1
|
Rai SN, Dutta T. Role of Yrn2 under oxidative stress in Deinococcus radiodurans. Biochem Biophys Res Commun 2024; 723:150169. [PMID: 38815487 DOI: 10.1016/j.bbrc.2024.150169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
Among the two Y RNAs in Deinococcus radiodurans, the functional properties of Yrn2 are still not known. Yrn2 although consists of a long stem-loop for Rsr binding, differs from Yrn1 in the effector binding site. An initial study on Yrn2 delineated it to be a UV-induced noncoding RNA. Apart from that Yrn2 has scarcely been investigated. In the current study, we identified Yrn2 as an γ-radiation induced Y RNA, which is also induced upon H2O2 and mitomycin treatment. Ectopically expressed Yrn2 appeared to be nontoxic to the cell growth. An overabundance of Yrn2 was found to ameliorate cell survival under oxidative stress through the detoxification of intracellular reactive oxygen species with a subsequent decrease in total protein carbonylation. A significant accumulation of intracellular Mn(II) with unaltered Fe(II) and Zn(II) with detected while Yrn2 is overabundant in the cells. This study identified the role of a novel Yrn2 under oxidative stress in D. radiodurans.
Collapse
Affiliation(s)
- Shiv Narayan Rai
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| |
Collapse
|
2
|
Almeida PP, Moraes JA, Barja-Fidalgo TC, Renovato-Martins M. Extracellular vesicles as modulators of monocyte and macrophage function in tumors. AN ACAD BRAS CIENC 2024; 96:e20231212. [PMID: 38922279 DOI: 10.1590/0001-3765202420231212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/17/2024] [Indexed: 06/27/2024] Open
Abstract
The tumor microenvironment (TME) harbors several cell types, such as tumor cells, immune cells, and non-immune cells. These cells communicate through several mechanisms, such as cell-cell contact, cytokines, chemokines, and extracellular vesicles (EVs). Tumor-derived vesicles are known to have the ability to modulate the immune response. Monocytes are a subset of circulating innate immune cells and play a crucial role in immune surveillance, being recruited to tissues where they differentiate into macrophages. In the context of tumors, it has been observed that tumor cells can attract monocytes to the TME and induce their differentiation into tumor-associated macrophages with a pro-tumor phenotype. Tumor-derived EVs have emerged as essential structures mediating this process. Through the transfer of specific molecules and signaling factors, tumor-derived EVs can shape the phenotype and function of monocytes, inducing the expression of cytokines and molecules by these cells, thus modulating the TME towards an immunosuppressive environment.
Collapse
Affiliation(s)
- Palloma P Almeida
- Universidade Federal Fluminense, Departamento de Biologia Celular e Molecular, Instituto de Biologia, Laboratório de Inflamação e Metabolismo, Rua Professor Marcos Waldemar de Freitas Reis, s/n, 24020-140 Niterói, RJ, Brazil
- Universidade Federal do Rio de Janeiro, Instituto de Ciências Biomédicas, Laboratório de Biologia Redox, Av. Carlos Chagas Filho, 373, Prédio do ICB - Anexo B1F3, Ilha do Fundão, 21941-902 Rio de Janeiro, RJ, Brazil
- Universidade do Estado do Rio de Janeiro, Departamento de Biologia Celular, Instituto de Biologia Roberto Alcantara Gomes - IBRAG, Laboratório de Farmacologia Celular e Molecular, Av. 28 de setembro, 87, 20551-030 Rio de Janeiro, RJ, Brazil
| | - João Alfredo Moraes
- Universidade Federal do Rio de Janeiro, Instituto de Ciências Biomédicas, Laboratório de Biologia Redox, Av. Carlos Chagas Filho, 373, Prédio do ICB - Anexo B1F3, Ilha do Fundão, 21941-902 Rio de Janeiro, RJ, Brazil
| | - Thereza Christina Barja-Fidalgo
- Universidade do Estado do Rio de Janeiro, Departamento de Biologia Celular, Instituto de Biologia Roberto Alcantara Gomes - IBRAG, Laboratório de Farmacologia Celular e Molecular, Av. 28 de setembro, 87, 20551-030 Rio de Janeiro, RJ, Brazil
| | - Mariana Renovato-Martins
- Universidade Federal Fluminense, Departamento de Biologia Celular e Molecular, Instituto de Biologia, Laboratório de Inflamação e Metabolismo, Rua Professor Marcos Waldemar de Freitas Reis, s/n, 24020-140 Niterói, RJ, Brazil
| |
Collapse
|
3
|
Taube M, Lisiak N, Totoń E, Rubiś B. Human Vault RNAs: Exploring Their Potential Role in Cellular Metabolism. Int J Mol Sci 2024; 25:4072. [PMID: 38612882 PMCID: PMC11012908 DOI: 10.3390/ijms25074072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Non-coding RNAs have been described as crucial regulators of gene expression and guards of cellular homeostasis. Some recent papers focused on vault RNAs, one of the classes of non-coding RNA, and their role in cell proliferation, tumorigenesis, apoptosis, cancer response to therapy, and autophagy, which makes them potential therapy targets in oncology. In the human genome, four vault RNA paralogues can be distinguished. They are associated with vault complexes, considered the largest ribonucleoprotein complexes. The protein part of these complexes consists of a major vault protein (MVP) and two minor vault proteins (vPARP and TEP1). The name of the complex, as well as vault RNA, comes from the hollow barrel-shaped structure that resembles a vault. Their sequence and structure are highly evolutionarily conserved and show many similarities in comparison with different species, but vault RNAs have various roles. Vaults were discovered in 1986, and their functions remained unclear for many years. Although not much is known about their contribution to cell metabolism, it has become clear that vault RNAs are involved in various processes and pathways associated with cancer progression and modulating cell functioning in normal and pathological stages. In this review, we discuss known functions of human vault RNAs in the context of cellular metabolism, emphasizing processes related to cancer and cancer therapy efficacy.
Collapse
Affiliation(s)
| | | | | | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Rokietnicka 3, 60-806 Poznan, Poland; (M.T.); (N.L.); (E.T.)
| |
Collapse
|
4
|
Michael FS, Hamouda MB, Stupak J, Li J, Pearson A, Sauvageau J. Identification of glycosylated nucleosides in small synthetic glyco-RNAs. Chembiochem 2024; 25:e202300784. [PMID: 38116890 DOI: 10.1002/cbic.202300784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Recently, the post-transcriptional modification of RNA with N-glycans was reported, changing the paradigm that RNAs are not commonly N-glycosylated. Moreover, glycan modifications of RNA are investigated for therapeutic targeting purposes. But the glyco-RNA field is in its infancy with many challenges to overcome. One question is how to accurately characterize glycosylated RNA constructs. Thus, we generated glycosylated forms of Y5 RNA mimics, a short non-coding RNA. The simple glycans lactose and sialyllactose were attached to the RNA backbone using azide-alkyne cycloadditions. Using nuclease digestion followed by LC-MS, we confirmed the presence of the glycosylated nucleosides, and characterized the chemical linkage. Next, we probed if glycosylation would affect the cellular response to Y5 RNA. We treated human foreskin fibroblasts in culture with the generated compounds. Key transcripts in the innate immune response were quantified by RT-qPCR. We found that under our experimental conditions, exposure of cells to the Y5 RNA did not trigger an interferon response, and glycosylation of this RNA did not have an impact. Thus, we have identified a successful approach to chemically characterize synthetic glyco-RNAs, which will be critical for further studies to elucidate how the presence of complex glycans on RNA affects the cellular response.
Collapse
Affiliation(s)
- Frank St Michael
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Maha Ben Hamouda
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531, boul. des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Jacek Stupak
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Jianjun Li
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Angela Pearson
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531, boul. des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Janelle Sauvageau
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| |
Collapse
|
5
|
Extracellular Vesicles of Mesenchymal Stem Cells Are More Effectively Accessed through Polyethylene Glycol-Based Precipitation than by Ultracentrifugation. Stem Cells Int 2022; 2022:3577015. [PMID: 36110890 PMCID: PMC9470370 DOI: 10.1155/2022/3577015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Extracellular vesicles (EVs) have been identified as cell-cell communication agents, and EVs derived from mesenchymal stem cells (MSCs) exhibit therapeutic effects similar to those of the cells of origin. Precipitation methods have been used extensively for EV harvests, such as UC- (ultracentrifugation-) or PEG- (polyethylene glycol-) based methods, and the difference in EVs derived from MSCs by UC and PEG is not fully understood. We harvested EVs from amniotic fluid MSCs (AF-MSCs) by UC- or PEG-based precipitation methods and conducted a comparison study of those EVs derived by the two methods: output, RNA, and protein expression of EVs and EV biological reaction in a THP-1-cell model of LPS induction, which was considered an infection model. There was no difference in morphology, size, or specific marker-positive ratio of PEG-EVs and UC-EVs, but PEG obtained more EV particles, protein, and RNA than the UC method. In our THP-1 model of LPS induction, MSC-EVs did not lead to a change in protein expression but inhibited the LPS-induced increase in cytokine secretion. UC-EVs were more effective for TNF-α inhibition, and PEG-EVs were more effective for IL10 inhibition. Thus, our findings provide evidence that PEG-based precipitation is a more efficient mesenchymal stem cell-extracellular vesicle-derived method than UC.
Collapse
|
6
|
Vabret N, Najburg V, Solovyov A, Gopal R, McClain C, Šulc P, Balan S, Rahou Y, Beauclair G, Chazal M, Varet H, Legendre R, Sismeiro O, Sanchez David RY, Chauveau L, Jouvenet N, Markowitz M, van der Werf S, Schwartz O, Tangy F, Bhardwaj N, Greenbaum BD, Komarova AV. Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. iScience 2022; 25:104599. [PMID: 35789859 PMCID: PMC9250025 DOI: 10.1016/j.isci.2022.104599] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/01/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Pattern recognition receptors (PRRs) protect against microbial invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. Although microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation remains overlooked. Here, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors (RLRs) upon infection by different RNA viruses. In each infection, several RNAs transcribed by RNA polymerase III (Pol3) specifically engaged RLRs, particularly the family of Y RNAs. Sensing of Y RNAs was dependent on their mimicking of viral secondary structure and their 5'-triphosphate extremity. Further, we found that HIV-1 triggered a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, inducing a transcriptome-wide change of cellular RNA 5'-triphosphorylation that licenses Y RNA immunogenicity. Overall, our work uncovers the contribution of endogenous RNAs to antiviral immunity and demonstrates the importance of this pathway in HIV-1 infection.
Collapse
Affiliation(s)
- Nicolas Vabret
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Valérie Najburg
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Alexander Solovyov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ramya Gopal
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher McClain
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Petr Šulc
- Center for Molecular Design and Biomimetics at the Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sreekumar Balan
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yannis Rahou
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Guillaume Beauclair
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Maxime Chazal
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Hugo Varet
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub Informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, Université de Paris, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Rachel Legendre
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub Informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, Université de Paris, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Raul Y. Sanchez David
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Lise Chauveau
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Nolwenn Jouvenet
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY, USA
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Frédéric Tangy
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Extra-mural Member, Parker Institute of Cancer Immunotherapy, USA
| | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Physiology, Biophysics, & Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anastassia V. Komarova
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| |
Collapse
|
7
|
Inhibition of Respiratory Syncytial Virus Infection by Small Non-Coding RNA Fragments. Int J Mol Sci 2022; 23:ijms23115990. [PMID: 35682669 PMCID: PMC9180592 DOI: 10.3390/ijms23115990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in infants, immunocompromised individuals and the elderly. As the only current specific treatment options for RSV are monoclonal antibodies, there is a need for efficacious antiviral treatments against RSV to be developed. We have previously shown that a group of synthetic non-coding single-stranded DNA oligonucleotides with lengths of 25–40 nucleotides can inhibit RSV infection in vitro and in vivo. Based on this, herein, we investigate whether naturally occurring single-stranded small non-coding RNA (sncRNA) fragments present in the airways have antiviral effects against RSV infection. From publicly available sequencing data, we selected sncRNA fragments such as YRNAs, tRNAs and rRNAs present in human bronchoalveolar lavage fluid (BALF) from healthy individuals. We utilized a GFP-expressing RSV to show that pre-treatment with the selected sncRNA fragments inhibited RSV infection in A549 cells in vitro. Furthermore, by using a flow cytometry-based binding assay, we demonstrate that these naturally occurring sncRNAs fragments inhibit viral infection most likely by binding to the RSV entry receptor nucleolin and thereby preventing the virus from binding to host cells, either directly or via steric hindrance. This finding highlights a new function of sncRNAs and displays the possibility of using naturally occurring sncRNAs as treatments against RSV.
Collapse
|
8
|
Leypold NA, Speicher MR. Evolutionary conservation in noncoding genomic regions. Trends Genet 2021; 37:903-918. [PMID: 34238591 DOI: 10.1016/j.tig.2021.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/25/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022]
Abstract
Humans may share more genomic commonalities with other species than previously thought. According to current estimates, ~5% of the human genome is functionally constrained, which is a much larger fraction than the ~1.5% occupied by annotated protein-coding genes. Hence, ~3.5% of the human genome comprises likely functional conserved noncoding elements (CNEs) preserved among organisms, whose common ancestors existed throughout hundreds of millions of years of evolution. As whole-genome sequencing emerges as a standard procedure in genetic analyses, interpretation of variations in CNEs, including the elucidation of mechanistic and functional roles, becomes a necessity. Here, we discuss the phenomenon of noncoding conservation via four dimensions (sequence, regulatory conservation, spatiotemporal expression, and structure) and the potential significance of CNEs in phenotype variation and disease.
Collapse
Affiliation(s)
- Nicole A Leypold
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, Graz, Austria.
| |
Collapse
|
9
|
Identification of a short form of a Caenorhabditis elegans Y RNA homolog Cel7 RNA. Biochem Biophys Res Commun 2021; 557:104-109. [PMID: 33862452 DOI: 10.1016/j.bbrc.2021.03.143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 11/23/2022]
Abstract
Cel7 RNA is a member of the Caenorhabditis elegans stem-bulge RNAs (sbRNAs) that are classified into the Y RNA family based on their structural similarity. We identified a 15-nucleotide-shorter form of Cel7 RNA and designated it Cel7s RNA. Both Cel7 and Cel7s RNAs increased during the development of worms from L1 to adult. Cel7s RNA was notably more abundant in embryos than in L1 to L3 larvae. Cel7 RNA in embryo was less than those in L2 to adult. The ratio of cellular level of Cel7 RNA to that of Cel7s RNA was higher in L1 to L4, but reversed in embryos and adults. In rop-1 mutants, in which the gene for the C. elegans Ro60 homolog, ROP-1, was disrupted, Cel7s RNA decreased similar to CeY RNA, another C. elegans Y RNA homolog. Surprisingly, Cel7 RNA, existed stably in the absence of ROP-1, unlike Cel7s and CeY RNAs. Gel-shift assays demonstrated that Cel7 and Cel7s RNAs bound to ROP-1 in a similar manner, which was much weaker than CeY RNA. The 5'-terminal 15-nt of Cel7 RNA could be folded into a short stem-loop structure, probably contributing to the stability of Cel7 RNA in vivo and the distinct expression patterns of the 2 RNAs.
Collapse
|
10
|
Leng Y, Sim S, Magidson V, Wolin SL. Noncoding Y RNAs regulate the levels, subcellular distribution and protein interactions of their Ro60 autoantigen partner. Nucleic Acids Res 2020; 48:6919-6930. [PMID: 32469055 DOI: 10.1093/nar/gkaa414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 12/31/2022] Open
Abstract
Noncoding Y RNAs are abundant in animal cells and present in many bacteria. These RNAs are bound and stabilized by Ro60, a ring-shaped protein that is a target of autoantibodies in patients with systemic lupus erythematosus. Studies in bacteria revealed that Y RNA tethers Ro60 to a ring-shaped exoribonuclease, forming a double-ringed RNP machine specialized for structured RNA degradation. In addition to functioning as a tether, the bacterial RNA gates access of substrates to the Ro60 cavity. To identify roles for Y RNAs in mammals, we used CRISPR to generate mouse embryonic stem cells lacking one or both of the two murine Y RNAs. Despite reports that animal cell Y RNAs are essential for DNA replication, cells lacking these RNAs divide normally. However, Ro60 levels are reduced, revealing that Y RNA binding is required for Ro60 to accumulate to wild-type levels. Y RNAs regulate the subcellular location of Ro60, since Ro60 is reduced in the cytoplasm and increased in nucleoli when Y RNAs are absent. Last, we show that Y RNAs tether Ro60 to diverse effector proteins to generate specialized RNPs. Together, our data demonstrate that the roles of Y RNAs are intimately connected to that of their Ro60 partner.
Collapse
Affiliation(s)
- Yuanyuan Leng
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| |
Collapse
|
11
|
Abstract
Ro60 ribonucleoproteins (RNPs), composed of the ring-shaped Ro 60-kDa (Ro60) protein and noncoding RNAs called Y RNAs, are present in all three domains of life. Ro60 was first described as an autoantigen in patients with rheumatic disease, and Ro60 orthologs have been identified in 3% to 5% of bacterial genomes, spanning the majority of phyla. Their functions have been characterized primarily in Deinococcus radiodurans, the first sequenced bacterium with a recognizable ortholog. In D. radiodurans, the Ro60 ortholog enhances the ability of 3'-to-5' exoribonucleases to degrade structured RNA during several forms of environmental stress. Y RNAs are regulators that inhibit or allow the interactions of Ro60 with other proteins and RNAs. Studies of Ro60 RNPs in other bacteria hint at additional functions, since the most conserved Y RNA contains a domain that is a close tRNA mimic and Ro60 RNPs are often encoded adjacent to components of RNA repair systems.
Collapse
Affiliation(s)
- Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Kevin Hughes
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Xinguo Chen
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| |
Collapse
|
12
|
Y RNA: An Overview of Their Role as Potential Biomarkers and Molecular Targets in Human Cancers. Cancers (Basel) 2020; 12:cancers12051238. [PMID: 32423154 PMCID: PMC7281143 DOI: 10.3390/cancers12051238] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Y RNA are a class of small non-coding RNA that are largely conserved. Although their discovery was almost 40 years ago, their function is still under investigation. This is evident in cancer biology, where their role was first studied just a dozen years ago. Since then, only a few contributions were published, mostly scattered across different tumor types and, in some cases, also suffering from methodological limitations. Nonetheless, these sparse data may be used to make some estimations and suggest routes to better understand the role of Y RNA in cancer formation and characterization. Here we summarize the current knowledge about Y RNA in multiple types of cancer, also including a paragraph about tumors that might be included in this list in the future, if more evidence becomes available. The picture arising indicates that Y RNA might be useful in tumor characterization, also relying on non-invasive methods, such as the analysis of the content of extracellular vesicles (EV) that are retrieved from blood plasma and other bodily fluids. Due to the established role of Y RNA in DNA replication, it is possible to hypothesize their therapeutic targeting to inhibit cell proliferation in oncological patients.
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Boccitto M, Wolin SL. Ro60 and Y RNAs: structure, functions, and roles in autoimmunity. Crit Rev Biochem Mol Biol 2019; 54:133-152. [PMID: 31084369 DOI: 10.1080/10409238.2019.1608902] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ro60, also known as SS-A or TROVE2, is an evolutionarily conserved RNA-binding protein that is found in most animal cells, approximately 5% of sequenced prokaryotic genomes and some archaea. Ro60 is present in cells as both a free protein and as a component of a ribonucleoprotein complex, where its best-known partners are members of a class of noncoding RNAs called Y RNAs. Structural and biochemical analyses have revealed that Ro60 is a ring-shaped protein that binds Y RNAs on its outer surface. In addition to Y RNAs, Ro60 binds misfolded and aberrant noncoding RNAs in some animal cell nuclei. Although the fate of these defective Ro60-bound noncoding RNAs in animal cells is not well-defined, a bacterial Ro60 ortholog functions with 3' to 5' exoribonucleases to assist structured RNA degradation. Studies of Y RNAs have revealed that these RNAs regulate the subcellular localization of Ro60, tether Ro60 to effector proteins and regulate the access of other RNAs to its central cavity. As both mammalian cells and bacteria lacking Ro60 are sensitized to ultraviolet irradiation, Ro60 function may be important during exposure to some environmental stressors. Here we summarize the current knowledge regarding the functions of Ro60 and Y RNAs in animal cells and bacteria. Because the Ro60 RNP is a clinically important target of autoantibodies in patients with rheumatic diseases such as Sjogren's syndrome, systemic lupus erythematosus, and neonatal lupus, we also discuss potential roles for Ro60 RNPs in the initiation and pathogenesis of systemic autoimmune rheumatic disease.
Collapse
Affiliation(s)
- Marco Boccitto
- a RNA Biology Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , MD , USA
| | - Sandra L Wolin
- a RNA Biology Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , MD , USA
| |
Collapse
|
17
|
Duarte Junior FF, Bueno PSA, Pedersen SL, Rando FDS, Pattaro Júnior JR, Caligari D, Ramos AC, Polizelli LG, Lima AFDS, de Lima Neto QA, Krude T, Seixas FAV, Fernandez MA. Identification and characterization of stem-bulge RNAs in Drosophila melanogaster. RNA Biol 2019; 16:330-339. [PMID: 30666901 DOI: 10.1080/15476286.2019.1572439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Non-coding Y RNAs and stem-bulge RNAs are homologous small RNAs in vertebrates and nematodes, respectively. They share a conserved function in the replication of chromosomal DNA in these two groups of organisms. However, functional homologues have not been found in insects, despite their common early evolutionary history. Here, we describe the identification and functional characterization of two sbRNAs in Drosophila melanogaster, termed Dm1 and Dm2. The genes coding for these two RNAs were identified by a computational search in the genome of D. melanogaster for conserved sequence motifs present in nematode sbRNAs. The predicted secondary structures of Dm1 and Dm2 partially resemble nematode sbRNAs and show stability in molecular dynamics simulations. Both RNAs are phylogenetically closer related to nematode sbRNAs than to vertebrate Y RNAs. Dm1, but not Dm2 sbRNA is abundantly expressed in D. melanogaster S2 cells and adult flies. Only Dm1, but not Dm2 sbRNA can functionally replace Y RNAs in a human cell-free DNA replication initiation system. Therefore, Dm1 is the first functional sbRNA described in insects, allowing future investigations into the physiological roles of sbRNAs in the genetically tractable model organism D. melanogaster.
Collapse
Affiliation(s)
| | - Paulo Sérgio Alves Bueno
- b Departamento de Tecnologia , Universidade Estadual de Maringá, campus Umuarama , Umuarama , Paraná , Brazil
| | - Sofia L Pedersen
- c Department of Zoology , University of Cambridge , Cambridge , UK
| | - Fabiana Dos Santos Rando
- d Center for Molecular, Structural and Functional Biology - CBM/COMCAP , Universidade Estadual de Maringá , Maringá , Paraná , Brazil
| | - José Renato Pattaro Júnior
- b Departamento de Tecnologia , Universidade Estadual de Maringá, campus Umuarama , Umuarama , Paraná , Brazil
| | - Daniel Caligari
- a Departamento de Biotecnologia, Genética e Biologia Celular , Universidade Estadual de Maringá , Maringá , Paraná , Brazil
| | - Anelise Cardoso Ramos
- a Departamento de Biotecnologia, Genética e Biologia Celular , Universidade Estadual de Maringá , Maringá , Paraná , Brazil
| | - Lorena Gomes Polizelli
- a Departamento de Biotecnologia, Genética e Biologia Celular , Universidade Estadual de Maringá , Maringá , Paraná , Brazil
| | | | - Quirino Alves de Lima Neto
- a Departamento de Biotecnologia, Genética e Biologia Celular , Universidade Estadual de Maringá , Maringá , Paraná , Brazil
| | - Torsten Krude
- c Department of Zoology , University of Cambridge , Cambridge , UK
| | | | - Maria Aparecida Fernandez
- a Departamento de Biotecnologia, Genética e Biologia Celular , Universidade Estadual de Maringá , Maringá , Paraná , Brazil
| |
Collapse
|
18
|
Abstract
Y RNAs are noncoding RNAs (ncRNAs) that are present in most animal cells and also in many bacteria. These RNAs were discovered because they are bound by the Ro60 protein, a major target of autoantibodies in patients with some systemic autoimmune rheumatic diseases. Studies of Ro60 and Y RNAs in Deinococcus radiodurans, the first sequenced bacterium with a Ro60 ortholog, revealed that they function with 3'-to-5' exoribonucleases to alter the composition of RNA populations during some forms of environmental stress. In the best-characterized example, Y RNA tethers the Ro60 protein to the exoribonuclease polynucleotide phosphorylase, allowing this exoribonuclease to degrade structured RNAs more effectively. Y RNAs can also function as gates to regulate access of other RNAs to the Ro60 central cavity. Recent studies in the enteric bacterium Salmonella enterica serovar Typhimurium resulted in the discovery that Y RNAs are widely present in bacteria. Remarkably, the most-conserved subclass of bacterial Y RNAs contains a domain that mimics tRNA. In this review, we discuss the structure, conservation, and known functions of bacterial Y RNAs as well as the certainty that more bacterial Y RNAs and additional roles for these ncRNAs remain to be uncovered.
Collapse
|
19
|
Kami D, Kitani T, Nakamura A, Wakui N, Mizutani R, Ohue M, Kametani F, Akimitsu N, Gojo S. The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency. PLoS One 2018; 13:e0203708. [PMID: 30273347 PMCID: PMC6166933 DOI: 10.1371/journal.pone.0203708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/24/2018] [Indexed: 12/30/2022] Open
Abstract
Cellular transitions and differentiation processes require mRNAs supporting the new phenotype but also the clearance of existing mRNAs for the parental phenotype. Cellular reprogramming from fibroblasts to induced pluripotent stem cells (iPSCs) occurs at the early stage of mesenchymal epithelial transition (MET) and involves drastic morphological changes. We examined the molecular mechanism for MET, focusing on RNA metabolism. DDX6, an RNA helicase, was indispensable for iPSC formation, in addition to RO60 and RNY1, a non-coding RNA, which form complexes involved in intracellular nucleotide sensing. RO60/RNY1/DDX6 complexes formed prior to processing body formation, which is central to RNA metabolism. The abrogation of DDX6 expression inhibited iPSC generation, which was mediated by RNA decay targeting parental mRNAs supporting mesenchymal phenotypes, along with microRNAs, such as miR-302b-3p. These results show that parental mRNA clearance is a prerequisite for cellular reprogramming and that DDX6 plays a central role in this process.
Collapse
Affiliation(s)
- Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoya Kitani
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akihiro Nakamura
- Department of Pediatric Cardiology and Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naoki Wakui
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan
| | - Rena Mizutani
- Radioisotope Center, The University of Tokyo, Tokyo, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan
| | - Fuyuki Kametani
- Department of Dementia and Higher Brain Function, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | | | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail:
| |
Collapse
|
20
|
Abstract
SIGNIFICANCE Platelets are anucleate blood cells that are involved in hemostasis and thrombosis. Although no longer able to generate ribonucleic acid (RNA) de novo, platelets contain messenger RNA (mRNA), YRNA fragments, and premature microRNAs (miRNAs) that they inherit from megakaryocytes. Recent Advances: Novel sequencing techniques have helped identify the unexpectedly large number of RNA species present in platelets. Throughout their life time, platelets can process the pre-existing pool of premature miRNA to give the fully functional miRNA that can regulate platelet protein expression and function. CRITICAL ISSUES Platelets make a major contribution to the circulating miRNA pool but platelet activation can have major consequences on Dicer levels and thus miRNA maturation, which has implications for studies that are focused on screening-stored platelets. FUTURE DIRECTIONS It will be important to determine the importance of platelets as donors for miRNA-containing microvesicles that can be taken up and processed by other (particularly vascular) cells, thus contributing to homeostasis as well as disease progression. Antioxid. Redox Signal. 29, 902-921.
Collapse
Affiliation(s)
- Amro Elgheznawy
- 1 Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University , Frankfurt am Main, Germany .,2 German Center for Cardiovascular Research (DZHK) , Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Ingrid Fleming
- 1 Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University , Frankfurt am Main, Germany .,2 German Center for Cardiovascular Research (DZHK) , Partner site Rhein-Main, Frankfurt am Main, Germany
| |
Collapse
|
21
|
Tebaldi T, Zuccotti P, Peroni D, Köhn M, Gasperini L, Potrich V, Bonazza V, Dudnakova T, Rossi A, Sanguinetti G, Conti L, Macchi P, D'Agostino V, Viero G, Tollervey D, Hüttelmaier S, Quattrone A. HuD Is a Neural Translation Enhancer Acting on mTORC1-Responsive Genes and Counteracted by the Y3 Small Non-coding RNA. Mol Cell 2018; 71:256-270.e10. [PMID: 30029004 PMCID: PMC6060611 DOI: 10.1016/j.molcel.2018.06.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/24/2018] [Accepted: 06/21/2018] [Indexed: 01/19/2023]
Abstract
The RNA-binding protein HuD promotes neurogenesis and favors recovery from peripheral axon injury. HuD interacts with many mRNAs, altering both stability and translation efficiency. We generated a nucleotide resolution map of the HuD RNA interactome in motor neuron-like cells, identifying HuD target sites in 1,304 mRNAs, almost exclusively in the 3' UTR. HuD binds many mRNAs encoding mTORC1-responsive ribosomal proteins and translation factors. Altered HuD expression correlates with the translation efficiency of these mRNAs and overall protein synthesis, in a mTORC1-independent fashion. The predominant HuD target is the abundant, small non-coding RNA Y3, amounting to 70% of the HuD interaction signal. Y3 functions as a molecular sponge for HuD, dynamically limiting its recruitment to polysomes and its activity as a translation and neuron differentiation enhancer. These findings uncover an alternative route to the mTORC1 pathway for translational control in motor neurons that is tunable by a small non-coding RNA.
Collapse
Affiliation(s)
- Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Paola Zuccotti
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Daniele Peroni
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Marcel Köhn
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle 06120, Germany; Julius-Bernstein-Institute of Physiology, Martin-Luther-University Halle-Wittenberg, Halle 06097, Germany
| | - Lisa Gasperini
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Valentina Potrich
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Veronica Bonazza
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Tatiana Dudnakova
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Annalisa Rossi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK
| | - Luciano Conti
- Laboratory of Stem Cell Biology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Paolo Macchi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Vito D'Agostino
- Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Trento 38123, Italy
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle 06120, Germany
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy.
| |
Collapse
|
22
|
Irimie AI, Zimta AA, Ciocan C, Mehterov N, Dudea D, Braicu C, Berindan-Neagoe I. The Unforeseen Non-Coding RNAs in Head and Neck Cancer. Genes (Basel) 2018; 9:genes9030134. [PMID: 29494516 PMCID: PMC5867855 DOI: 10.3390/genes9030134] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/18/2022] Open
Abstract
Previously ignored non-coding RNAs (ncRNAs) have become the subject of many studies. However, there is an imbalance in the amount of consideration that ncRNAs are receiving. Some transcripts such as microRNAs (miRNAs) or small interfering RNAs (siRNAs) have gained much attention, but it is necessary to investigate other “pieces of the RNA puzzle”. These can offer a more complete view over normal and pathological cell behavior. The other ncRNA species are less studied, either due to their recent discovery, such as stable intronic sequence RNA (sisRNA), YRNA, miRNA-offset RNAs (moRNA), telomerase RNA component (TERC), natural antisense transcript (NAT), transcribed ultraconserved regions (T-UCR), and pseudogene transcript, or because they are still largely seen as non-coding transcripts with no relevance to pathogenesis. Moreover, some are still considered housekeeping RNAs, for instance small nucleolar RNAs (snoRNAs) and TERC. Our review summarizes the biogenesis, mechanism of action and potential role of less known ncRNAs in head and neck cancer, with a particular focus on the installment and progress for this particular cancer type.
Collapse
Affiliation(s)
- Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Alina-Andreea Zimta
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cristina Ciocan
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University Plovdiv, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
- Technological Center for Emergency Medicine, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
| | - Diana Dudea
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34 Street, 400015 Cluj-Napoca, Romania.
| |
Collapse
|
23
|
Abstract
Noncoding RNAs have essential biochemical functions in different areas of cellular metabolism, including protein synthesis, RNA splicing, protein secretion, and DNA replication. We have successfully used Morpholino antisense oligonucleotides for the functional inactivation of small noncoding RNAs required for DNA replication (Y RNAs in vertebrates and stem-bulge RNAs in nematodes). Here we discuss specific issues of targeting functional noncoding RNAs for inactivation by Morpholino antisense oligonucleotides. We present protocols for the design, preparation, and efficacy controls of Morpholino antisense oligonucleotides, as well as brief descriptions for their delivery into vertebrate and nematode embryos.
Collapse
|
24
|
SMORE: Synteny Modulator of Repetitive Elements. Life (Basel) 2017; 7:life7040042. [PMID: 29088079 PMCID: PMC5745555 DOI: 10.3390/life7040042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/27/2017] [Accepted: 10/28/2017] [Indexed: 12/19/2022] Open
Abstract
Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny. The evolution of tRNAs in primates as well as the history of the Y RNA family in vertebrates and nematodes are used to showcase the method. The pipeline is freely available.
Collapse
|
25
|
Sunderland N, Skroblin P, Barwari T, Huntley RP, Lu R, Joshi A, Lovering RC, Mayr M. MicroRNA Biomarkers and Platelet Reactivity: The Clot Thickens. Circ Res 2017; 120:418-435. [PMID: 28104774 DOI: 10.1161/circresaha.116.309303] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 12/16/2022]
Abstract
Over the last few years, several groups have evaluated the potential of microRNAs (miRNAs) as biomarkers for cardiometabolic disease. In this review, we discuss the emerging literature on the role of miRNAs and other small noncoding RNAs in platelets and in the circulation, and the potential use of miRNAs as biomarkers for platelet activation. Platelets are a major source of miRNAs, YRNAs, and circular RNAs. By harnessing multiomics approaches, we may gain valuable insights into their potential function. Because not all miRNAs are detectable in the circulation, we also created a gene ontology annotation for circulating miRNAs using the gene ontology term extracellular space as part of blood plasma. Finally, we share key insights for measuring circulating miRNAs. We propose ways to standardize miRNA measurements, in particular by using platelet-poor plasma to avoid confounding caused by residual platelets in plasma or by adding RNase inhibitors to serum to reduce degradation. This should enhance comparability of miRNA measurements across different cohorts. We provide recommendations for future miRNA biomarker studies, emphasizing the need for accurate interpretation within a biological and methodological context.
Collapse
Affiliation(s)
- Nicholas Sunderland
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (N.S., P.S., T.B., R.L., A.J., M.M.); and Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (R.P.H., R.C.L.)
| | - Philipp Skroblin
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (N.S., P.S., T.B., R.L., A.J., M.M.); and Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (R.P.H., R.C.L.)
| | - Temo Barwari
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (N.S., P.S., T.B., R.L., A.J., M.M.); and Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (R.P.H., R.C.L.)
| | - Rachael P Huntley
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (N.S., P.S., T.B., R.L., A.J., M.M.); and Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (R.P.H., R.C.L.)
| | - Ruifang Lu
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (N.S., P.S., T.B., R.L., A.J., M.M.); and Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (R.P.H., R.C.L.)
| | - Abhishek Joshi
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (N.S., P.S., T.B., R.L., A.J., M.M.); and Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (R.P.H., R.C.L.)
| | - Ruth C Lovering
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (N.S., P.S., T.B., R.L., A.J., M.M.); and Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (R.P.H., R.C.L.)
| | - Manuel Mayr
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (N.S., P.S., T.B., R.L., A.J., M.M.); and Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (R.P.H., R.C.L.).
| |
Collapse
|
26
|
Simon CR, Siviero F, Monesi N. Beyond DNA puffs: What can we learn from studying sciarids? Genesis 2016; 54:361-78. [PMID: 27178805 DOI: 10.1002/dvg.22946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/07/2022]
Abstract
Members of the Sciaridae family attracted the interest of researchers because of the demonstration that the DNA puff regions, which are formed in the salivary gland polytene chromosomes at the end of the fourth larval instar, constitute sites of developmentally regulated gene amplification. Besides contributing to a deeper understanding of the process of gene amplification, the study of sciarids has also provided important insights on other biological processes such as sex determination, programmed cell death, insect immunity, telomere maintenance, and nucleolar organizing regions (NOR) formation. Open questions in sciarids include among others, early development, the role of noncoding RNAs in gene amplification and the relationship between gene amplification and transcription in DNA puff forming regions. These and other questions can now be pursued with next generation sequencing techniques and experiments using RNAi experiments, since this latter technique has been shown to be feasible in sciarids. These new perspectives in the field of sciarid biology open the opportunity to consolidate sciarid species as important emerging models. genesis 54:361-378, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Claudio Roberto Simon
- Departamento de Biologia Estrutural, Universidade Federal do Triângulo Mineiro-UFTM, Instituto de Ciências Biológicas e Naturais, Uberaba, MG, Brazil, CEP 38025-015
| | - Fábio Siviero
- Departamento de Biologia Celular e do Desenvolvimento, Universidade de São Paulo, Instituto de Ciências Biomédicas, São Paulo, SP, Brazil, CEP 05508-900
| | - Nadia Monesi
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| |
Collapse
|
27
|
de Lima Neto QA, Duarte Junior FF, Bueno PSA, Seixas FAV, Kowalski MP, Kheir E, Krude T, Fernandez MA. Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells: identification, molecular dynamics simulations and DNA replication initiation assays. BMC Mol Biol 2016; 17:1. [PMID: 26733090 PMCID: PMC4702372 DOI: 10.1186/s12867-015-0053-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/21/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is available about Y RNAs in Chinese hamster cells, which have already been used to detect replication origins and alternative DNA structures around these sites. Here, we report the gene sequences and predicted structural characteristics of the Chinese hamster Y RNAs, and analyze their ability to support the initiation of chromosomal DNA replication in vitro. RESULTS We identified DNA sequences in the Chinese hamster genome of four Y RNAs (chY1, chY3, chY4 and chY5) with upstream promoter sequences, which are homologous to the four main types of vertebrate Y RNAs. The chY1, chY3 and chY5 genes were highly conserved with their vertebrate counterparts, whilst the chY4 gene showed a relatively high degree of diversification from the other vertebrate Y4 genes. Molecular dynamics simulations suggest that chY4 RNA is structurally stable despite its evolutionarily divergent predicted stem structure. Of the four Y RNA genes present in the hamster genome, we found that only the chY1 and chY3 RNA were strongly expressed in the Chinese hamster GMA32 cell line, while expression of the chY4 and chY5 RNA genes was five orders of magnitude lower, suggesting that they may in fact not be expressed. We synthesized all four chY RNAs and showed that any of these four could support the initiation of DNA replication in an established human cell-free system. CONCLUSIONS These data therefore establish that non-coding chY RNAs are stable structures and can substitute for human Y RNAs in a reconstituted cell-free DNA replication initiation system. The pattern of Y RNA expression and functionality is consistent with Y RNAs of other rodents, including mouse and rat.
Collapse
Affiliation(s)
- Quirino Alves de Lima Neto
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil.
| | - Francisco Ferreira Duarte Junior
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil.
| | | | | | | | - Eyemen Kheir
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
| | - Maria Aparecida Fernandez
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil.
| |
Collapse
|
28
|
Chakrabortty SK, Prakash A, Nechooshtan G, Hearn S, Gingeras TR. Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. RNA (NEW YORK, N.Y.) 2015; 21:1966-79. [PMID: 26392588 PMCID: PMC4604435 DOI: 10.1261/rna.053629.115] [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: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 05/22/2023]
Abstract
Extracellular vesicles (EVs) have been proposed as a means to promote intercellular communication. We show that when human primary cells are exposed to cancer cell EVs, rapid cell death of the primary cells is observed, while cancer cells treated with primary or cancer cell EVs do not display this response. The active agents that trigger cell death are 29- to 31-nucleotide (nt) or 22- to 23-nt processed fragments of an 83-nt primary transcript of the human RNY5 gene that are highly likely to be formed within the EVs. Primary cells treated with either cancer cell EVs, deproteinized total RNA from either primary or cancer cell EVs, or synthetic versions of 31- and 23-nt fragments trigger rapid cell death in a dose-dependent manner. The transfer of processed RNY5 fragments through EVs may reflect a novel strategy used by cancer cells toward the establishment of a favorable microenvironment for their proliferation and invasion.
Collapse
Affiliation(s)
| | - Ashwin Prakash
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gal Nechooshtan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Stephen Hearn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Thomas R Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| |
Collapse
|
29
|
Ødum Nielsen I, Hartwig Trier N, Friis T, Houen G. Characterization of continuous monoclonal antibody epitopes in the N-terminus of Ro60. Biopolymers 2015; 106:62-71. [PMID: 26506479 DOI: 10.1002/bip.22758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/12/2015] [Accepted: 10/17/2015] [Indexed: 11/06/2022]
Abstract
One of the major targets of the autoimmune response in the rheumatic autoimmune diseases, Systemic Lupus Erythematosus and Sjögrens Syndrome, is the protein Ro60. Ro60 is known to associate with small misfolded RNAs, and is involved in RNA quality control and in enhancing cell survival during cellular stress, e.g. after ultaviolet irradiation. In this study, six monoclonal antibodies to Ro60 were analyzed in order to identify antigenic regions and the nature of these. Preliminary analyses revealed that two of the antibodies recognized continuous epitopes, while the remaining antibodies most likely recognized conformational epitopes. The continuous epitopes of Ro60 were characterised by modified immunoassays employing resin-bound peptides and free peptides. Peptide screenings located the epitopes to the N-terminus of Ro60, and further analyses indicated that the epitopes of the monoclonal antibodies TROVE2 and SSI-HYB 358-02 were located to amino acids 8-17 and 34-49, respectively. Moreover, charged amino acids were found to be especially important for antibody reactivity, although antibody reactivity of the monoclonal antibody TROVE2 primarily was found to be epitope backbone-dependent.
Collapse
Affiliation(s)
- Inger Ødum Nielsen
- Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Nicole Hartwig Trier
- Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Tina Friis
- Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Gunnar Houen
- Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| |
Collapse
|
30
|
Synaptic vesicles contain small ribonucleic acids (sRNAs) including transfer RNA fragments (trfRNA) and microRNAs (miRNA). Sci Rep 2015; 5:14918. [PMID: 26446566 PMCID: PMC4597359 DOI: 10.1038/srep14918] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/08/2015] [Indexed: 12/29/2022] Open
Abstract
Synaptic vesicles (SVs) are neuronal presynaptic organelles that load and release neurotransmitter at chemical synapses. In addition to classic neurotransmitters, we have found that synaptic vesicles isolated from the electric organ of Torpedo californica, a model cholinergic synapse, contain small ribonucleic acids (sRNAs), primarily the 5' ends of transfer RNAs (tRNAs) termed tRNA fragments (trfRNAs). To test the evolutionary conservation of SV sRNAs we examined isolated SVs from the mouse central nervous system (CNS). We found abundant levels of sRNAs in mouse SVs, including trfRNAs and micro RNAs (miRNAs) known to be involved in transcriptional and translational regulation. This discovery suggests that, in addition to inducing changes in local dendritic excitability through the release of neurotransmitters, SVs may, through the release of specific trfRNAs and miRNAs, directly regulate local protein synthesis. We believe these findings have broad implications for the study of chemical synaptic transmission.
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
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: 151] [Impact Index Per Article: 16.8] [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.
Collapse
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.
| |
Collapse
|
33
|
Spurlock CF, Tossberg JT, Guo Y, Sriram S, Crooke PS, Aune TM. Defective structural RNA processing in relapsing-remitting multiple sclerosis. Genome Biol 2015; 16:58. [PMID: 25885816 PMCID: PMC4403723 DOI: 10.1186/s13059-015-0629-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 03/11/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Surveillance of integrity of the basic elements of the cell including DNA, RNA, and proteins is a critical element of cellular physiology. Mechanisms of surveillance of DNA and protein integrity are well understood. Surveillance of structural RNAs making up the vast majority of RNA in a cell is less well understood. Here, we sought to explore integrity of processing of structural RNAs in relapsing remitting multiple sclerosis (RRMS) and other inflammatory diseases. RESULTS We employed mononuclear cells obtained from subjects with RRMS and cell lines. We used quantitative-PCR and whole genome RNA sequencing to define defects in structural RNA surveillance and siRNAs to deplete target proteins. We report profound defects in surveillance of structural RNAs in RRMS exemplified by elevated levels of poly(A) + Y1-RNA, poly(A) + 18S rRNA and 28S rRNAs, elevated levels of misprocessed 18S and 28S rRNAs and levels of the U-class of small nuclear RNAs. Multiple sclerosis is also associated with genome-wide defects in mRNA splicing. Ro60 and La proteins, which exist in ribonucleoprotein particles and play different roles in quality control of structural RNAs, are also deficient in RRMS. In cell lines, silencing of the genes encoding Ro60 and La proteins gives rise to these same defects in surveillance of structural RNAs. CONCLUSIONS Our results establish that profound defects in structural RNA surveillance exist in RRMS and establish a causal link between Ro60 and La proteins and integrity of structural RNAs.
Collapse
Affiliation(s)
- Charles F Spurlock
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
| | - John T Tossberg
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
| | - Yan Guo
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
| | - Subramaniam Sriram
- Department of Neurology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
| | - Philip S Crooke
- Department of Mathematics, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Thomas M Aune
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Medical Center North T3113, Vanderbilt University Medical Center, 1161 21st Avenue South, Nashville, TN, USA.
| |
Collapse
|
34
|
Ryu KW, Kim DS, Kraus WL. New facets in the regulation of gene expression by ADP-ribosylation and poly(ADP-ribose) polymerases. Chem Rev 2015; 115:2453-81. [PMID: 25575290 PMCID: PMC4378458 DOI: 10.1021/cr5004248] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Keun Woo Ryu
- Laboratory of Signaling and Gene
Regulation, Cecil H. and Ida Green
Center for Reproductive Biology Sciences, Division of Basic Research, Department
of Obstetrics and Gynecology, and Graduate School of Biomedical Sciences, Program
in Genetics and Development, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Dae-Seok Kim
- Laboratory of Signaling and Gene
Regulation, Cecil H. and Ida Green
Center for Reproductive Biology Sciences, Division of Basic Research, Department
of Obstetrics and Gynecology, and Graduate School of Biomedical Sciences, Program
in Genetics and Development, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - W. Lee Kraus
- Laboratory of Signaling and Gene
Regulation, Cecil H. and Ida Green
Center for Reproductive Biology Sciences, Division of Basic Research, Department
of Obstetrics and Gynecology, and Graduate School of Biomedical Sciences, Program
in Genetics and Development, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| |
Collapse
|
35
|
Dalgard CL, Jacobowitz DM, Singh VK, Saleem KS, Ursano RJ, Starr JM, Pollard HB. A novel analytical brain block tool to enable functional annotation of discriminatory transcript biomarkers among discrete regions of the fronto-limbic circuit in primate brain. Brain Res 2015; 1600:42-58. [DOI: 10.1016/j.brainres.2014.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 01/05/2023]
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
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.
Collapse
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.
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Gupta Y, Witte M, Möller S, Ludwig RJ, Restle T, Zillikens D, Ibrahim SM. ptRNApred: computational identification and classification of post-transcriptional RNA. Nucleic Acids Res 2014; 42:e167. [PMID: 25303994 PMCID: PMC4267668 DOI: 10.1093/nar/gku918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED Non-coding RNAs (ncRNAs) are known to play important functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as classification tools, offer a fast and reliable way for such screening and multiple classifiers have already been developed to predict well-defined subfamilies of RNA. So far, however, out of all the ncRNAs, only tRNA, miRNA and snoRNA can be predicted with a satisfying sensitivity and specificity. We here present ptRNApred, a tool to detect and classify subclasses of non-coding RNA that are involved in the regulation of post-transcriptional modifications or DNA replication, which we here call post-transcriptional RNA (ptRNA). It (i) detects RNA sequences coding for post-transcriptional RNA from the genomic sequence with an overall sensitivity of 91% and a specificity of 94% and (ii) predicts ptRNA-subclasses that exist in eukaryotes: snRNA, snoRNA, RNase P, RNase MRP, Y RNA or telomerase RNA. AVAILABILITY The ptRNApred software is open for public use on http://www.ptrnapred.org/.
Collapse
Affiliation(s)
- Yask Gupta
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Mareike Witte
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Steffen Möller
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Ralf J Ludwig
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Tobias Restle
- Institute for Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Saleh M Ibrahim
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| |
Collapse
|
39
|
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] [MESH Headings] [Track Full Text] [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.
Collapse
Affiliation(s)
- Iren Wang
- Institute of Biological Chemistry, Academia Sinica , 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | | | | | | | | | | | | |
Collapse
|
40
|
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.
Collapse
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.
| |
Collapse
|
41
|
Deschamps-Francoeur G, Garneau D, Dupuis-Sandoval F, Roy A, Frappier M, Catala M, Couture S, Barbe-Marcoux M, Abou-Elela S, Scott MS. Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency. Nucleic Acids Res 2014; 42:10073-85. [PMID: 25074380 PMCID: PMC4150776 DOI: 10.1093/nar/gku664] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are among the first discovered and most extensively studied group of small non-coding RNA. However, most studies focused on a small subset of snoRNAs that guide the modification of ribosomal RNA. In this study, we annotated the expression pattern of all box C/D snoRNAs in normal and cancer cell lines independent of their functions. The results indicate that C/D snoRNAs are expressed as two distinct forms differing in their ends with respect to boxes C and D and in their terminal stem length. Both forms are overexpressed in cancer cell lines but display a conserved end distribution. Surprisingly, the long forms are more dependent than the short forms on the expression of the core snoRNP protein NOP58, thought to be essential for C/D snoRNA production. In contrast, a subset of short forms are dependent on the splicing factor RBFOX2. Analysis of the potential secondary structure of both forms indicates that the k-turn motif required for binding of NOP58 is less stable in short forms which are thus less likely to mature into a canonical snoRNP. Taken together the data suggest that C/D snoRNAs are divided into at least two groups with distinct maturation and functional preferences.
Collapse
Affiliation(s)
- Gabrielle Deschamps-Francoeur
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Daniel Garneau
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Fabien Dupuis-Sandoval
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Audrey Roy
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Marie Frappier
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Mathieu Catala
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sonia Couture
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Mélissa Barbe-Marcoux
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou-Elela
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| |
Collapse
|
42
|
Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J. Structured RNAs and synteny regions in the pig genome. BMC Genomics 2014; 15:459. [PMID: 24917120 PMCID: PMC4124155 DOI: 10.1186/1471-2164-15-459] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 05/02/2014] [Indexed: 11/25/2022] Open
Abstract
Background Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals. Results We present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58 lncRNA loci, 11 conflicts of annotation, and 3,183 ncRNA genes. The ncRNA genes comprise 359 miRNAs, 8 ribozymes, 185 rRNAs, 638 snoRNAs, 1,030 snRNAs, 810 tRNAs and 153 ncRNA genes not belonging to the here fore mentioned classes. When running the pipeline on a local shuffled version of the genome, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated annotation. To further enhance the reliability, 571 of the 3,556 structured RNAs were manually curated by methods depending on the RNA class while 1,581 were declared as pseudogenes. We further created a multiple alignment of pig against 20 representative vertebrates, from which RNAz predicted 83,859 de novo RNA loci with conserved RNA structures. 528 of the RNAz predictions overlapped with the homology based annotation or novel miRNAs. We further present a substantial synteny analysis which includes 1,004 lineage specific de novo RNA loci and 4 ncRNA loci in the known annotation specific for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog). Conclusions We have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the complete annotation is available at
http://rth.dk/resources/rnannotator/susscr102/version1.02. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-459) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, University of Copenhagen, DK-1870 Frederiksberg, Denmark.
| |
Collapse
|
43
|
Yamazaki F, Kim HH, Lau P, Hwang CK, Iuvone PM, Klein D, Clokie SJH. pY RNA1-s2: a highly retina-enriched small RNA that selectively binds to Matrin 3 (Matr3). PLoS One 2014; 9:e88217. [PMID: 24558381 PMCID: PMC3928194 DOI: 10.1371/journal.pone.0088217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/03/2014] [Indexed: 12/22/2022] Open
Abstract
The purpose of this study was to expand our knowledge of small RNAs, which are known to function within protein complexes to modulate the transcriptional output of the cell. Here we describe two previously unrecognized, small RNAs, termed pY RNA1-s1 and pY RNA1-s2 (processed Y RNA1-stem −1 and −2), thereby expanding the list of known small RNAs. pY RNA1-s1 and pY RNA1-s2 were discovered by RNA sequencing and found to be 20-fold more abundant in the retina than in 14 other rat tissues. Retinal expression of pY RNAs is highly conserved, including expression in the human retina, and occurs in all retinal cell layers. Mass spectrometric analysis of pY RNA1-S2 binding proteins in retina indicates that pY RNA1-s2 selectively binds the nuclear matrix protein Matrin 3 (Matr3) and to a lesser degree to hnrpul1 (heterogeneous nuclear ribonucleoprotein U-like protein). In contrast, pY RNA1-s1 does not bind these proteins. Accordingly, the molecular mechanism of action of pY RNA1-s2 is likely be through an action involving Matr3; this 95 kDa protein has two RNA recognition motifs (RRMs) and is implicated in transcription and RNA-editing. The high affinity binding of pY RNA1-s2 to Matr3 is strongly dependent on the sequence of the RNA and both RRMs of Matr3. Related studies also indicate that elements outside of the RRM region contribute to binding specificity and that phosphorylation enhances pY RNA-s2/Matr3 binding. These observations are of significance because they reveal that a previously unrecognized small RNA, pY RNA1-s2, binds selectively to Matr3. Hypothetically, pY RNA1-S2 might act to modulate cellular function through this molecular mechanism. The retinal enrichment of pY RNA1-s2 provides reason to suspect that the pY RNA1-s2/Matr3 interaction could play a role in vision.
Collapse
Affiliation(s)
- Fumiyoshi Yamazaki
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hyun Hee Kim
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Pierre Lau
- Division of intramural research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher K. Hwang
- Departments of Ophthalmology and Pharmacology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - P. Michael Iuvone
- Departments of Ophthalmology and Pharmacology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - David Klein
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Samuel J. H. Clokie
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
44
|
Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Mote P, Martin DIK. 5′-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma. Physiol Genomics 2013; 45:990-8. [DOI: 10.1152/physiolgenomics.00129.2013] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small noncoding RNAs carry out a variety of functions in eukaryotic cells, and in multiple species they can travel between cells, thus serving as signaling molecules. In mammals multiple small RNAs have been found to circulate in the blood, although in most cases the targets of these RNAs, and even their functions, are not well understood. YRNAs are small (84–112 nt) RNAs with poorly characterized functions, best known because they make up part of the Ro ribonucleoprotein autoantigens in connective tissue diseases. In surveying small RNAs present in the serum of healthy adult humans, we have found YRNA fragments of lengths 27 nt and 30–33 nt, derived from the 5′-ends of specific YRNAs and generated by cleavage within a predicted internal loop. Many of the YRNAs from which these fragments are derived were previously annotated only as pseudogenes, or predicted informatically. These 5′-YRNA fragments make up a large proportion of all small RNAs (including miRNAs) present in human serum. They are also present in plasma, are not present in exosomes or microvesicles, and circulate as part of a complex with a mass between 100 and 300 kDa. Mouse serum contains far fewer 5′-YRNA fragments, possibly reflecting the much greater copy number of YRNA genes and pseudogenes in humans. The function of the 5′-YRNA fragments is at present unknown, but the processing and secretion of specific YRNAs to produce 5′-end fragments that circulate in stable complexes are consistent with a signaling function.
Collapse
Affiliation(s)
- Joseph M. Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - Stephen R. Spindler
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - Hani Atamna
- Department of Basic Sciences, Neuroscience, The Commonwealth Medical College, Scranton, Pennsylvania
| | - Dario Boffelli
- Center for Genetics, Childrens Hospital Oakland Research Institute, Oakland, California
| | - Patricia Mote
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - David I. K. Martin
- Center for Genetics, Childrens Hospital Oakland Research Institute, Oakland, California
| |
Collapse
|
45
|
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
|
46
|
Wolin SL, Belair C, Boccitto M, Chen X, Sim S, Taylor DW, Wang HW. Non-coding Y RNAs as tethers and gates: Insights from bacteria. RNA Biol 2013; 10:1602-8. [PMID: 24036917 DOI: 10.4161/rna.26166] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) called Y RNAs are abundant components of both animal cells and a variety of bacteria. In all species examined, these ~100 nt RNAs are bound to the Ro 60 kDa (Ro60) autoantigen, a ring-shaped protein that also binds misfolded ncRNAs in some vertebrate nuclei. Although the function of Ro60 RNPs has been mysterious, we recently reported that a bacterial Y RNA tethers Ro60 to the 3' to 5' exoribonuclease polynucleotide phosphorylase (PNPase) to form RYPER (Ro60/Y RNA/PNPase Exoribonuclease RNP), a new RNA degradation machine. PNPase is a homotrimeric ring that degrades single-stranded RNA, and Y RNA-mediated tethering of Ro60 increases the effectiveness of PNPase in degrading structured RNAs. Single particle electron microscopy of RYPER suggests that RNA threads through the Ro60 ring into the PNPase cavity. Further studies indicate that Y RNAs may also act as gates to regulate entry of RNA substrates into the Ro60 channel. These findings reveal novel functions for Y RNAs and raise questions about how the bacterial findings relate to the roles of these ncRNAs in animal cells. Here we review the literature on Y RNAs, highlighting their close relationship with Ro60 proteins and the hypothesis that these ncRNAs function generally to tether Ro60 rings to diverse RNA-binding proteins.
Collapse
Affiliation(s)
- Sandra L Wolin
- Department of Cell Biology; Yale School of Medicine; New Haven, CT USA; Department of Molecular Biophysics and Biochemistry; Yale School of Medicine; New Haven, CT USA
| | - Cedric Belair
- Department of Cell Biology; Yale School of Medicine; New Haven, CT USA
| | - Marco Boccitto
- Department of Cell Biology; Yale School of Medicine; New Haven, CT USA
| | - Xinguo Chen
- Department of Cell Biology; Yale School of Medicine; New Haven, CT USA
| | - Soyeong Sim
- Department of Cell Biology; Yale School of Medicine; New Haven, CT USA
| | - David W Taylor
- Department of Molecular Biophysics and Biochemistry; Yale School of Medicine; New Haven, CT USA
| | - Hong-Wei Wang
- Department of Molecular Biophysics and Biochemistry; Yale School of Medicine; New Haven, CT USA; Tsinghua-Peking Center for Life Sciences; School of Life Sciences; Tsinghua University; Beijing, P.R. China
| |
Collapse
|
47
|
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.
Collapse
Affiliation(s)
- P Perez
- Sjögren's Clinic, Molecular Physiology & Therapeutics, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | | | | |
Collapse
|
48
|
Chen X, Taylor DW, Fowler CC, Galan JE, Wang HW, Wolin SL. An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA. Cell 2013; 153:166-77. [PMID: 23540697 DOI: 10.1016/j.cell.2013.02.037] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 01/10/2013] [Accepted: 02/19/2013] [Indexed: 11/18/2022]
Abstract
Many bacteria contain an ortholog of the Ro autoantigen, a ring-shaped protein that binds noncoding RNAs (ncRNAs) called Y RNAs. In the only studied bacterium, Deinococcus radiodurans, the Ro ortholog Rsr functions in heat-stress-induced ribosomal RNA (rRNA) maturation and starvation-induced rRNA decay. However, the mechanism by which this conserved protein and its associated ncRNAs act has been obscure. We report that Rsr and the exoribonuclease polynucleotide phosphorylase (PNPase) form an RNA degradation machine that is scaffolded by Y RNA. Single-particle electron microscopy, followed by docking of atomic models into the reconstruction, suggests that Rsr channels single-stranded RNA into the PNPase cavity. Biochemical assays reveal that Rsr and Y RNA adapt PNPase for effective degradation of structured RNAs. A Ro ortholog and ncRNA also associate with PNPase in Salmonella Typhimurium. Our studies identify another ribonucleoprotein machine and demonstrate that ncRNA, by tethering a protein cofactor, can alter the substrate specificity of an enzyme.
Collapse
Affiliation(s)
- Xinguo Chen
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA
| | | | | | | | | | | |
Collapse
|
49
|
Seychelles LH, Doiron K, Audet C, Tremblay R, Pernet F, Lemarchand K. Impact of arachidonic acid enrichment of live rotifer prey on bacterial communities in rotifer and larval fish cultures. Can J Microbiol 2013; 59:189-96. [DOI: 10.1139/cjm-2012-0564] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rotifers (Brachionus plicatilis), commonly used at first feeding in commercial fish hatcheries, carry a large bacteria load. Because they are relatively poor in essential fatty acids, it is common practice to enrich them with fatty acids, including arachidonic acid (AA). This study aims to determine whether prey enrichment with AA may act as a prebiotic and modify the microbial community composition either in AA-enriched rotifer cultures or in larval-rearing water using winter flounder (Pseudopleuronectes americanus) as a larval fish model. AA enrichment modified the bacterial community composition in both the rotifer culture tanks and the larval-rearing tanks. We observed an increase in the number of cultivable bacteria on TCBS (thiosulfate–citrate–bile salts–sucrose) agar, used as a proxy for the abundance of Vibrio sp. The results suggest that AA may also play an indirect role in larval health.
Collapse
Affiliation(s)
- Laurent H. Seychelles
- Phytopathology Institute, Working group in aquaculture, Kiel University, Olshausenstraße 40-60, 24118 Kiel, Germany
| | - Kim Doiron
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Réjean Tremblay
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Fabrice Pernet
- Ifremer, UMR LEMAR 6539 - Technopole de Brest-Iroise, B.P. 70, 29280 Plouzané, France
| | - Karine Lemarchand
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| |
Collapse
|
50
|
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.
Collapse
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.
| |
Collapse
|