RNAs with ∼80% cross-validation accuracy. Analysis by CoRAL revealed that microRNAs, small nucleolar and transposon-derived RNAs are highly discernible and consistent across all human tissue types assessed, whereas long intergenic ncRNAs, small cytoplasmic RNAs and small nuclear RNAs show less consistent patterns. The ability to reliably annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using small RNA sequencing data in less well-characterized organisms.
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Affiliation(s)
- Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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34
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Moore A. BioEssays in non-coding RNAs: A special collection of recent content. Bioessays 2013; 35:304. [DOI: 10.1002/bies.201390011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Köhn M, Pazaitis N, Hüttelmaier S. Why YRNAs? About Versatile RNAs and Their Functions. Biomolecules 2013; 3:143-56. [PMID: 24970161 PMCID: PMC4030889 DOI: 10.3390/biom3010143] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 01/27/2013] [Accepted: 01/31/2013] [Indexed: 11/20/2022] Open
Abstract
Y RNAs constitute a family of highly conserved small noncoding RNAs (in humans: 83-112 nt; Y1, Y3, Y4 and Y5). They are transcribed from individual genes by RNA-polymerase III and fold into conserved stem-loop-structures. Although discovered 30 years ago, insights into the cellular and physiological role of Y RNAs remains incomplete. In this review, we will discuss knowledge on the structural properties, associated proteins and discuss proposed functions of Y RNAs. We suggest Y RNAs to be an integral part of ribonucleoprotein networks within cells and could therefore have substantial influence on many different cellular processes. Putative functions of Y RNAs include small RNA quality control, DNA replication, regulation of the cellular stress response and proliferation. This suggests Y RNAs as essential regulators of cell fate and indicates future avenues of research, which will provide novel insights into the role of small noncoding RNAs in gene expression.
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Affiliation(s)
- Marcel Köhn
- Martin-Luther-University Halle-Wittenberg, Institute of Molecular Medicine, Section Molecular Cell Biology, ZAMED, Heinrich-Damerow-Str.1, D-6120 Halle, Germany.
| | - Nikolaos Pazaitis
- Martin-Luther-University Halle-Wittenberg, Institute of Molecular Medicine, Section Molecular Cell Biology, ZAMED, Heinrich-Damerow-Str.1, D-6120 Halle, Germany.
| | - Stefan Hüttelmaier
- Martin-Luther-University Halle-Wittenberg, Institute of Molecular Medicine, Section Molecular Cell Biology, ZAMED, Heinrich-Damerow-Str.1, D-6120 Halle, Germany.
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36
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Langenberger D, Çakir MV, Hoffmann S, Stadler PF. Dicer-processed small RNAs: rules and exceptions. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 320:35-46. [PMID: 23165937 DOI: 10.1002/jez.b.22481] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/15/2012] [Accepted: 09/13/2012] [Indexed: 01/08/2023]
Abstract
Canonical microRNAs are excised from their hairpin-shaped precursors by Dicer. In order to find possible exceptions to this rule and to identify additional substrates for Dicer processing we re-evaluate the small RNA sequencing data of the Dicer knockdown experiment in MCF-7 cells orignally published by Friedländer et al. [Friedländer et al., 2012, Nucleic Acids Res 40:37-52]. While the well-known non-Dicer mir-451 is not sufficiently expressed in these experiments, there are several additional Dicer-independent microRNAs, among them the important tumor supressor mir-663a. We recover previously described examples of non-miRNA Dicer substrates such as tRNA-Gln and several snoRNAs. Interestingly, sdRNAs derived from box C/D snoRNAs are Dicer-independent, while those derived from box H/ACA snoRNAs are often Dicer dependent. Several pol-III transcripts, in particular the vault RNAs and the great ape specific snaRs are processed by Dicer, while the small RNAs originating from Y RNAs seem to be Dicer independent.
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Affiliation(s)
- David Langenberger
- LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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37
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Dieci G, Conti A, Pagano A, Carnevali D. Identification of RNA polymerase III-transcribed genes in eukaryotic genomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:296-305. [PMID: 23041497 DOI: 10.1016/j.bbagrm.2012.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/20/2012] [Accepted: 09/21/2012] [Indexed: 12/16/2022]
Abstract
The RNA polymerase (Pol) III transcription system is devoted to the production of short, generally abundant noncoding (nc) RNAs in all eukaryotic cells. Previously thought to be restricted to a few housekeeping genes easily detectable in genome sequences, the set of known Pol III-transcribed genes (class III genes) has been expanding in the last ten years, and the issue of their detection, annotation and actual expression has been stimulated and revived by the results of recent high-resolution genome-wide location analyses of the mammalian Pol III machinery, together with those of Pol III-centered computational studies and of ncRNA-focused transcriptomic approaches. In this article, we provide an outline of distinctive features of Pol III-transcribed genes that have allowed and currently allow for their detection in genome sequences, we critically review the currently practiced strategies for the identification of novel class III genes and transcripts, and we discuss emerging themes in Pol III transcription regulation which might orient future transcriptomic studies. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Giorgio Dieci
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy.
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38
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Hu S, Wu J, Chen L, Shan G. Signals from noncoding RNAs: unconventional roles for conventional pol III transcripts. Int J Biochem Cell Biol 2012; 44:1847-51. [PMID: 22819850 DOI: 10.1016/j.biocel.2012.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/06/2012] [Accepted: 07/09/2012] [Indexed: 12/29/2022]
Abstract
A range of noncoding RNAs are transcribed by pol III. A lot of them such as tRNA, 7SL RNA, 7SK RNA, 5S RNA, MRP RNA, Y RNAs, H1 RNA, and vault RNAs are considered as "house keeping" RNAs essential for eukaryotic cells. In recent years, researchers started to recognize the existence of unconventional functions of many pol III transcripts other than classical "house keeping" roles. Therefore, these ncRNAs could now be viewed as molecules with functional regulatory signals as well as cellular building blocks. These noncoding RNAs, all transcribed by pol III, may assemble regulatory networks with analogy to signaling pathways in eukaryotic cells. In this review we discuss these unconventional roles of pol III transcripts.
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Affiliation(s)
- Shanshan Hu
- School of Life Science, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui Province 230027, China
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39
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Current world literature. Curr Opin Rheumatol 2012; 24:435-40. [PMID: 22653148 DOI: 10.1097/bor.0b013e3283556515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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40
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Bortolin-Cavaillé ML, Cavaillé J. The SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters at the imprinted Prader-Willi locus generate canonical box C/D snoRNAs. Nucleic Acids Res 2012; 40:6800-7. [PMID: 22495932 PMCID: PMC3413130 DOI: 10.1093/nar/gks321] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The imprinted Snurf–Snrpn chromosomal domain contains two large arrays of tandemly repeated, paternally expressed box C/D small-nucleolar RNA (snoRNA) genes: the SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters believed to play key roles in the fine-tuning of serotonin receptor (5-HT2C) pre-mRNA processing and in the etiology of the Prader–Willi Syndrome (PWS), respectively. SNORD115 and SNORD116 were recently proposed to undergo significant conversion into shorter RNA species, the so-called psnoRNAs. Here, we provide evidence that argues against the existence of abundant psnoRNAs in human or mouse brain. Instead, we characterize a previously unsuspected low-abundance, fibrillarin-associated SNORD115-derived smaller RNA species. Based on these findings, we strongly recommend that PWS-encoded SNORD115 and SNORD116 be considered as bona fide box C/D snoRNAs.
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41
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Nicolas FE, Hall AE, Csorba T, Turnbull C, Dalmay T. Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway. FEBS Lett 2012; 586:1226-30. [PMID: 22575660 DOI: 10.1016/j.febslet.2012.03.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 03/13/2012] [Accepted: 03/15/2012] [Indexed: 12/30/2022]
Abstract
Y RNAs are approximately 100 nucleotide long conserved cytoplasmic non-coding RNAs, which produce smaller RNA fragments during apoptosis. Here we show that these smaller RNA molecules are also produced in non-stressed cells and in a range of human cancerous and non-cancerous cell types. Recent reports have speculated that the cleavage products of Y RNAs enter the microRNA pathway. We tested this hypothesis and found that Y5 and Y3 RNA fragments are Dicer independent, they are in different complexes than microRNAs and that they are not co-immunoprecipitated with Ago2. Therefore we conclude that Y RNA fragments do not enter the microRNA pathway.
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42
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Cifuentes RA, Restrepo-Montoya D, Anaya JM. The autoimmune tautology: an in silico approach. Autoimmune Dis 2012; 2012:792106. [PMID: 22474574 PMCID: PMC3303588 DOI: 10.1155/2012/792106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 11/26/2011] [Indexed: 11/17/2022] Open
Abstract
There is genetic evidence of similarities and differences among autoimmune diseases (AIDs) that warrants looking at a general panorama of what has been published. Thus, our aim was to determine the main shared genes and to what extent they contribute to building clusters of AIDs. We combined a text-mining approach to build clusters of genetic concept profiles (GCPs) from the literature in MedLine with knowledge of protein-protein interactions to confirm if genes in GCP encode proteins that truly interact. We found three clusters in which the genes with the highest contribution encoded proteins that showed strong and specific interactions. After projecting the AIDs on a plane, two clusters could be discerned: Sjögren's syndrome-systemic lupus erythematosus, and autoimmune thyroid disease-type1 diabetes-rheumatoid arthritis. Our results support the common origin of AIDs and the role of genes involved in apoptosis such as CTLA4, FASLG, and IL10.
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Affiliation(s)
- Ricardo A. Cifuentes
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24, No. 63-69 piso 3, Bogotá, Colombia
| | - Daniel Restrepo-Montoya
- Bioinformatics and Intelligent Systems Research Laboratory (BIOLISI), Universidad Nacional, Avenida Carrera 30, No. 45-03, Bogotá, Colombia
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24, No. 63-69 piso 3, Bogotá, Colombia
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43
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Circulating microRNAs involved in multiple sclerosis. Mol Biol Rep 2012; 39:6219-25. [PMID: 22231906 DOI: 10.1007/s11033-011-1441-7] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 12/26/2011] [Indexed: 12/18/2022]
Abstract
Multiple sclerosis (MS) is an immune-mediated, demyelinating and neurodegenerative disease of the central nervous system. After traumatic brain injury, it is the leading cause of neurology disability in young adults. Considerable advances have been made in identifying genes involved in MS but the genetic and phenotypic complexity associated with this disease significantly hinders any progress. A novel class of small RNA molecules, microRNAs (miRNAs) has acquired much attention because they regulate the expression of up to 30% of protein-coding genes and may play a pivotal role in the development of many, if not all, complex diseases. Seven published studies investigated miRNAs from peripheral blood mononuclear cells, CD4+, CD8+ T cell, B lymphocytes, peripheral blood leukocytes, whole blood and brain astrocytes with MS risk. The absence of MS studies investigating plasma miRNA prompted the current investigation of identifying a circulating miRNA signature in MS. We conducted a microarray analysis of over 900 known miRNA transcripts from plasma samples collected from four MS individuals and four sex-aged and ethnicity matched healthy controls. We identified six plasma miRNA (miR-614, miR-572, miR-648, miR-1826, miR-422a and miR-22) that were significantly up-regulated and one plasma miRNA (miR-1979) that was significantly down-regulated in MS individuals. Both miR-422a and miR-22 have previously been implicated in MS. The present study is the first to show a circulating miRNA signature involved in MS that could serve as a potential prognostic and diagnostic biomarker for MS.
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