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Hasanzadeh A, Ebadati A, Saeedi S, Kamali B, Noori H, Jamei B, Hamblin MR, Liu Y, Karimi M. Nucleic acid-responsive smart systems for controlled cargo delivery. Biotechnol Adv 2024; 74:108393. [PMID: 38825215 DOI: 10.1016/j.biotechadv.2024.108393] [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: 08/21/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arefeh Ebadati
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Molecular and Cell Biology, University of California, Merced, Merced, USA
| | - Sara Saeedi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kamali
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnam Jamei
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Yong Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
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2
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Velázquez-Flores MÁ, Ruiz Esparza-Garrido R. Fragments derived from non-coding RNAs: how complex is genome regulation? Genome 2024. [PMID: 38684113 DOI: 10.1139/gen-2023-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.
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Affiliation(s)
- Miguel Ángel Velázquez-Flores
- Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
| | - Ruth Ruiz Esparza-Garrido
- Investigadora por México, Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
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3
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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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4
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Pliatsika V, Cherlin T, Loher P, Vlantis P, Nagarkar P, Nersisyan S, Rigoutsos I. MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs). Nucleic Acids Res 2024; 52:D229-D238. [PMID: 37843123 PMCID: PMC10767805 DOI: 10.1093/nar/gkad833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
We describe the Mitochondrial and Nuclear rRNA fragment database (MINRbase), a knowledge repository aimed at facilitating the study of ribosomal RNA-derived fragments (rRFs). MINRbase provides interactive access to the profiles of 130 238 expressed rRFs arising from the four human nuclear rRNAs (18S, 5.8S, 28S, 5S), two mitochondrial rRNAs (12S, 16S) or four spacers of 45S pre-rRNA. We compiled these profiles by analyzing 11 632 datasets, including the GEUVADIS and The Cancer Genome Atlas (TCGA) repositories. MINRbase offers a user-friendly interface that lets researchers issue complex queries based on one or more criteria, such as parental rRNA identity, nucleotide sequence, rRF minimum abundance and metadata keywords (e.g. tissue type, disease). A 'summary' page for each rRF provides a granular breakdown of its expression by tissue type, disease, sex, ancestry and other variables; it also allows users to create publication-ready plots at the click of a button. MINRbase has already allowed us to generate support for three novel observations: the internal spacers of 45S are prolific producers of abundant rRFs; many abundant rRFs straddle the known boundaries of rRNAs; rRF production is regimented and depends on 'personal attributes' (sex, ancestry) and 'context' (tissue type, tissue state, disease). MINRbase is available at https://cm.jefferson.edu/MINRbase/.
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Affiliation(s)
- Venetia Pliatsika
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Tess Cherlin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Panagiotis Vlantis
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Parth Nagarkar
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Stepan Nersisyan
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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5
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Böğürcü-Seidel N, Ritschel N, Acker T, Németh A. Beyond ribosome biogenesis: noncoding nucleolar RNAs in physiology and tumor biology. Nucleus 2023; 14:2274655. [PMID: 37906621 PMCID: PMC10730139 DOI: 10.1080/19491034.2023.2274655] [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: 07/31/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The nucleolus, the largest subcompartment of the nucleus, stands out from the nucleoplasm due to its exceptionally high local RNA and low DNA concentrations. Within this central hub of nuclear RNA metabolism, ribosome biogenesis is the most prominent ribonucleoprotein (RNP) biogenesis process, critically determining the structure and function of the nucleolus. However, recent studies have shed light on other roles of the nucleolus, exploring the interplay with various noncoding RNAs that are not directly involved in ribosome synthesis. This review focuses on this intriguing topic and summarizes the techniques to study and the latest findings on nucleolar long noncoding RNAs (lncRNAs) as well as microRNAs (miRNAs) in the context of nucleolus biology beyond ribosome biogenesis. We particularly focus on the multifaceted roles of the nucleolus and noncoding RNAs in physiology and tumor biology.
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Affiliation(s)
| | - Nadja Ritschel
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Till Acker
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Attila Németh
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
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6
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Lai H, Feng N, Zhai Q. Discovery of the major 15-30 nt mammalian small RNAs, their biogenesis and function. Nat Commun 2023; 14:5796. [PMID: 37723159 PMCID: PMC10507107 DOI: 10.1038/s41467-023-41554-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
Small RNAs (sRNAs) within 15-30 nt such as miRNA, tsRNA, srRNA with 3'-OH have been identified. However, whether these sRNAs are the major 15-30 nt sRNAs is still unknown. Here we show about 90% mammalian sRNAs within 15-30 nt end with 2',3'-cyclic phosphate (3'-cP). TANT-seq was developed to simultaneously profile sRNAs with 3'-cP (sRNA-cPs) and sRNA-OHs, and huge amount of sRNA-cPs were detected. Surprisingly, sRNA-cPs and sRNA-OHs usually have distinct sequences. The data from TANT-seq were validated by a novel method termed TE-qPCR, and Northern blot. Furthermore, we found that Angiogenin and RNase 4 contribute to the biogenesis of sRNA-cPs. Moreover, much more sRNA-cPs than sRNA-OHs bind to Ago2, and can regulate gene expression. Particularly, snR-2-cP regulates Bcl2 by targeting to its 3'UTR dependent on Ago2, and subsequently regulates apoptosis. In addition, sRNA-cPs can guide the cleavage of target RNAs in Ago2 complex as miRNAs without the requirement of 3'-cP. Our discovery greatly expands the repertoire of mammalian sRNAs, and provides strategies and powerful tools towards further investigation of sRNA-cPs.
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Affiliation(s)
- Hejin Lai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ning Feng
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiwei Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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7
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Gou LT, Zhu Q, Liu MF. Small RNAs: An expanding world with therapeutic promises. FUNDAMENTAL RESEARCH 2023; 3:676-682. [PMID: 38933305 PMCID: PMC11197668 DOI: 10.1016/j.fmre.2023.03.003] [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: 12/09/2022] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 04/09/2023] Open
Abstract
Small non-coding RNAs (sncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), and transfer RNA (tRNA)-derived small RNAs (tsRNAs), play essential roles in regulating various cellular and developmental processes. Over the past three decades, researchers have identified novel sncRNA species from various organisms. These molecules demonstrate dynamic expression and diverse functions, and they are subject to intricate regulation through RNA modifications in both healthy and diseased states. Notably, certain sncRNAs in gametes, particularly sperm, respond to environmental stimuli and facilitate epigenetic inheritance. Collectively, the in-depth understanding of sncRNA functions and mechanisms has accelerated the development of small RNA-based therapeutics. In this review, we present the recent advances in the field, including new sncRNA species and the regulatory influences of RNA modifications. We also discuss the current limitations and challenges associated with using small RNAs as either biomarkers or therapeutic drugs.
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Affiliation(s)
- Lan-Tao Gou
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qifan Zhu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
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8
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Natali L, Luna Pizarro G, Moyano S, de la Cruz-Thea B, Musso J, Rópolo AS, Eichner N, Meister G, Musri MM, Feliziani C, Touz MC. The Exosome-like Vesicles of Giardia Assemblages A, B, and E Are Involved in the Delivering of Distinct Small RNA from Parasite to Parasite. Int J Mol Sci 2023; 24:ijms24119559. [PMID: 37298511 DOI: 10.3390/ijms24119559] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 06/12/2023] Open
Abstract
The genetically related assemblages of the intestinal protozoa parasite Giardia lamblia are morphologically indistinguishable and are often derived from specific hosts. The Giardia assemblages are separated by large genetic distances, which might account for their relevant biological and pathogenic differences. In this work, we analyzed the RNAs cargo released into exosomal-like vesicles (ElVs) by the assemblages A and B, which differentially infect humans, and the assemblage E, which infects hoofed animals. The RNA sequencing analysis revealed that the ElVs of each assemblage contained distinct small RNA (sRNA) biotypes, suggesting a preference for specific packaging in each assemblage. These sRNAs were classified into three categories, ribosomal-small RNAs (rsRNAs), messenger-small RNAs (msRNAs), and transfer-small RNAs (tsRNAs), which may play a regulatory role in parasite communication and contribute to host-specificity and pathogenesis. Uptake experiments showed, for the first time, that ElVs were successfully internalized by the parasite trophozoites. Furthermore, we observed that the sRNAs contained inside these ElVs were first located below the plasma membrane but then distributed along the cytoplasm. Overall, the study provides new insights into the molecular mechanisms underlying the host-specificity and pathogenesis of G. lamblia and highlights the potential role of sRNAs in parasite communication and regulation.
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Affiliation(s)
- Lautaro Natali
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Gabriel Luna Pizarro
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Sofía Moyano
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Benjamin de la Cruz-Thea
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Juliana Musso
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Andrea S Rópolo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Norbert Eichner
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Melina M Musri
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Constanza Feliziani
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - María C Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
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9
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Karvinen S, Korhonen T, Sievänen T, Karppinen JE, Juppi H, Jakoaho V, Kujala UM, Laukkanen JA, Lehti M, Laakkonen EK. Extracellular vesicles and high-density lipoproteins: Exercise and oestrogen-responsive small RNA carriers. J Extracell Vesicles 2023; 12:e12308. [PMID: 36739598 PMCID: PMC9899444 DOI: 10.1002/jev2.12308] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 12/22/2022] [Accepted: 01/22/2023] [Indexed: 02/06/2023] Open
Abstract
Decreased systemic oestrogen levels (i.e., menopause) affect metabolic health. However, the detailed mechanisms underlying this process remain unclear. Both oestrogens and exercise have been shown to improve metabolic health, which may be partly mediated by circulating microRNA (c-miR) signalling. In recent years, extracellular vesicles (EV) have increased interest in the field of tissue crosstalk. However, in many studies on EV-carried miRs, the co-isolation of high-density lipoprotein (HDL) particles with EVs has not been considered, potentially affecting the results. Here, we demonstrate that EV and HDL particles have distinct small RNA (sRNA) content, including both host and nonhost sRNAs. Exercise caused an acute increase in relative miR abundancy in EVs, whereas in HDL particles, it caused an increase in transfer RNA-derived sRNA. Furthermore, we demonstrate that oestrogen-based hormonal therapy (HT) allows the acute exercise-induced miR-response to occur in both EV and HDL particles in postmenopausal women, while the response was absent in nonusers.
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Affiliation(s)
- Sira Karvinen
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Tia‐Marje Korhonen
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Tero Sievänen
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Jari E. Karppinen
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Hanna‐Kaarina Juppi
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Veera Jakoaho
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Urho M. Kujala
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Jari A. Laukkanen
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland,Institute of Clinical MedicineUniversity of Eastern FinlandKuopioFinland
| | - Maarit Lehti
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Eija K. Laakkonen
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
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10
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Zhu Q, Jiang F, Song Y, Lu L, He F, Huang S, Huang Z, Yao J, Lei N, Huang J, Lu S. Small noncoding RNA dysregulation is implicated in manganism in a rat model of methylcyclopentadienyl manganese tricarbonyl-induced unrepaired striatum damage. J Toxicol Sci 2023; 48:535-546. [PMID: 37778982 DOI: 10.2131/jts.48.535] [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] [Indexed: 10/03/2023]
Abstract
The accumulation of excessively high manganese levels within the brain can contribute to a series of Parkinsonian symptoms referred to as manganism. The gasoline antiknock additive Methylcyclopentadienyl Manganese Tricarbonyl (MMT) is an environmental source of manganese exposure and can induce manganism in rats. While some prior reports have demonstrated the differential expression of small noncoding RNAs (sncRNAs) in patients with Parkinson's disease (PD), the degree of sncRNA dysfunction in manganism has yet to be clearly documented. As sncRNAs such as transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) exhibit high levels of modifications such as 3' terminal 3'-phosphate and 2',3'-cyclic phosphate modifications that disrupt the process of adapter ligation and m1A, m3C, m1G, and m22G RNA methylation, these transcripts are not detected in traditional small RNA-sequencing studies. Here, differential sncRNA expression was analyzed by comparing a rat model of MMT-induced unrepaired striatum damage to appropriate control samples via PANDORA-Seq, which can detect highly modified sncRNAs. Following the removal of sncRNA modifications, this approach identified 599 sncRNAs that were differentially expressed in the striatum of MMT-exposed rats relative to controls, as well as 1155 sncRNAs that were differentially expressed in Mn-treated and control rats. Additional functional analyses were performed to predict the putative targets of these sncRNAs, implicating a role for such sncRNA dysregulation in the pathogenesis of manganism in this rat model system.
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Affiliation(s)
- Qifeng Zhu
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Fan Jiang
- Department of Rehabilitation medicine, the First Institute of Clinical Medicine Guangxi Medical University, China
| | - Yuanbo Song
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Lili Lu
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Fajian He
- RnD Department, Wilking Biotechnology Co., Ltd, China
| | - Shuqi Huang
- RnD Department, Wilking Biotechnology Co., Ltd, China
| | - Zhaoying Huang
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Jing Yao
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Ningning Lei
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Jianmin Huang
- Department of Neurology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
| | - Shijin Lu
- Department of Centre for Translational Medical Research in Integrative Chinese and Western Medicine, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, China
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11
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Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA 2022; 8:ncrna8040054. [PMID: 35893237 PMCID: PMC9326685 DOI: 10.3390/ncrna8040054] [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: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
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12
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Tchurikov NA, Klushevskaya ES, Alembekov IR, Bukreeva AS, Kretova AN, Chechetkin VR, Kravatskaya GI, Kravatsky YV. Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs. Int J Mol Sci 2022; 23:ijms23063014. [PMID: 35328433 PMCID: PMC8954558 DOI: 10.3390/ijms23063014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
Small noncoding RNAs of different origins and classes play several roles in the regulation of gene expression. Here, we show that diverged and rearranged fragments of rDNA units are scattered throughout the human genome and that endogenous small noncoding RNAs are processed by the Microprocessor complex from specific regions of ribosomal RNAs shaping hairpins. These small RNAs correspond to particular sites inside the fragments of rDNA that mostly reside in intergenic regions or the introns of about 1500 genes. The targets of these small ribosomal RNAs (srRNAs) are characterized by a set of epigenetic marks, binding sites of Pol II, RAD21, CBP, and P300, DNase I hypersensitive sites, and by enrichment or depletion of active histone marks. In HEK293T cells, genes that are targeted by srRNAs (srRNA target genes) are involved in differentiation and development. srRNA target genes are enriched with more actively transcribed genes. Our data suggest that remnants of rDNA sequences and srRNAs may be involved in the upregulation or downregulation of a specific set of genes in human cells. These results have implications for diverse fields, including epigenetics and gene therapy.
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Affiliation(s)
- Nickolai A. Tchurikov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Correspondence:
| | - Elena S. Klushevskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Ildar R. Alembekov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Anastasiia S. Bukreeva
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Antonina N. Kretova
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Vladimir R. Chechetkin
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Galina I. Kravatskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Yuri V. Kravatsky
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
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13
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Touchette D, Altshuler I, Gostinčar C, Zalar P, Raymond-Bouchard I, Zajc J, McKay CP, Gunde-Cimerman N, Whyte LG. Novel Antarctic yeast adapts to cold by switching energy metabolism and increasing small RNA synthesis. THE ISME JOURNAL 2022; 16:221-232. [PMID: 34294882 PMCID: PMC8692454 DOI: 10.1038/s41396-021-01030-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 05/17/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023]
Abstract
The novel extremophilic yeast Rhodotorula frigidialcoholis, formerly R. JG1b, was isolated from ice-cemented permafrost in University Valley (Antarctic), one of coldest and driest environments on Earth. Phenotypic and phylogenetic analyses classified R. frigidialcoholis as a novel species. To characterize its cold-adaptive strategies, we performed mRNA and sRNA transcriptomic analyses, phenotypic profiling, and assessed ethanol production at 0 and 23 °C. Downregulation of the ETC and citrate cycle genes, overexpression of fermentation and pentose phosphate pathways genes, growth without reduction of tetrazolium dye, and our discovery of ethanol production at 0 °C indicate that R. frigidialcoholis induces a metabolic switch from respiration to ethanol fermentation as adaptation in Antarctic permafrost. This is the first report of microbial ethanol fermentation utilized as the major energy pathway in response to cold and the coldest temperature reported for natural ethanol production. R. frigidialcoholis increased its diversity and abundance of sRNAs when grown at 0 versus 23 °C. This was consistent with increase in transcription of Dicer, a key protein for sRNA processing. Our results strongly imply that post-transcriptional regulation of gene expression and mRNA silencing may be a novel evolutionary fungal adaptation in the cryosphere.
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Affiliation(s)
- D Touchette
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - I Altshuler
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - C Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China
| | - P Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - I Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - J Zajc
- Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - C P McKay
- NASA Ames Research Center, Moffett Field, CA, USA
| | - N Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - L G Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
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14
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Small Noncoding RNAs in Reproduction and Infertility. Biomedicines 2021; 9:biomedicines9121884. [PMID: 34944700 PMCID: PMC8698561 DOI: 10.3390/biomedicines9121884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/20/2022] Open
Abstract
Infertility has been reported as one of the most common reproductive impairments, affecting nearly one in six couples worldwide. A large proportion of infertility cases are diagnosed as idiopathic, signifying a deficit in information surrounding the pathology of infertility and necessity of medical intervention such as assisted reproductive therapy. Small noncoding RNAs (sncRNAs) are well-established regulators of mammalian reproduction. Advanced technologies have revealed the dynamic expression and diverse functions of sncRNAs during mammalian germ cell development. Mounting evidence indicates sncRNAs in sperm, especially microRNAs (miRNAs) and transfer RNA (tRNA)-derived small RNAs (tsRNAs), are sensitive to environmental changes and mediate the inheritance of paternally acquired metabolic and mental traits. Here, we review the critical roles of sncRNAs in mammalian germ cell development. Furthermore, we highlight the functions of sperm-borne sncRNAs in epigenetic inheritance. We also discuss evidence supporting sncRNAs as promising biomarkers for fertility and embryo quality in addition to the present limitations of using sncRNAs for infertility diagnosis and treatment.
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15
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Abstract
In human cells, each rDNA unit consists of the ~13 kb long ribosomal part and ~30 kb long intergenic spacer (IGS). The ribosomal part, transcribed by RNA polymerase I (pol I), includes genes coding for 18S, 5.8S, and 28S RNAs of the ribosomal particles, as well as their four transcribed spacers. Being highly repetitive, intensively transcribed, and abundantly methylated, rDNA is a very fragile site of the genome, with high risk of instability leading to cancer. Multiple small mutations, considerable expansion or contraction of the rDNA locus, and abnormally enhanced pol I transcription are usual symptoms of transformation. Recently it was found that both IGS and the ribosomal part of the locus contain many functional/potentially functional regions producing non-coding RNAs, which participate in the pol I activity regulation, stress reactions, and development of the malignant phenotype. Thus, there are solid reasons to believe that rDNA locus plays crucial role in carcinogenesis. In this review we discuss the data concerning the human rDNA and its closely associated factors as both targets and drivers of the pathways essential for carcinogenesis. We also examine whether variability in the structure of the locus may be blamed for the malignant transformation. Additionally, we consider the prospects of therapy focused on the activity of rDNA.
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16
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Sellem E, Jammes H, Schibler L. Sperm-borne sncRNAs: potential biomarkers for semen fertility? Reprod Fertil Dev 2021; 34:160-173. [PMID: 35231268 DOI: 10.1071/rd21276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Semen infertility or sub-fertility, whether in humans or livestock species, remains a major concern for clinicians and technicians involved in reproduction. Indeed, they can cause tragedies in human relationships or have a dramatic overall negative impact on the sustainability of livestock breeding. Understanding and predicting semen fertility issues is therefore crucial and quality control procedures as well as biomarkers have been proposed to ensure sperm fertility. However, their predictive values appeared to be too limited and additional relevant biomarkers are still required to diagnose sub-fertility efficiently. During the last decade, the study of molecular mechanisms involved in spermatogenesis and sperm maturation highlighted the regulatory role of a variety of small non-coding RNAs (sncRNAs) and led to the discovery that sperm sncRNAs comprise both remnants from spermatogenesis and post-testicular sncRNAs acquired through interactions with extracellular vesicles along epididymis. This has led to the hypothesis that sncRNAs may be a source of relevant biomarkers, associated either with sperm functionality or embryo development. This review aims at providing a synthetic overview of the current state of knowledge regarding implication of sncRNA in spermatogenesis defects and their putative roles in sperm maturation and embryo development, as well as exploring their use as fertility biomarkers.
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Affiliation(s)
- Eli Sellem
- R&D Department, ALLICE, 149 rue de Bercy, 75012 Paris, France
| | - Hélène Jammes
- Université Paris Saclay, UVSQ, INRAE, BREED, 78350 Jouy en Josas, France; and Ecole Nationale Vétérinaire d'Alfort, BREED, 94700 Maisons-Alfort, France
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17
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Stenum TS, Kongstad M, Holmqvist E, Kallipolitis B, Svenningsen SL, Sørensen MA. Three Ribosomal Operons of Escherichia coli Contain Genes Encoding Small RNAs That Interact With Hfq and CsrA in vitro. Front Microbiol 2021; 12:625585. [PMID: 34046019 PMCID: PMC8144298 DOI: 10.3389/fmicb.2021.625585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/09/2021] [Indexed: 01/08/2023] Open
Abstract
Three out of the seven ribosomal RNA operons in Escherichia coli end in dual terminator structures. Between the two terminators of each operon is a short sequence that we report here to be an sRNA gene, transcribed as part of the ribosomal RNA primary transcript by read-through of the first terminator. The sRNA genes (rrA, rrB and rrF) from the three operons (rrnA, rrnB and rrnD) are more than 98% identical, and pull-down experiments show that their transcripts interact with Hfq and CsrA. Deletion of rrA, B, F, as well as overexpression of rrB, only modestly affect known CsrA-regulated phenotypes like biofilm formation, pgaA translation and glgC translation, and the role of the sRNAs in vivo may not yet be fully understood. Since RrA, B, F are short-lived and transcribed along with the ribosomal RNA components, their concentration reflect growth-rate regulation at the ribosomal RNA promoters and they could function to fine-tune other growth-phase-dependent processes in the cell. The primary and secondary structure of these small RNAs are conserved among species belonging to different genera of Enterobacteriales.
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Affiliation(s)
| | - Mette Kongstad
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Erik Holmqvist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Birgitte Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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18
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Shi J, Zhang Y, Tan D, Zhang X, Yan M, Zhang Y, Franklin R, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, Zhao W, Zhao L, Zhou C, Gu W, Murn J, Guo J, Carrell DT, Wang Y, Chen X, Cairns BR, Yang XL, Schimmel P, Zernicka-Goetz M, Cheloufi S, Zhang Y, Zhou T, Chen Q. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat Cell Biol 2021; 23:424-436. [PMID: 33820973 PMCID: PMC8236090 DOI: 10.1038/s41556-021-00652-7] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
Although high-throughput RNA sequencing (RNA-seq) has greatly advanced small non-coding RNA (sncRNA) discovery, the currently widely used complementary DNA library construction protocol generates biased sequencing results. This is partially due to RNA modifications that interfere with adapter ligation and reverse transcription processes, which prevent the detection of sncRNAs bearing these modifications. Here, we present PANDORA-seq (panoramic RNA display by overcoming RNA modification aborted sequencing), employing a combinatorial enzymatic treatment to remove key RNA modifications that block adapter ligation and reverse transcription. PANDORA-seq identified abundant modified sncRNAs-mostly transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs)-that were previously undetected, exhibiting tissue-specific expression across mouse brain, liver, spleen and sperm, as well as cell-specific expression across embryonic stem cells (ESCs) and HeLa cells. Using PANDORA-seq, we revealed unprecedented landscapes of microRNA, tsRNA and rsRNA dynamics during the generation of induced pluripotent stem cells. Importantly, tsRNAs and rsRNAs that are downregulated during somatic cell reprogramming impact cellular translation in ESCs, suggesting a role in lineage differentiation.
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Affiliation(s)
- Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Yunfang Zhang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Dongmei Tan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Xudong Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Menghong Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- Pudong Medical Center, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Reuben Franklin
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA
| | - Marta Shahbazi
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kirsty Mackinlay
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Shichao Liu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Emma R James
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Liwen Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yongcun Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiwei Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Wenxin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Changcheng Zhou
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Weifeng Gu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, USA
| | - Jernej Murn
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA
| | - Jingtao Guo
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Douglas T Carrell
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sihem Cheloufi
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA.
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- The Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA.
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MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis. Biochem Soc Trans 2021; 48:595-612. [PMID: 32267487 PMCID: PMC7200637 DOI: 10.1042/bst20190854] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/14/2022]
Abstract
Ribosome biogenesis is the fine-tuned, essential process that generates mature ribosomal subunits and ultimately enables all protein synthesis within a cell. Novel regulators of ribosome biogenesis continue to be discovered in higher eukaryotes. While many known regulatory factors are proteins or small nucleolar ribonucleoproteins, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) are emerging as a novel modulatory layer controlling ribosome production. Here, we summarize work uncovering non-coding RNAs (ncRNAs) as novel regulators of ribosome biogenesis and highlight their links to diseases of defective ribosome biogenesis. It is still unclear how many miRNAs or lncRNAs are involved in phenotypic or pathological disease outcomes caused by impaired ribosome production, as in the ribosomopathies, or by increased ribosome production, as in cancer. In time, we hypothesize that many more ncRNA regulators of ribosome biogenesis will be discovered, which will be followed by an effort to establish connections between disease pathologies and the molecular mechanisms of this additional layer of ribosome biogenesis control.
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20
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Wu J, Nagy LE, Liangpunsakul S, Wang L. Non-coding RNA crosstalk with nuclear receptors in liver disease. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166083. [PMID: 33497819 DOI: 10.1016/j.bbadis.2021.166083] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/28/2020] [Accepted: 01/16/2021] [Indexed: 02/06/2023]
Abstract
The dysregulation of nuclear receptors (NRs) underlies the pathogenesis of a variety of liver disorders. Non-coding RNAs (ncRNAs) are defined as RNA molecules transcribed from DNA but not translated into proteins. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two types of ncRNAs that have been extensively studied for regulating gene expression during diverse cellular processes. NRs as therapeutic targets in liver disease have been exemplified by the successful application of their pharmacological ligands in clinics. MiRNA-based reagents or drugs are emerging as flagship products in clinical trials. Advancing our understanding of the crosstalk between NRs and ncRNAs is critical to the development of diagnostic and therapeutic strategies. This review summarizes recent findings on the reciprocal regulation between NRs and ncRNAs (mainly on miRNAs and lncRNAs) and their implication in liver pathophysiology, which might be informative to the translational medicine of targeting NRs and ncRNAs in liver disease.
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Affiliation(s)
- Jianguo Wu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America; Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH, United States of America.
| | - Laura E Nagy
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America; Department of Gastroenterology and Hepatology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America; Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States of America; Roudebush Veterans Administration Medical Center, Indianapolis, IN, United States of America; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Li Wang
- Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, CT, United States of America
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21
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Terletskaya NV, Shcherban AB, Nesterov MA, Perfil’ev RN, Salina EA, Altayeva NA, Blavachinskaya IV. Drought Stress Tolerance and Photosynthetic Activity of Alloplasmic Lines T. dicoccum x T. aestivum. Int J Mol Sci 2020; 21:E3356. [PMID: 32397492 PMCID: PMC7246993 DOI: 10.3390/ijms21093356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 11/29/2022] Open
Abstract
Tetraploid species T. dicoccum Shuebl is a potential source of drought tolerance for cultivated wheat, including common wheat. This paper describes the genotyping of nine stable allolines isolated in the offspring from crossing of T. dicoccum x T. aestivum L. using 21 microsatellite (simple sequence repeats-SSR) markers and two cytoplasmic mitochondrial markers to orf256, rps19-p genes; evaluation of drought tolerance of allolines at different stages of ontogenesis (growth parameters, relative water content, quantum efficiency of Photosystem II, electron transport rate, energy dissipated in Photosystem II); and the study of drought tolerance regulator gene Dreb-1 with allele-specific PCR (AS-MARKER) and partial sequence analysis. Most allolines differ in genomic composition and T. dicoccum introgressions. Four allolines-D-b-05, D-d-05, D-d-05b, and D-41-05-revealed signs of drought tolerance of varying degrees. The more drought tolerant D-41-05 line was also characterized by Dreb-B1 allele introgression from T. dicoccum. A number of non-specific patterns and significant differences in allolines in regulation of physiological parameters in drought conditions is identified. Changes in photosynthetic activity in stress-drought are shown to reflect the level of drought tolerance of the forms studied. The contribution of different combinations of nuclear/cytoplasmic genome and alleles of Dreb-1 gene in allolines to the formation of stress tolerance and photosynthetic activity is discussed.
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Affiliation(s)
- Nina V. Terletskaya
- Department of Biodiversity and Biological Resources, Faculty of Biology and Biotechnology Al-Farabi Kazakh National University, Al-Farabi av., 71, Almaty 050040, Kazakhstan;
- Institute of Plant Biology and Biotechnology, Timiryazev str. 45, Almaty 050040, Kazakhstan;
| | - Andrey B. Shcherban
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Lavrentiev av., 10, 630090 Novosibirsk, Russia; (A.B.S.); (M.A.N.); (R.N.P.); (E.A.S.)
| | - Michail A. Nesterov
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Lavrentiev av., 10, 630090 Novosibirsk, Russia; (A.B.S.); (M.A.N.); (R.N.P.); (E.A.S.)
| | - Roman N. Perfil’ev
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Lavrentiev av., 10, 630090 Novosibirsk, Russia; (A.B.S.); (M.A.N.); (R.N.P.); (E.A.S.)
| | - Elena A. Salina
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Lavrentiev av., 10, 630090 Novosibirsk, Russia; (A.B.S.); (M.A.N.); (R.N.P.); (E.A.S.)
| | - Nazira A. Altayeva
- Institute of Plant Biology and Biotechnology, Timiryazev str. 45, Almaty 050040, Kazakhstan;
| | - Irina V. Blavachinskaya
- Department of Biodiversity and Biological Resources, Faculty of Biology and Biotechnology Al-Farabi Kazakh National University, Al-Farabi av., 71, Almaty 050040, Kazakhstan;
- Central Laboratory for Biocontrol, Certification and Preclinical Trials, Al-Farabi av., 93, Almaty 050040, Kazakhstan
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22
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Rosace D, López J, Blanco S. Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer. RNA Biol 2020; 17:1196-1213. [PMID: 32186461 DOI: 10.1080/15476286.2020.1737442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The term small non-coding RNAs (ncRNAs) refers to all those RNAs that even without encoding for a protein, can play important functional roles. Transfer RNA and ribosomal RNA-derived fragments (tRFs and rRFs, respectively) are an emerging class of ncRNAs originally considered as simple degradation products, which though play important roles in stress responses, signalling, or gene expression. They control all levels of gene expression regulating transcription and translation and affecting RNA processing and maturation. They have been linked to pivotal cellular processes such as self-renewal, differentiation, and proliferation. For this reason, mis-regulation of this novel class of ncRNAs can lead to various pathological processes such as neurodegenerative and development diseases, metabolism and immune system disorders, and cancer. In this review, we summarise the classification, biogenesis, and functions of tRFs and rRFs with a special focus on their role in immunity and cancer.
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Affiliation(s)
- Domenico Rosace
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Judith López
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Sandra Blanco
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
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23
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Stolyarenko AD. Nuclear Argonaute Piwi Gene Mutation Affects rRNA by Inducing rRNA Fragment Accumulation, Antisense Expression, and Defective Processing in Drosophila Ovaries. Int J Mol Sci 2020; 21:ijms21031119. [PMID: 32046213 PMCID: PMC7037970 DOI: 10.3390/ijms21031119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 12/26/2022] Open
Abstract
Drosophila key nuclear piRNA silencing pathway protein Piwi of the Argonaute family has been classically studied as a factor controlling transposable elements and fertility. Piwi has been shown to concentrate in the nucleolus for reasons largely unknown. Ribosomal RNA is the main component of the nucleolus. In this work the effect of a piwi mutation on rRNA is described. This work led to three important conclusions: A mutation in piwi induces antisense 5S rRNA expression, a processing defect of 2S rRNA orthologous to the 3′-end of eukaryotic 5.8S rRNA, and accumulation of fragments of all five rRNAs in Drosophilamelanogaster ovaries. Hypotheses to explain these phenomena are proposed, possibly involving the interaction of the components of the piRNA pathway with the RNA surveillance machinery.
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Affiliation(s)
- Anastasia D Stolyarenko
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., Moscow 123182, Russia
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24
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Interpreting and integrating big data in non-coding RNA research. Emerg Top Life Sci 2019; 3:343-355. [PMID: 33523206 DOI: 10.1042/etls20190004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
In the last two decades, we have witnessed an impressive crescendo of non-coding RNA studies, due to both the development of high-throughput RNA-sequencing strategies and an ever-increasing awareness of the involvement of newly discovered ncRNA classes in complex regulatory networks. Together with excitement for the possibility to explore previously unknown layers of gene regulation, these advancements led to the realization of the need for shared criteria of data collection and analysis and for novel integrative perspectives and tools aimed at making biological sense of very large bodies of molecular information. In the last few years, efforts to respond to this need have been devoted mainly to the regulatory interactions involving ncRNAs as direct or indirect regulators of protein-coding mRNAs. Such efforts resulted in the development of new computational tools, allowing the exploitation of the information spread in numerous different ncRNA data sets to interpret transcriptome changes under physiological and pathological cell responses. While experimental validation remains essential to identify key RNA regulatory interactions, the integration of ncRNA big data, in combination with systematic literature mining, is proving to be invaluable in identifying potential new players, biomarkers and therapeutic targets in cancer and other diseases.
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25
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Nguyen Q, Iritani A, Ohkita S, Vu BV, Yokoya K, Matsubara A, Ikeda KI, Suzuki N, Nakayashiki H. A fungal Argonaute interferes with RNA interference. Nucleic Acids Res 2019; 46:2495-2508. [PMID: 29309640 PMCID: PMC5946944 DOI: 10.1093/nar/gkx1301] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/19/2017] [Indexed: 11/25/2022] Open
Abstract
Small RNA (sRNA)-mediated gene silencing phenomena, exemplified by RNA interference (RNAi), require a unique class of proteins called Argonautes (AGOs). An AGO protein typically forms a protein–sRNA complex that contributes to gene silencing using the loaded sRNA as a specificity determinant. Here, we show that MoAGO2, one of the three AGO genes in the fungus Pyricularia oryzae (Magnaporthe oryzae) interferes with RNAi. Gene knockout (KO) studies revealed that MoAGO1 and MoAGO3 additively or redundantly played roles in hairpin RNA- and retrotransposon (MAGGY)-triggered RNAi while, surprisingly, the KO mutants of MoAGO2 (Δmoago2) showed elevated levels of gene silencing. Consistently, transcript levels of MAGGY and mycoviruses were drastically reduced in Δmoago2, supporting the idea that MoAGO2 impeded RNAi against the parasitic elements. Deep sequencing analysis revealed that repeat- and mycovirus-derived small interfering RNAs were mainly associated with MoAGO2 and MoAGO3, and their populations were very similar based on their size distribution patterns and positional base preference. Site-directed mutagenesis studies indicated that sRNA binding but not slicer activity of MoAGO2 was essential for the ability to diminish the efficacy of RNAi. Overall, these results suggest a possible interplay between distinct sRNA-mediated gene regulation pathways through a competition for sRNA.
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Affiliation(s)
- Quyet Nguyen
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Akihide Iritani
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Shuhei Ohkita
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Ba V Vu
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Kana Yokoya
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Ai Matsubara
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Ken-Ichi Ikeda
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
| | - Nobuhiro Suzuki
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Hitoshi Nakayashiki
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe 657-8501, Japan
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26
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Hong J, Blenkiron C, Tsai P, Premkumar R, Nachkebia S, Tun SM, Petzer A, Windsor JA, Hickey AJ, Phillips AR. Extracellular RNA Profile in Mesenteric Lymph from Exemplar Rat Models of Acute and Critical Illness. Lymphat Res Biol 2019; 17:512-517. [PMID: 30864890 DOI: 10.1089/lrb.2018.0044] [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: 12/28/2022] Open
Abstract
Background: Mesenteric lymph (ML) has been implicated in the development of multiple organ dysfunction syndrome in critical illness. Extracellular RNAs play a role in cell-to-cell communication during physiological and disease processes but they are rarely studied in ML. We aimed at examining the RNA profiles of peripheral plasma, ML, and ML's extracellular vesicle (ML-EV) and triglyceride-rich lipoprotein (ML-TRL) fractions, obtained from rodent models of critical illness. Methods and Results: We collected ML for 5 hours from rodent models of critical illness [Acute Pancreatitis, Cecal Ligation and Incision (CLI), Gut Ischemia-Reperfusion (IR)] and matching Sham control rats. ML-EV and ML-TRL fractions were also isolated. RNA sequencing was performed on the RNA extracted from ML, ML-EV, ML-TRL, and plasma by using the Ion Torrent Personal Genome Machine platform. RNA sequences were searched using the Basic Local Alignment Search Tool against rat genome and RefSeq, microRNA (miRNA), genomic tRNA, functional RNA, and Genbank nucleotide databases, and the read counts were analyzed. Each sample type had a distinct RNA profile. ML contained more RNA per volume and a larger proportion of tRNA fragments than plasma. ML-EVs were enriched with miRNA, whereas ML-TRLs contained low absolute amounts of RNA. The RNA size profiles for CLI and Gut IR were different from Sham. ML carried intestinal RNAs and in a CLI model it was significantly enriched with bacterial RNA sequences. Conclusions: We found the distinct but diverse RNA profiles of ML and its compartments, and their different profiles in critical illness. Intestinal-derived small RNAs in ML may have a direct role in critical illness and utility as potential biomarkers.
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Affiliation(s)
- Jiwon Hong
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Surgical and Translational Research Center, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Cherie Blenkiron
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Peter Tsai
- Department of Molecular Medicine and Pathology, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Rakesh Premkumar
- Surgical and Translational Research Center, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Shorena Nachkebia
- Surgical and Translational Research Center, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Soe M Tun
- Surgical and Translational Research Center, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Amorita Petzer
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - John A Windsor
- Surgical and Translational Research Center, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Anthony J Hickey
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Anthony R Phillips
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Surgical and Translational Research Center, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
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27
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Small Non-Coding RNAs Derived From Eukaryotic Ribosomal RNA. Noncoding RNA 2019; 5:ncrna5010016. [PMID: 30720712 PMCID: PMC6468398 DOI: 10.3390/ncrna5010016] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/24/2019] [Accepted: 01/27/2019] [Indexed: 12/13/2022] Open
Abstract
The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will present a nonexhaustive list of referenced small non-coding RNAs (ncRNAs) derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs). We will focus on the rRFs that are experimentally verified, and discuss their origin, length, structure, biogenesis, association with known regulatory proteins, and potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences-because of their overabundance-from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because no one could believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.
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28
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A ribosomal DNA-hosted microRNA regulates zebrafish embryonic angiogenesis. Angiogenesis 2019; 22:211-221. [PMID: 30656567 DOI: 10.1007/s10456-019-09663-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/08/2019] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are single-stranded small non-coding RNAs, generally 18-25 nucleotides in length, that act as repressors of gene expression. miRNAs are encoded by independent genes or processed from a variety of different RNA species. So far, there is no evidence showing that the ribosomal DNA-hosted microRNA is implicated in vertebrate development. Currently, we found a highly expressed small RNA hosted in ribosomal DNA was predicted as a novel miRNA, named miR-ntu1, in zebrafish endothelial cells by deep sequencing analysis. The miRNA was validated by custom-designed Taqman PCR, Northern Blot, and in silico analysis. Furthermore, we demonstrated that miR-ntu1 played a crucial role in zebrafish angiogenesis via modulation of Notch signaling. Our findings provide a notable case that a miRNA hosted in ribosomal DNA is involved in vertebrate development.
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29
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Arya S, Dubey V, Sen D, Sharma A, Pathania R. Computational Prediction of sRNA in Acinetobacter baumannii. Methods Mol Biol 2019; 1946:307-320. [PMID: 30798565 DOI: 10.1007/978-1-4939-9118-1_27] [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] [Indexed: 06/09/2023]
Abstract
Small RNAs in bacteria are noncoding RNAs that act as posttranscriptional regulators of gene expression. Over time, they have gained importance as fine-tuners of expression of genes involved in critical biological processes like metabolism, fitness, virulence, and antibiotic resistance. The availability of various high-throughput strategies enable the detection of these molecules but are technically challenging and time-intensive. Thus, to fulfil the need of a simple computational algorithm pipeline to predict these sRNAs in bacterial species, we detail a user-friendly ensemble method with specific application in Acinetobacter spp. The developed algorithms primarily look for intergenic regions in the genome of related Acinetobacter spp., thermodynamic stability, and conservation of RNA secondary structures to generate a model input for the sRNAPredict3 tool which utilizes all this information to generate a list of putative sRNA. We confirmed the accuracy of the method by comparing its output with the RNA-seq data and found the method to be faster and more accurate for Acinetobacter baumannii ATCC 17978. Thus, this method improves the identification of sRNA in Acinetobacter and other bacterial species.
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Affiliation(s)
- Sankalp Arya
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India
- Division of Agricultural and Environmental Sciences, University of Nottingham, Nottingham, UK
| | - Vineet Dubey
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India
| | - Deepak Sen
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India
| | - Atin Sharma
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India
| | - Ranjana Pathania
- Department of Biotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India.
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30
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The nucleolar transcriptome regulates Piwi shuttling between the nucleolus and the nucleoplasm. Chromosome Res 2018; 27:141-152. [DOI: 10.1007/s10577-018-9595-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 01/25/2023]
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31
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Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome. Sci Rep 2018; 8:10813. [PMID: 30018314 PMCID: PMC6050237 DOI: 10.1038/s41598-018-28485-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) mediate cell-to-cell communication by delivering or displaying macromolecules to their recipient cells. While certain broad-spectrum EV effects reflect their protein cargo composition, others have been attributed to individual EV-loaded molecules such as specific miRNAs. In this work, we have investigated the contents of vesicular cargo using small RNA sequencing of cells and EVs from HEK293T, RD4, C2C12, Neuro2a and C17.2. The majority of RNA content in EVs (49–96%) corresponded to rRNA-, coding- and tRNA fragments, corroborating with our proteomic analysis of HEK293T and C2C12 EVs which showed an enrichment of ribosome and translation-related proteins. On the other hand, the overall proportion of vesicular small RNA was relatively low and variable (2-39%) and mostly comprised of miRNAs and sequences mapping to piRNA loci. Importantly, this is one of the few studies, which systematically links vesicular RNA and protein cargo of vesicles. Our data is particularly useful for future work in unravelling the biological mechanisms underlying vesicular RNA and protein sorting and serves as an important guide in developing EVs as carriers for RNA therapeutics.
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32
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Shi J, Ko EA, Sanders KM, Chen Q, Zhou T. SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:144-151. [PMID: 29730207 PMCID: PMC6112344 DOI: 10.1016/j.gpb.2018.04.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/25/2018] [Accepted: 04/07/2018] [Indexed: 01/07/2023]
Abstract
High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipelineoptimized for rRNA- and tRNA-derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users' input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.
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Affiliation(s)
- Junchao Shi
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
| | - Eun-A Ko
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Kenton M Sanders
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
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33
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Fowler EK, Mohorianu I, Smith DT, Dalmay T, Chapman T. Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues. PLoS One 2018; 13:e0191966. [PMID: 29474379 PMCID: PMC5825024 DOI: 10.1371/journal.pone.0191966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/15/2018] [Indexed: 12/31/2022] Open
Abstract
RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues.
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Affiliation(s)
- Emily K. Fowler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
- School of Computing Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Damian T. Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
- * E-mail:
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34
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Locati MD, Pagano JFB, Abdullah F, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Spaink HP, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM. Identifying small RNAs derived from maternal- and somatic-type rRNAs in zebrafish development. Genome 2018; 61:371-378. [PMID: 29425468 DOI: 10.1139/gen-2017-0202] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
rRNAs are non-coding RNAs present in all prokaryotes and eukaryotes. In eukaryotes there are four rRNAs: 18S, 5.8S, 28S, originating from a common precursor (45S), and 5S. We have recently discovered the existence of two distinct developmental types of rRNA: a maternal-type, present in eggs and a somatic-type, expressed in adult tissues. Lately, next-generation sequencing has allowed the discovery of new small-RNAs deriving from longer non-coding RNAs, including small-RNAs from rRNAs (srRNAs). Here, we systemically investigated srRNAs of maternal- or somatic-type 18S, 5.8S, 28S, with small-RNAseq from many zebrafish developmental stages. We identified new srRNAs for each rRNA. For 5.8S, we found srRNA consisting of the 5' or 3' halves, with only the latter having different sequence for the maternal- and somatic-types. For 18S, we discovered 21 nt srRNA from the 5' end of the 18S rRNA with a striking resemblance to microRNAs; as it is likely processed from a stem-loop precursor and present in human and mouse Argonaute-complexed small-RNA. For 28S, an abundant 80 nt srRNA from the 3' end of the 28S rRNA was found. The expression levels during embryogenesis of these srRNA indicate they are not generated from rRNA degradation and might have a role in the zebrafish development.
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Affiliation(s)
- Mauro D Locati
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Johanna F B Pagano
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Farah Abdullah
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Wim A Ensink
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Marina van Olst
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Selina van Leeuwen
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Ulrike Nehrdich
- b Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, the Netherlands
| | - Herman P Spaink
- b Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, the Netherlands
| | - Han Rauwerda
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Martijs J Jonker
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Rob J Dekker
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Timo M Breit
- a RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
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35
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Computational investigation of small RNAs in the establishment of root nodules and arbuscular mycorrhiza in leguminous plants. SCIENCE CHINA-LIFE SCIENCES 2018; 61:706-717. [DOI: 10.1007/s11427-017-9203-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
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36
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Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea. GENOMICS DATA 2017; 14:114-125. [PMID: 29124009 PMCID: PMC5671611 DOI: 10.1016/j.gdata.2017.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 10/15/2017] [Accepted: 10/17/2017] [Indexed: 12/22/2022]
Abstract
Small noncoding RNAs play a pivotal role in the regulation of gene expression, and are key regulators of animal development. Freshwater planarian exhibits an extraordinary ability to regenerate any missing body parts, representing an emerging model for studying mechanism underlying stem cell regulation and tissue regeneration. Here, we utilized next-generation sequencing (NGS) to identify small RNAs that are expressed in planarian adult stem cells, and are implicated in tissue regeneration. We profiled microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small rDNA-derived RNAs (srRNAs) and endogenous interfering RNAs (endo-siRNAs) population from size 18–30 nt, measured the expression of 244 conserved miRNAs, and identified 41 novel miRNAs and 64 novel endo-siRNAs. Expression profiling analyses revealed that most piRNAs and srRNAs are up-regulated during regeneration, and that the most abundantly expressed srRNAs are from 5.8s and 28s rRNA. Furthermore, a target prediction method was adopted to investigate the anti-correlation of small RNAs and mRNA expression. We built up a gene regulatory network based on the genes that are targeted by dynamically changed small RNAs. These results expand the known small RNA repertoire in planarian, and provide valuable insights and a rich resource for understanding the small RNAs landscape in stem cell-mediated regeneration.
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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Li Y, Zeng A, Li G, Guan YN, Yang HT, Shen B, Jing Q. Dynamic regulation of small RNAome during the early stage of cardiac differentiation from pluripotent embryonic stem cells. GENOMICS DATA 2017; 12:136-145. [PMID: 28540181 PMCID: PMC5432660 DOI: 10.1016/j.gdata.2017.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/09/2017] [Accepted: 05/03/2017] [Indexed: 11/16/2022]
Abstract
Embryonic stem cells (mESCs), having potential to differentiate into three germ-layer cells including cardiomyocytes, shall be a perfect model to help understanding heart development. Here, using small RNA deep sequencing, we studied the small RNAome in the early stage of mouse cardiac differentiation. We found that the expression pattern of most microRNA (miRNA) were highly enriched at the beginning and declined thereafter, some were still insufficiently expressed on day 6, and most miRNAs recovered in the following days. When pluripotent embryonic stem cells are differentiating to cardiomyocytes, targeted genes are concentrated on TGF, WNT and cytoskeletal remodeling pathway. The pathway and network of dynamically changed target genes of the miRNAs at different time points were also investigated. Furthermore, we demonstrated that small rDNA-derived RNAs (srRNAs) were significantly up-regulated during differentiation, especially in stem cells. The pathways of srRNAs targeted genes were also presented. We described the existence and the differential expression of transfer RNA (tRNA), Piwi-interacting RNA (piRNA) and Endogenous siRNAs (endo-siRNAs) in this process. This study reports the genome-wide small RNAome profile, and provides a uniquely comprehensive view of the small RNA regulatory network that governs embryonic stem cell differentiation and cardiac development.
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Affiliation(s)
- Yue Li
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China
- Correspondence to: Y. Li, Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China.Key Laboratory of Stem Cell BiologyInstitute of Health SciencesShanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological ScienceChinese Academy of SciencesShanghai200031China
| | - An Zeng
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ge Li
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ya-Na Guan
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huang-Tian Yang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
- Corresponding author.
| | - Qing Jing
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China
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Asha S, Soniya EV. The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages. Sci Rep 2017; 7:41052. [PMID: 28145468 PMCID: PMC5286533 DOI: 10.1038/srep41052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 12/16/2016] [Indexed: 01/27/2023] Open
Abstract
Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5' end of the putative long form of 5.8S rRNA (5.8SLrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5' consensus sequence of the 5.8S rRNA. The major cleavage process mapped identically among the different tissues of the same plant. The differential expression and cleavage of 5'5.8S srRNAs in Phytophthora capsici infected P. nigrum tissues indicated the critical biological functions of these srRNAs during stress response. The non-canonical short hairpin precursor structure, the association with Argonaute proteins, and the potential targets of 5'5.8S srRNAs reinforced their regulatory role in the RNAi pathway in plants. In addition, this novel lineage specific small RNAs may have tremendous biological potential in the taxonomic profiling of plants.
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Affiliation(s)
- Srinivasan Asha
- Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - E V Soniya
- Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
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Variety of RNAs in Peripheral Blood Cells, Plasma, and Plasma Fractions. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7404912. [PMID: 28127559 PMCID: PMC5239830 DOI: 10.1155/2017/7404912] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/25/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023]
Abstract
Human peripheral blood contains RNA in cells and in extracellular membrane vesicles, microvesicles and exosomes, as well as in cell-free ribonucleoproteins. Circulating mRNAs and noncoding RNAs, being internalized, possess the ability to modulate vital processes in recipient cells. In this study, with SOLiD sequencing technology, we performed identification, classification, and quantification of RNAs from blood fractions: cells, plasma, plasma vesicles pelleted at 16,000g and 160,000g, and vesicle-depleted plasma supernatant of healthy donors and non-small cell lung cancer (NSCLC) patients. It was determined that 16,000g blood plasma vesicles were enriched with cell-free mitochondria and with a set of mitochondrial RNAs. The variable RNA set of blood plasma 160,000g pellets reflected the prominent contribution of U1, U5, and U6 small nuclear RNAs' fragments and at the same time was characterized by a remarkable depletion of small nucleolar RNAs. Besides microRNAs, the variety of fragments of mRNAs and snoRNAs dominated in the set of circulating RNAs differentially expressed in blood fractions of NSCLC patients. Taken together, our data emphasize that not only extracellular microRNAs but also circulating fragments of messenger and small nuclear/nucleolar RNAs represent prominent classes of circulating regulatory ncRNAs as well as promising circulating biomarkers for the development of disease diagnostic approaches.
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Fiskaa T, Knutsen E, Nikolaisen MA, Jørgensen TE, Johansen SD, Perander M, Seternes OM. Distinct Small RNA Signatures in Extracellular Vesicles Derived from Breast Cancer Cell Lines. PLoS One 2016; 11:e0161824. [PMID: 27579604 PMCID: PMC5006963 DOI: 10.1371/journal.pone.0161824] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/14/2016] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is a heterogeneous disease, and different subtypes of breast cancer show distinct cellular morphology, gene expression, metabolism, motility, proliferation, and metastatic potential. Understanding the molecular features responsible for this heterogeneity is important for correct diagnosis and better treatment strategies. Extracellular vesicles (EVs) and their associated molecules have gained much attention as players in intercellular communication, ability to precondition specific organs for metastatic invasion, and for their potential role as circulating cancer biomarkers. EVs are released from the cells and contain proteins, DNA, and long and small RNA species. Here we show by high-throughput small RNA-sequencing that EVs from nine different breast cancer cell lines share common characteristics in terms of small RNA content that are distinct from their originating cells. Most strikingly, a highly abundant small RNA molecule derived from the nuclear 28S rRNA is vastly enriched in EVs. The miRNA profiles in EVs correlate with the cellular miRNA expression pattern, but with a few exceptions that includes miR-21. This cancer-associated miRNA is retained in breast cancer cell lines. Finally, we report that EVs from breast cancer cell lines cluster together based on their small RNA signature when compared to EVs derived from other cancer cell lines. Altogether, our data demonstrate that breast cancer cell lines manifest a specific small RNA signature in their released EVs. This opens up for further evaluation of EVs as breast cancer biomarkers.
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Affiliation(s)
- Tonje Fiskaa
- Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
- * E-mail:
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
| | - Marlen Aas Nikolaisen
- Department of Pharmacy, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
| | - Tor Erik Jørgensen
- Marine Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Steinar Daae Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
- Marine Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
| | - Ole Morten Seternes
- Department of Pharmacy, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
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De Paola D, Zuluaga DL, Sonnante G. The miRNAome of durum wheat: isolation and characterisation of conserved and novel microRNAs and their target genes. BMC Genomics 2016; 17:505. [PMID: 27448633 PMCID: PMC4957382 DOI: 10.1186/s12864-016-2838-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/15/2016] [Indexed: 11/17/2022] Open
Abstract
Background The allotetraploid durum wheat [Triticum turgidum subsp. durum (Desf.) Husn.] is a highly economically important species especially in the Mediterranean basin. However, its genomics, transcriptomics and in particular microRNAome are still largely unknown. Results In the present work, two small RNA libraries from durum wheat Ciccio and Svevo cultivars were generated from different tissues at the late milk (Z77) developmental stage. A total of 167 conserved and 98 potential novel miRNAs were identified in the two libraries and interestingly, three novel miRNAs were found to be derived from ribosomal RNA. Putative target genes were predicted for conserved and novel miRNAs, the majority of which interact with nucleic acids, according to GO terms relative to molecular function. Quantitative qPCR analysis showed that several miRNAs identified were differentially expressed in the mature (Z77) developmental stage compared to young (Z14) tissues. Moreover, target gene expression analysis suggested that in roots, the putative genes encoding for the SQUAMOSA SPL2 and TGA1 proteins are regulated by ttu-miR156n, while MYB3 transcription factor by ttu-miR319f. Additionally, the Photosystem II P680 chlorophyll A apoprotein gene showed an expression level negatively correlated to that of ttu-novel-48 in leaves. Conclusion Our results suggest that, in durum wheat, these genes may play important roles in root/leaf development and are subjected to miRNA regulation. The prediction of novel miRNAs putatively derived from ribosomal RNA opens new perspectives on the study of plant miRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2838-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Domenico De Paola
- Institute of Biosciences and Bioresources, National Research Council, Via G. Amendola 165/A, 70126, Bari, Italy
| | - Diana L Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Via G. Amendola 165/A, 70126, Bari, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via G. Amendola 165/A, 70126, Bari, Italy.
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Human Ribosomal RNA-Derived Resident MicroRNAs as the Transmitter of Information upon the Cytoplasmic Cancer Stress. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7562085. [PMID: 27517048 PMCID: PMC4969525 DOI: 10.1155/2016/7562085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/19/2016] [Indexed: 12/13/2022]
Abstract
Dysfunction of ribosome biogenesis induces divergent ribosome-related diseases including ribosomopathy and occasionally results in carcinogenesis. Although many defects in ribosome-related genes have been investigated, little is known about contribution of ribosomal RNA (rRNA) in ribosome-related disorders. Meanwhile, microRNA (miRNA), an important regulator of gene expression, is derived from both coding and noncoding region of the genome and is implicated in various diseases. Therefore, we performed in silico analyses using M-fold, TargetScan, GeneCoDia3, and so forth to investigate RNA relationships between rRNA and miRNA against cellular stresses. We have previously shown that miRNA synergism is significantly correlated with disease and the miRNA package is implicated in memory for diseases; therefore, quantum Dynamic Nexus Score (DNS) was also calculated using MESer program. As a result, seventeen RNA sequences identical with known miRNAs were detected in the human rRNA and termed as rRNA-hosted miRNA analogs (rmiRNAs). Eleven of them were predicted to form stem-loop structures as pre-miRNAs, and especially one stem-loop was completely identical with hsa-pre-miR-3678 located in the non-rDNA region. Thus, these rmiRNAs showed significantly high DNS values, participation in regulation of cancer-related pathways, and interaction with nucleolar RNAs, suggesting that rmiRNAs may be stress-responsible resident miRNAs which transmit stress-tuning information in multiple levels.
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Wang Y, Lan Q, Zhao X, Xu W, Li F, Wang Q, Chen R. Comparative Profiling of microRNA Expression in Soybean Seeds from Genetically Modified Plants and their Near-Isogenic Parental Lines. PLoS One 2016; 11:e0155896. [PMID: 27214227 PMCID: PMC4876996 DOI: 10.1371/journal.pone.0155896] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 05/05/2016] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) have been widely demonstrated to play fundamental roles in gene regulation in most eukaryotes. To date, there has been no study describing the miRNA composition in genetically modified organisms (GMOs). In this study, small RNAs from dry seeds of two GM soybean lines and their parental cultivars were investigated using deep sequencing technology and bioinformatic approaches. As a result, several differentially expressed gma-miRNAs were found between the GM and non-GM soybeans. Meanwhile, more differentially expressed gma-miRNAs were identified between distantly relatednon-GM soybeans, indicating that the miRNA components of soybean seeds varied among different soybean lines, including the GM and non-GM soybeans, and the extent of difference might be related to their genetic relationship. Additionally, fourteen novel gma-miRNA candidates were predicted in soybean seeds including a potential bidirectionally transcribed miRNA family with two genomic loci (gma-miR-N1). Our findings firstly provided useful data for miRNA composition in edible GM crops and also provided valuable information for soybean miRNA research.
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Affiliation(s)
- Yong Wang
- College of Plant Protection, Agricultural University of Hebei, Baoding, 071001, China
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Qingkuo Lan
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Xin Zhao
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Wentao Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Feiwu Li
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qinying Wang
- College of Plant Protection, Agricultural University of Hebei, Baoding, 071001, China
| | - Rui Chen
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
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Wang Y, Li H, Sun Q, Yao Y. Characterization of Small RNAs Derived from tRNAs, rRNAs and snoRNAs and Their Response to Heat Stress in Wheat Seedlings. PLoS One 2016; 11:e0150933. [PMID: 26963812 PMCID: PMC4786338 DOI: 10.1371/journal.pone.0150933] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 02/22/2016] [Indexed: 12/21/2022] Open
Abstract
Small RNAs (sRNAs) derived from non-coding RNAs (ncRNAs), such as tRNAs, rRNAs and snoRNAs, have been identified in various organisms. Several observations have indicated that cleavage of tRNAs and rRNAs is induced by various stresses. To clarify whether sRNAs in wheat derived from tRNAs (stRNAs), rRNAs (srRNAs) and snoRNAs (sdRNAs) are produced specifically in association with heat stress responses, we carried out a bioinformatic analysis of sRNA libraries from wheat seedlings and performed comparisons between control and high-temperature-treated samples to measure the differential abundance of stRNAs, srRNAs and sdRNAs. We found that the production of sRNAs from tRNAs, 5.8S rRNAs, and 28S rRNAs was more specific than that from 5S rRNAs and 18S rRNAs, and more than 95% of the stRNAs were processed asymmetrically from the 3’ or 5’ ends of mature tRNAs. We identified 333 stRNAs and 8,822 srRNAs that were responsive to heat stress. Moreover, the expression of stRNAs derived from tRNA-Val-CAC, tRNA-Thr-UGU, tRNA-Tyr-GUA and tRNA-Ser-UGA was not only up-regulated under heat stress but also induced by osmotic stress, suggesting that the increased cleavage of tRNAs might be a mechanism that developed in wheat seedlings to help them cope with adverse environmental conditions.
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Affiliation(s)
- Yu Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongxia Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qixin Sun
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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Asha S, Soniya EV. Transfer RNA Derived Small RNAs Targeting Defense Responsive Genes Are Induced during Phytophthora capsici Infection in Black Pepper (Piper nigrum L.). FRONTIERS IN PLANT SCIENCE 2016; 7:767. [PMID: 27313593 PMCID: PMC4887504 DOI: 10.3389/fpls.2016.00767] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 05/17/2016] [Indexed: 05/09/2023]
Abstract
Small RNAs derived from transfer RNAs were recently assigned as potential gene regulatory candidates for various stress responses in eukaryotes. In this study, we report on the cloning and identification of tRNA derived small RNAs from black pepper plants in response to the infection of the quick wilt pathogen, Phytophthora capsici. 5'tRFs cloned from black pepper were validated as highly expressed during P. capsici infection. A high-throughput systematic analysis of the small RNAome (sRNAome) revealed the predominance of 5'tRFs in the infected leaf and root. The abundance of 5'tRFs in the sRNAome and the defense responsive genes as their potential targets indicated their regulatory role during stress response in black pepper. The 5'Ala(CGC) tRF mediated cleavage was experimentally mapped at the tRF binding sites on the mRNA targets of Non-expresser of pathogenesis related protein (NPR1), which was down-regulated during pathogen infection. Comparative sRNAome further demonstrated sequence conservation of 5'Ala tRFs across the angiosperm plant groups, and many important genes in the defense response were identified in silico as their potential targets. Our findings uncovered the diversity, differential expression and stress responsive functional role of tRNA-derived small RNAs during Phytophthora infection in black pepper.
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SncRNA715 Inhibits Schwann Cell Myelin Basic Protein Synthesis. PLoS One 2015; 10:e0136900. [PMID: 26317513 PMCID: PMC4552632 DOI: 10.1371/journal.pone.0136900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/10/2015] [Indexed: 01/03/2023] Open
Abstract
Myelin basic proteins (MBP) are major constituents of the myelin sheath in the central nervous system (CNS) and the peripheral nervous system (PNS). In the CNS Mbp translation occurs locally at the axon-glial contact site in a neuronal activity-dependent manner. Recently we identified the small non-coding RNA 715 (sncRNA715) as a key inhibitor of Mbp translation during transport in oligodendrocytes. Mbp mRNA localization in Schwann cells has been observed, but has not been investigated in much detail. Here we could confirm translational repression of Mbp mRNA in Schwann cells. We show that sncRNA715 is expressed and its levels correlate inversely with MBP in cultured Schwann cells and in the sciatic nerve in vivo. Furthermore we could reduce MBP protein levels in cultured Schwann cells by increasing the levels of the inhibitory sncRNA715. Our findings suggest similarities in sncRNA715-mediated translational repression of Mbp mRNA in oligodendrocytes and Schwann cells.
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Müller C, Schäfer I, Luhmann HJ, White R. Oligodendroglial Argonaute protein Ago2 associates with molecules of the Mbp mRNA localization machinery and is a downstream target of Fyn kinase. Front Cell Neurosci 2015; 9:328. [PMID: 26379499 PMCID: PMC4548153 DOI: 10.3389/fncel.2015.00328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/10/2015] [Indexed: 01/10/2023] Open
Abstract
Oligodendrocytes myelinate neuronal axons in the central nervous system (CNS) facilitating rapid transmission of action potentials by saltatory conduction. Myelin basic protein (MBP) is an essential component of myelin and its absence results in severe hypomyelination in the CNS of rodents. Mbp mRNA is not translated immediately after exit from the nucleus in the cytoplasm, but is transported to the plasma membrane in RNA transport granules in a translationally silenced state. We have previously identified the small non-coding RNA 715 (sncRNA715) as an inhibitor of Mbp translation associated with RNA granules. Argonaute (Ago) proteins and small RNAs form the minimal core of the RNA induced silencing complex and together recognize target mRNAs to be translationally inhibited or degraded. Recently, tyrosine phosphorylation of Ago2 was reported to be a regulator of small RNA binding. The oligodendroglial non-receptor tyrosine kinase Fyn is activated by neuronal signals and stimulates the translation of Mbp mRNA at the axon-glial contact site. Here we analyzed the expression of Ago proteins in oligodendrocytes, if they associate with Mbp mRNA transport granules and are tyrosine phosphorylated by Fyn. We show that all Ago proteins (Ago1-4) are expressed by oligodendrocytes and that Ago2 colocalizes with hnRNP A2 in granular cytoplasmic structures. Ago2 associates with hnRNP A2, Mbp mRNA, sncRNA715 and Fyn kinase and is tyrosine phosphorylated in response to Fyn activity. Our findings suggest an involvement of Ago2 in the translational regulation of Mbp. The identification of Ago proteins as Fyn targets will foster further research to understand in more molecular detail how Fyn activity regulates Mbp translation.
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Affiliation(s)
| | | | | | - Robin White
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, MainzGermany
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49
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Genome-wide analysis of small RNAs in the wheat pathogenic fungus Zymoseptoria tritici. Fungal Biol 2015; 119:631-40. [DOI: 10.1016/j.funbio.2015.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/08/2015] [Accepted: 03/30/2015] [Indexed: 11/23/2022]
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50
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Gvozdev VA, Stolyarenko AD, Klenov MS. Functions of piRNAs and the Piwi protein in Drosophila. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415040055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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