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Zhang B, Zhang C, Zhang J, Lu S, Zhao H, Jiang Y, Ma W. Regulatory roles of long non-coding RNAs in short-term heat stress in adult worker bees. BMC Genomics 2024; 25:506. [PMID: 38778290 PMCID: PMC11110378 DOI: 10.1186/s12864-024-10399-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial modulators of post-transcriptional gene expression regulation, cell fate determination, and disease development. However, lncRNA functions during short-term heat stress in adult worker bees are poorly understood. Here, we performed deep sequencing and bioinformatic analyses of honeybee lncRNAs. RNA interference was performed by using siRNA targeting the most highly expressed lncRNA. The silencing effect on lncRNA and the relative expression levels of seven heat shock protein (HSP) genes, were subsequently examined. Overall, 7,842 lncRNAs and 115 differentially expressed lncRNAs (DELs) were identified in adult worker bees following heat stress exposure. Structural analysis revealed that the overall expression abundance, length of transcripts, exon number, and open reading frames of lncRNAs were lower than those of mRNAs. GO analysis revealed that the target genes were mainly involved in "metabolism," "protein folding," "response to stress," and "signal transduction" pathways. KEGG analysis indicated that the "protein processing in endoplasmic reticulum" and "longevity regulating pathway-multiple species" pathways were most enriched. Quantitative real-time polymerase chain reaction (qRT-PCR) detection of the selected DELs confirmed the reliability of the sequencing data. Moreover, the siRNA experiment indicated that feeding siRNA yielded a silencing efficiency of 77.51% for lncRNA MSTRG.9645.5. Upon silencing this lncRNA, the expression levels of three HSP genes were significantly downregulated (p < 0.05), whereas those of three other HSP genes were significantly upregulated (p < 0.05). Our results provide a new perspective for understanding the regulatory mechanisms of lncRNAs in adult worker bees under short-term heat stress.
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Affiliation(s)
- Bing Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Chaoying Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Jiangchao Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Surong Lu
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Huiting Zhao
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Yusuo Jiang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Weihua Ma
- College of Horticulture, Shanxi Agricultural University, Taiyuan, Shanxi, China.
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2
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Čáp M, Palková Z. Non-Coding RNAs: Regulators of Stress, Ageing, and Developmental Decisions in Yeast? Cells 2024; 13:599. [PMID: 38607038 PMCID: PMC11012152 DOI: 10.3390/cells13070599] [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: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.
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Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
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3
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Fonseca-Carvalho M, Veríssimo G, Lopes M, Ferreira D, Louzada S, Chaves R. Answering the Cell Stress Call: Satellite Non-Coding Transcription as a Response Mechanism. Biomolecules 2024; 14:124. [PMID: 38254724 PMCID: PMC10813801 DOI: 10.3390/biom14010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Organisms are often subjected to conditions that promote cellular stress. Cell responses to stress include the activation of pathways to defend against and recover from the stress, or the initiation of programmed cell death to eliminate the damaged cells. One of the processes that can be triggered under stress is the transcription and variation in the number of copies of satellite DNA sequences (satDNA), which are involved in response mechanisms. Satellite DNAs are highly repetitive tandem sequences, mainly located in the centromeric and pericentromeric regions of eukaryotic chromosomes, where they form the constitutive heterochromatin. Satellite non-coding RNAs (satncRNAs) are important regulators of cell processes, and their deregulation has been associated with disease. Also, these transcripts have been associated with stress-response mechanisms in varied eukaryotic species. This review intends to explore the role of satncRNAs when cells are subjected to adverse conditions. Studying satDNA transcription under various stress conditions and deepening our understanding of where and how these sequences are involved could be a key factor in uncovering important facts about the functions of these sequences.
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Affiliation(s)
- Marisa Fonseca-Carvalho
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Gabriela Veríssimo
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Mariana Lopes
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Daniela Ferreira
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Sandra Louzada
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Raquel Chaves
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
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4
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 343] [Impact Index Per Article: 343.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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5
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Wimalasiri-Yapa BMCR, Huang B, Ross PA, Hoffmann AA, Ritchie SA, Frentiu FD, Warrilow D, van den Hurk AF. Differences in gene expression in field populations of Wolbachia-infected Aedes aegypti mosquitoes with varying release histories in northern Australia. PLoS Negl Trop Dis 2023; 17:e0011222. [PMID: 36989319 PMCID: PMC10085034 DOI: 10.1371/journal.pntd.0011222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/10/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Aedes aegypti is the principal mosquito vector of dengue, yellow fever, Zika and chikungunya viruses. The wMel strain of the endosymbiotic bacteria Wolbachia pipientis was introduced into the vector as a novel biocontrol strategy to stop transmission of these viruses. Mosquitoes with Wolbachia have been released in the field in Northern Queensland, Australia since 2011, at various locations and over several years, with populations remaining stably infected. Wolbachia infection is known to alter gene expression in its mosquito host, but whether (and how) this changes over the long-term in the context of field releases remains unknown. We sampled mosquitoes from Wolbachia-infected populations with three different release histories along a time gradient and performed RNA-seq to investigate gene expression changes in the insect host. We observed a significant impact on gene expression in Wolbachia-infected mosquitoes versus uninfected controls. Fewer genes had significantly upregulated expression in mosquitoes from the older releases (512 and 486 from the 2011 and 2013/14 release years, respectively) versus the more recent releases (1154 from the 2017 release year). Nonetheless, a fundamental signature of Wolbachia infection on host gene expression was observed across all releases, comprising upregulation of immunity (e.g. leucine-rich repeats, CLIPs) and metabolism (e.g. lipid metabolism, iron transport) genes. There was limited downregulation of gene expression in mosquitoes from the older releases (84 and 71 genes from the 2011 and 2013/14 release years, respectively), but significantly more in the most recent release (509 from the 2017 release year). Our findings indicate that at > 8 years post-introgression into field populations, Wolbachia continues to profoundly impact expression of host genes, such as those involved in insect immune response and metabolism. If Wolbachia-mediated virus blocking is underpinned by these differential gene expression changes, our results suggest it may remain stable long-term.
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Affiliation(s)
- B M C Randika Wimalasiri-Yapa
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Open University of Sri Lanka, Nugegoda, Colombo, Sri Lanka
- School of Biomedical Sciences and Centre for Immunology and Infection Control, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Bixing Huang
- Public Health Virology, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, Queensland, Australia
| | - Perran A Ross
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Scott A Ritchie
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Francesca D Frentiu
- School of Biomedical Sciences and Centre for Immunology and Infection Control, Queensland University of Technology, Brisbane, Queensland, Australia
| | - David Warrilow
- Public Health Virology, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, Queensland, Australia
| | - Andrew F van den Hurk
- Public Health Virology, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, Queensland, Australia
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6
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Wolf IR, Marques LF, de Almeida LF, Lázari LC, de Moraes LN, Cardoso LH, Alves CCDO, Nakajima RT, Schnepper AP, Golim MDA, Cataldi TR, Nijland JG, Pinto CM, Fioretto MN, Almeida RO, Driessen AJM, Simōes RP, Labate MV, Grotto RMT, Labate CA, Fernandes Junior A, Justulin LA, Coan RLB, Ramos É, Furtado FB, Martins C, Valente GT. Integrative Analysis of the Ethanol Tolerance of Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24065646. [PMID: 36982719 PMCID: PMC10051466 DOI: 10.3390/ijms24065646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/25/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
Ethanol (EtOH) alters many cellular processes in yeast. An integrated view of different EtOH-tolerant phenotypes and their long noncoding RNAs (lncRNAs) is not yet available. Here, large-scale data integration showed the core EtOH-responsive pathways, lncRNAs, and triggers of higher (HT) and lower (LT) EtOH-tolerant phenotypes. LncRNAs act in a strain-specific manner in the EtOH stress response. Network and omics analyses revealed that cells prepare for stress relief by favoring activation of life-essential systems. Therefore, longevity, peroxisomal, energy, lipid, and RNA/protein metabolisms are the core processes that drive EtOH tolerance. By integrating omics, network analysis, and several other experiments, we showed how the HT and LT phenotypes may arise: (1) the divergence occurs after cell signaling reaches the longevity and peroxisomal pathways, with CTA1 and ROS playing key roles; (2) signals reaching essential ribosomal and RNA pathways via SUI2 enhance the divergence; (3) specific lipid metabolism pathways also act on phenotype-specific profiles; (4) HTs take greater advantage of degradation and membraneless structures to cope with EtOH stress; and (5) our EtOH stress-buffering model suggests that diauxic shift drives EtOH buffering through an energy burst, mainly in HTs. Finally, critical genes, pathways, and the first models including lncRNAs to describe nuances of EtOH tolerance are reported here.
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Affiliation(s)
- Ivan Rodrigo Wolf
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Lucas Farinazzo Marques
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Lauana Fogaça de Almeida
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
- Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil
| | - Lucas Cardoso Lázari
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil
| | - Leonardo Nazário de Moraes
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Luiz Henrique Cardoso
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Camila Cristina de Oliveira Alves
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Rafael Takahiro Nakajima
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Amanda Piveta Schnepper
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Marjorie de Assis Golim
- Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil
| | - Thais Regiani Cataldi
- Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil
| | - Jeroen G. Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Camila Moreira Pinto
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Matheus Naia Fioretto
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Rodrigo Oliveira Almeida
- Instituto Federal de Educação, Ciência e Tecnologia do Sudeste de Minas Gerais–Campus Muriaé, Muriaé 36884-036, Brazil
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Rafael Plana Simōes
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
| | - Mônica Veneziano Labate
- Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil
| | - Rejane Maria Tommasini Grotto
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (I.R.W.)
- Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil
| | - Carlos Alberto Labate
- Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil
| | - Ary Fernandes Junior
- Laboratory of Bacteriology, Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Luis Antonio Justulin
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Rafael Luiz Buogo Coan
- Department of Biophysics and Pharmacology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Érica Ramos
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Fabiana Barcelos Furtado
- Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
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7
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Recent Advances and Future Potential of Long Non-Coding RNAs in Insects. Int J Mol Sci 2023; 24:ijms24032605. [PMID: 36768922 PMCID: PMC9917219 DOI: 10.3390/ijms24032605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Over the last decade, long non-coding RNAs (lncRNAs) have witnessed a steep rise in interest amongst the scientific community. Because of their functional significance in several biological processes, i.e., alternative splicing, epigenetics, cell cycle, dosage compensation, and gene expression regulation, lncRNAs have transformed our understanding of RNA's regulatory potential. However, most knowledge concerning lncRNAs comes from mammals, and our understanding of the potential role of lncRNAs amongst insects remains unclear. Technological advances such as RNA-seq have enabled entomologists to profile several hundred lncRNAs in insect species, although few are functionally studied. This article will review experimentally validated lncRNAs from different insects and the lncRNAs identified via bioinformatic tools. Lastly, we will discuss the existing research challenges and the future of lncRNAs in insects.
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8
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Shi L, Li WL, Zeng HX, Shi Y, Liao XL. Systematic identification and functional analysis of long noncoding RNAs involved in indoxacarb resistance in Spodoptera litura. INSECT SCIENCE 2022; 29:1721-1736. [PMID: 35150054 DOI: 10.1111/1744-7917.13015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts that are more than 200 nucleotides long. They play essential roles in regulating a variety of biological processes in many species, including insects, and some lncRNAs have been found to be associated with insecticide resistance. However, the characteristics and biological functions of lncRNAs involved in indoxacarb resistance are unknown in Spodoptera litura. We performed RNA sequencing in the SS, InRS, and FInRS of S. litura and identified 11 978 lncRNAs, including 3 136 intergenic lncRNAs, 7 393 intronic lncRNAs, and 1 449 anti-sense lncRNAs. Compared with the SS, 51 lncRNAs were upregulated and 134 lncRNAs were downregulated in the two resistant strains, and 908 differentially expressed mRNAs were predicted as the target genes of the 185 differentially expressed lncRNAs. Further analysis showed that 112 of differentially expressed lncRNAs may be associated with indoxacarb resistance by regulating the expression of 14 P450s, seven CCEs, one GST, six UGTs, five ABC transporters, and 24 cuticle protein genes, and 79 of differentially expressed lncRNAs may regulate the expression of 14 detoxification genes and 19 cuticle protein genes to participate in indoxacarb resistance by sponging 10 microRNAs. Interestingly, 47 of differentially expressed lncRNAs may mediate indoxacarb resistance through both lncRNA-mRNA and lncRNA-miRNA-mRNA regulatory pathways. Furthermore, quantitative PCR, RNA interference, and indoxacarb bioassay analyses indicated that overexpressed LNC_004867 and LNC_006576 were involved in indoxacarb resistance. This study provides comprehensive information for lncRNAs of S. litura, and presents evidence that lncRNAs have key roles in conferring insecticide resistance in S. litura.
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Affiliation(s)
- Li Shi
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
| | - Wen-Lin Li
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
| | - Hai-Xin Zeng
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
| | - Yao Shi
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
| | - Xiao-Lan Liao
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
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9
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Vourc’h C, Dufour S, Timcheva K, Seigneurin-Berny D, Verdel A. HSF1-Activated Non-Coding Stress Response: Satellite lncRNAs and Beyond, an Emerging Story with a Complex Scenario. Genes (Basel) 2022; 13:genes13040597. [PMID: 35456403 PMCID: PMC9032817 DOI: 10.3390/genes13040597] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 12/21/2022] Open
Abstract
In eukaryotes, the heat shock response is orchestrated by a transcription factor named Heat Shock Factor 1 (HSF1). HSF1 is mostly characterized for its role in activating the expression of a repertoire of protein-coding genes, including the heat shock protein (HSP) genes. Remarkably, a growing set of reports indicate that, upon heat shock, HSF1 also targets various non-coding regions of the genome. Focusing primarily on mammals, this review aims at reporting the identity of the non-coding genomic sites directly bound by HSF1, and at describing the molecular function of the long non-coding RNAs (lncRNAs) produced in response to HSF1 binding. The described non-coding genomic targets of HSF1 are pericentric Satellite DNA repeats, (sub)telomeric DNA repeats, Short Interspersed Nuclear Element (SINE) repeats, transcriptionally active enhancers and the NEAT1 gene. This diverse set of non-coding genomic sites, which already appears to be an integral part of the cellular response to stress, may only represent the first of many. Thus, the study of the evolutionary conserved heat stress response has the potential to emerge as a powerful cellular context to study lncRNAs, produced from repeated or unique DNA regions, with a regulatory function that is often well-documented but a mode of action that remains largely unknown.
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Affiliation(s)
- Claire Vourc’h
- Université de Grenoble Alpes (UGA), 38700 La Tronche, France
- Correspondence: (C.V.); (A.V.)
| | - Solenne Dufour
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - Kalina Timcheva
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - Daphné Seigneurin-Berny
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - André Verdel
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
- Correspondence: (C.V.); (A.V.)
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10
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Singh A, Kandi AR, Jayaprakashappa D, Thuery G, Purohit DJ, Huelsmeier J, Singh R, Pothapragada SS, Ramaswami M, Bakthavachalu B. The Transcriptional Response to Oxidative Stress is Independent of Stress-Granule Formation. Mol Biol Cell 2022; 33:ar25. [PMID: 34985933 PMCID: PMC9250384 DOI: 10.1091/mbc.e21-08-0418] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cells respond to stress with translational arrest, robust transcriptional changes, and transcription-independent formation of mRNP assemblies termed stress granules (SGs). Despite considerable interest in the role of SGs in oxidative, unfolded-protein and viral stress responses, whether and how SGs contribute to stress-induced transcription has not been rigorously examined. To address this, we characterized transcriptional changes in Drosophila S2 cells induced by acute oxidative-stress and assessed how these were altered under conditions that disrupted SG assembly. Oxidative stress for 3-hours predominantly resulted in induction or upregulation of stress-responsive mRNAs whose levels peaked during recovery after stress cessation. The stress-transcriptome is enriched in mRNAs coding for chaperones, including HSP70s, small heat shock proteins, glutathione transferases, and several non-coding RNAs. Oxidative stress also induced cytoplasmic SGs that disassembled 3-hours after stress cessation. As expected, RNAi-mediated knockdown of the conserved G3BP1/Rasputin protein inhibited SG assembly. However, this disruption had no significant effect on the stress-induced transcriptional response or stress-induced translational arrest. Thus, SG assembly and stress-induced gene expression alterations appear to be driven by distinctive signaling processes. We suggest that while SG assembly represents a fast, transient mechanism, the transcriptional response enables a slower, longer-lasting mechanism for adaptation to and recovery from cell stress.
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Affiliation(s)
- Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Arvind Reddy Kandi
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore 560065, India
| | | | - Guillaume Thuery
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Devam J Purohit
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Rashi Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | | | - Mani Ramaswami
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India.,Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Baskar Bakthavachalu
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore 560065, India.,School of Basic Sciences, Indian Institute of Technology, Mandi 175005, India
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11
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Sheida A, Taghavi T, Shafabakhsh R, Ostadian A, Razaghi Bahabadi Z, Khaksary Mahabady M, Hamblin MR, Mirzaei H. Potential of natural products in the treatment of myocardial infarction: focus on molecular mechanisms. Crit Rev Food Sci Nutr 2022; 63:5488-5505. [PMID: 34978223 DOI: 10.1080/10408398.2021.2020720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although conventional drugs are widely used in the prevention and treatment of cardiovascular disease (CVD), they are being used less frequently due to concerns about possible side effects over the long term. There has been a renewed research interest in medicinal plant products, and their role in protecting the cardiovascular system and treating CVD, which are now being considered as potential alternatives to modern drugs. The most important mechanism causing damage to the myocardium after heart attack and reperfusion, is increased levels of free radicals and oxidative stress. Therefore, treatment approaches often focus on reducing free radicals or enhancing antioxidant defense mechanism. It has been previously reported that bioactive natural products can protect the heart muscle in myocardial infarction (MI). Since these compounds are readily available in fruits and vegetables, they could prevent the risk of MI if they are consumed daily. Although the benefits of a healthy diet are well known, many scientific studies have focused on whether pure natural compounds can prevent and treat MI. In this review we summarize the effects of curcumin, resveratrol, quercitin, berberine, and tanshinone on MI and CVD, and focus on their proposed molecular mechanisms of action.
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Affiliation(s)
- Amirhossein Sheida
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Amirreza Ostadian
- Department of Laboratory Medicine, School of Allied Medical Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Zahra Razaghi Bahabadi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Mahmood Khaksary Mahabady
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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12
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Chatterjee M, Viswanathan P. Long noncoding RNAs in the regulation of p53-mediated apoptosis in human cancers. Cell Biol Int 2021; 45:1364-1382. [PMID: 33760332 DOI: 10.1002/cbin.11597] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/02/2021] [Accepted: 03/21/2021] [Indexed: 02/05/2023]
Abstract
Long noncoding RNAs (lncRNAs) are widely known for their regulatory function in transcriptional and posttranscriptional processes. The involvement of such non-protein-coding RNAs in nuclear organization and chromatin remodeling is often associated with an increased risk of human malignancies. In cancer, lncRNAs either promote cell survival or may act as a growth suppressor, thus conferring a key regulatory function other than their established role in fundamental cellular processes. Interestingly, lncRNAs interfere with the stages of apoptosis and related pathways involving p53. Many of these molecules either regulate or are regulated by p53 while mounting oncogenic events. Consequently, they may confer both prosurvival or proapoptotic functions depending upon the tissue type. Since the mechanism of cell death is bypassed in many human cancers, it has emerged that the lncRNAs are either overexpressed or knocked down to sensitize cells to apoptotic stimuli. Nonetheless, the abundant expression of lncRNAs in tumor cells renders them suitable targets for anticancer therapies. Although the role of lncRNAs in the p53 network and apoptosis has been independently defined, their interplay in activating p53-target genes during cell cycle arrest remains unexplored. Thus, we have specifically reviewed the possible involvement of lncRNAs in the p53-mediated apoptosis of human cancer cells. In particular, we summarize the growing evidence from individual studies and analyze whether lncRNAs are essential to facilitate apoptosis in a p53-dependent manner. This may lead to the identification of p53-associated lncRNAs that are suitable therapeutic targets or diagnostic/prognostic markers.
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Affiliation(s)
- Manjima Chatterjee
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Pragasam Viswanathan
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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13
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Meng LW, Yuan GR, Chen ML, Dou W, Jing TX, Zheng LS, Peng ML, Bai WJ, Wang JJ. Genome-wide identification of long non-coding RNAs (lncRNAs) associated with malathion resistance in Bactrocera dorsalis. PEST MANAGEMENT SCIENCE 2021; 77:2292-2301. [PMID: 33423365 DOI: 10.1002/ps.6256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/09/2020] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play important roles in the regulation of biological processes and have been identified in many species including insects. However, the association between lncRNAs and pesticide resistance in insect species such as Bactrocera dorsalis is unknown. RESULTS RNA-seq was performed on malathion resistant (MR1) and susceptible (MS) strains of B. dorsalis and a total of 6171 lncRNAs transcripts were identified. These included 3728 lincRNAs, 653 antisense lncRNAs, 1402 intronic lncRNAs, and 388 sense lncRNAs. A total of 40 and 52 upregulated lncRNAs were found in females and males of the MR1 strain compared to 54 and 49 in the same sexes of the MS strain, respectively. Twenty-seven of these lncRNAs showed the same trend of expression in both females and males in the MR1 strain, in which 15 lncRNAs were upregulated and 12 were downregulated. RT-qPCR results indicated that the differentially expressed lncRNAs were associated with malathion resistance. The lnc15010.10 and lnc3774.2 were highly expressed in the cuticle of the MR1 strain, indicating that these two lncRNAs may be related to malathion resistance. RNAi of lnc3774.2 and a bioassay showed that malathion resistance was possibly influenced by changes in the B. dorsalis cuticle. CONCLUSION LncRNAs of B. dorsalis potentially related to the malathion resistance were identified. Two lncRNAs appear to influence malathion resistance via modulating the structure, or components, of the cuticle. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Li-Wei Meng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meng-Ling Chen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Tian-Xing Jing
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Li-Sha Zheng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meng-Lan Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wen-Jie Bai
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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14
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Jantrapirom S, Koonrungsesomboon N, Yoshida H, M Candeias M, Pruksakorn D, Lo Piccolo L. Long noncoding RNA-dependent methylation of nonhistone proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1661. [PMID: 33913612 DOI: 10.1002/wrna.1661] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/18/2021] [Accepted: 04/04/2021] [Indexed: 12/15/2022]
Abstract
In the last decade, an intriguing new paradigm of regulation has emerged in which some transcripts longer than 200 nucleotides and no coding potential, long noncoding RNA (lncRNAs), exhibit the capability to control posttranslational modifications of nonhistone proteins in both invertebrates and vertebrates. The extent of such a regulation is still largely unknown. We performed a systematic review to identify and evaluate the potential impact of lncRNA-dependent methylation of nonhistone proteins. Collectively, these lncRNAs primarily act as scaffolds upon which methyltransferases (MTases) and targets are brought in proximity. In this manner, the N-MTase activity of EZH2, protein arginine-MTase 1/4/5, and SMYD2 is exploited to modulate the stability or the compartmentalization of several nonhistone proteins with roles in cell signaling, gene expression, and RNA processing. Moreover, these lncRNAs can indirectly affect the methylation of nonhistone proteins by transcriptional or posttranscriptional regulation of MTases. Strikingly, the lncRNAs/MTases/nonhistone proteins networking seem to be relevant to carcinogenesis and neurological disorders. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Salinee Jantrapirom
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Drosophila Center for Human Diseases and Drug Discovery (DHD), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nut Koonrungsesomboon
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Musculoskeletal Science and Translational Research Center (MSTR), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Marco M Candeias
- MaRCU-Molecular and RNA Cancer Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Human Genetics, National Health Institute Dr Ricardo Jorge, Lisbon, Portugal
| | - Dumnoensun Pruksakorn
- Musculoskeletal Science and Translational Research Center (MSTR), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Omics Center for Health Science, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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15
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Chatterjee M, Viswanathan P. Long noncoding RNAs in the regulation of p53‐mediated apoptosis in human cancers. Cell Biol Int 2021. [DOI: https://doi.org/10.1002/cbin.11597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Manjima Chatterjee
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore Tamil Nadu India
| | - Pragasam Viswanathan
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore Tamil Nadu India
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16
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Chen M, Cai D, Gu H, Yang J, Fan L. MALAT1 rs619586 A/G polymorphisms are associated with decreased risk of lung cancer. Medicine (Baltimore) 2021; 100:e23716. [PMID: 33761627 PMCID: PMC9281991 DOI: 10.1097/md.0000000000023716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 11/16/2020] [Indexed: 01/05/2023] Open
Abstract
Lung cancer is the leading cause of cancer-associated mortality worldwide. Genetic factors are reported to play important roles in lung carcinogenesis. To evaluate genetic susceptibility, we conducted a hospital-based case-control study on the effects of functional single nucleotide polymorphisms (SNPs) in long non-coding RNAs (lncRNAs) and microRNAs on lung cancer development. A total of 917 lung cancer cases and 925 control subjects were recruited. The MALAT1 rs619586 A/G genotype frequencies between patient and control groups were significantly different (P < .001), specifically, 83.85% vs 75.88% (AA), 15.60% vs 21.79% (AG), and 0.55% vs 2.32% (GG). When the homozygous genotype MALAT1 rs619586 AA was used as the reference group, AG (AG vs AA: adjusted odds ratio [OR] 0.65, 95% confidential interval [CI] 0.51-0.83, P = .001) and GG genotypes were associated with significantly decreased risk of lung cancer (GG vs AA: adjusted OR 0.22, 95% CI 0.08-0.59, P = .003). In the dominant model, MALAT1 rs619586 AG/GG variants were also associated with a significantly decreased risk of lung cancer (adjusted OR 0.61, 95% CI 0.48-0.78, P < .001). In the recessive model, when MALAT1 rs619586 AA/AG genotypes were used as the reference group, the GG homozygous genotype was also associated with significantly decreased risk for lung cancer (adjusted OR 0.24, 95% CI 0.09-0.64, P = .004). Hsa-miR-34b/c rs4938723 T > C, pri-miR-124-1 rs531564 C > G and hsa-miR-423 rs6505162 C > A SNPs were not associated with lung cancer risk. Our collective data indicated that MALAT1 rs619586 A/G SNPs significantly reduced the risk of lung cancer. Large-scale studies on different ethnic populations and tissue-specific biological characterization are required to validate the current findings.
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Affiliation(s)
- Ming Chen
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Deng Cai
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyong Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Liming Fan
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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17
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Conservation of gene architecture and domains amidst sequence divergence in the hsrω lncRNA gene across the Drosophila genus: an in silico analysis. J Genet 2020. [DOI: 10.1007/s12041-020-01218-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Yang H, Xu D, Zhuo Z, Hu J, Lu B. SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae). PeerJ 2020; 8:e9133. [PMID: 32509454 PMCID: PMC7246026 DOI: 10.7717/peerj.9133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.
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Affiliation(s)
- Hongjun Yang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Danping Xu
- Sichuan Provincial Key Laboratory of Agricultural Products Processing and Preservative, College of Food Science, Sichuan Agricultural University, Yaan, Sichuan, China
| | - Zhihang Zhuo
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China.,Key Laboratory of Integrated Pest Management on Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiameng Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Baoqian Lu
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture China, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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19
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The Arabidopsis Hypoxia Inducible AtR8 Long Non-Coding RNA also Contributes to Plant Defense and Root Elongation Coordinating with WRKY Genes under Low Levels of Salicylic Acid. Noncoding RNA 2020; 6:ncrna6010008. [PMID: 32110879 PMCID: PMC7151572 DOI: 10.3390/ncrna6010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/22/2020] [Accepted: 02/23/2020] [Indexed: 12/13/2022] Open
Abstract
AtR8 lncRNA was previously identified in the flowering plant Arabidopsis thaliana as an abundant Pol III-transcribed long non-coding RNA (lncRNA) of approximately 260 nt. AtR8 lncRNA accumulation is responsive to hypoxic stress and salicylic acid (SA) treatment in roots, but its function has not yet been identified. In this study, microarray analysis of an atr8 mutant and wild-type Arabidopsis indicated a strong association of AtR8 lncRNA with the defense response. AtR8 accumulation exhibited an inverse correlation with an accumulation of two WRKY genes (WRKY53/WRKY70) when plants were exposed to exogenous low SA concentrations (20 µM), infected with Pseudomonas syringae, or in the early stage of development. The highest AtR8 accumulation was observed 5 days after germination, at which time no WRKY53 or WRKY70 mRNA was detectable. The presence of low levels of SA resulted in a significant reduction of root length in atr8 seedlings, whereas wrky53 and wrky70 mutants exhibited the opposite phenotype. Taken together, AtR8 lncRNA participates in Pathogenesis-Related Proteins 1 (PR-1)-independent defense and root elongation, which are related to the SA response. The mutual regulation of AtR8 lncRNA and WRKY53/WRKY70 is mediated by Nonexpressor of Pathogenesis-Related Gene 1 (NPR1).
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20
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Guan R, Li H, Zhang H, An S. Comparative analysis of dsRNA-induced lncRNAs in three kinds of insect species. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21640. [PMID: 31667893 DOI: 10.1002/arch.21640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/24/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) that have immune responses to various stimuli have been identified in some insects. One type of pathogen-associated molecular pattern, double-stranded RNA (dsRNA), can trigger the RNA interference (RNAi) pathway and immune response. Interestingly, there has been no research into characterizing the relationship between lncRNA and dsRNA-induced RNAi pathways. In this study, dsRNA-induced lncRNAs were investigated in two species of lepidopteran insects, Helicoverpa armigera and Plutella xylostella, and one species of coleopteran insects, Tribolium castaneum. Between untreated group and dsRNA-induced group; 3,463 H. armigera, 6,245 P. xylostella, and 3,067 T. castaneum differentially expressed lncRNAs were identified while 156 H. armigera, 247 P. xylostella, 415 T. castaneum lncRNAs and their putative target genes showed consistent changes in gene expression. In T. castaneum, most target genes of the differentially expressed lncRNAs are enriched in the cyclic adenosine monophosphate signaling pathway, ABC transporters, and Janus kinase-signal transducers and activators of the transcription signaling pathway. Conversely, in H. armigera and P. xylostella, the differentially expressed lncRNAs were mainly enriched in the metabolic, digestive, and synthetic signaling pathways. This result indicates that dsRNA-induced lncRNA is species-dependent. We also found that both Dicer-2 and the lncRNA that targets Dicer-2 were significantly upregulated after dsRNA treatment in P. xylostella, indicating that some lncRNAs may be involved in the regulation of the core RNAi pathway in insects. Our results are the first to identify a relationship between lncRNAs and dsRNA in various insect species with different RNAi efficiencies. These results provide a reference for future study of the dsRNA-induced RNAi pathway and different RNAi efficiencies among insect species.
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Affiliation(s)
- Ruobing Guan
- State Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Haichao Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hao Zhang
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Shiheng An
- State Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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21
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Liu B, Cao W, Xue J. LncRNA ANRIL protects against oxygen and glucose deprivation (OGD)-induced injury in PC-12 cells: potential role in ischaemic stroke. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:1384-1395. [PMID: 31174432 DOI: 10.1080/21691401.2019.1596944] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
lncRNA ANRIL was reported to be closely related to ischaemic stroke (IS). In this study, we used oxygen-glucose deprivation (OGD) to stimulate rat adrenal medulla-derived pheochromocytoma cell line PC-12 to construct an in vitro IS cell model and investigated the role of ANRIL and the underlying mechanism. PC-12 cells were stimulated by OGD and/or transfected with pc-ANRIL, si-ANRIL, miR-127 mimic, miR-127 inhibitor, pEX-Mcl-1, sh-Mcl-1 and their negative controls. Cell viability, apoptosis, mRNA and protein expression was detected using CCK-8 assay, flow cytometry assay, qRT-PCR and western blot, respectively. Results showed that OGD-induced PC-12 cell injury and decreased ANRIL expression. ANRIL overexpression significantly reduced OGD-induced PC-12 cell injury evidenced by increasing cell viability and decreasing apoptosis, while ANRIL silence led to the opposite results. Meanwhile, dysregulation of ANRIL altered the expression of apoptotic proteins. Furthermore, ANRIL negatively regulated miR-127 expression. miR-127 overexpression significantly enhanced OGD-induced PC-12 cell injury. In addition, Mcl-1 expression was negatively regulated by miR-127, besides ANRIL up-regulated Mcl-1 expression by down-regulation of miR-127. Mcl-1 overexpression alleviated cell injury and miR-127 silence up-regulated Mcl-1 expression. In conclusion, lncRNA ANRIL alleviated OGD-induced PC-12 cell injury as evidenced. PI3K/AKT pathway might be involved in this regulating progression.
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Affiliation(s)
- Bin Liu
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
| | - Wei Cao
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
| | - Jian Xue
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
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22
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Zeng Z, Pan Y, Wu W, Li L, Wu Z, Zhang Y, Deng B, Wei S, Zhang W, Lin F, Song Y. Myocardial hypertrophy is improved with berberine treatment via long non-coding RNA MIAT-mediated autophagy. J Pharm Pharmacol 2019; 71:1822-1831. [PMID: 31612504 DOI: 10.1111/jphp.13170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/01/2019] [Indexed: 01/01/2023]
Abstract
Abstract
Objectives
This study aimed to evaluate berberine (BBR) effects on myocardial hypertrophy (MH) and associated mechanisms.
Methods
BBR effects on MH were evaluated in rats with constriction of abdominal aorta (CAA). qRT-PCR assay was used to measure MH-related genes, long non-coding RNAs (lncRNAs) and autophagy-related genes expressions. Western blot was performed to detect autophagy markers expression. Filamentous actin and phalloidin expressions were detected using immunofluorescence assay.
Key findings
BBR significantly attenuated CAA-induced MH and cardiomyocyte enlargement. CAA upregulated β myosin heavy chain and atrial natriuretic peptide expressions in heart tissues, which was attenuated by BBR. BBR suppressed myocardial infarction associated transcript (MIAT) expression in rats with CAA. p62 mRNA expression was upregulated and beclin1 and autophagy related 5 were downregulated in CAA versus control groups. The effects were abolished by BBR. In vitro studies showed that BBR ameliorated angiotensin II-induced MH and attenuated Ang II-induced MIAT expression in H9C2 cells. Expressions of phosphorylated mTOR, phosphorylated AMPK and LC3 were upregulated in H9C2 cells after Ang II stimulation, and the effects were abolished by BBR.
Conclusions
BBR exerted beneficial effects on MH induced by CCA, and the mechanisms were associated with decreased MIAT expression and enhanced autophagy.
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Affiliation(s)
- Zhicong Zeng
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
| | - Yan Pan
- Diabetes Department, Bao'an TCM Hospital Group, Shenzhen, China
| | - Wei Wu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liang Li
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
- Graduate School, Guangzhou University of TCM, Guangzhou, China
| | - Zijun Wu
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
| | - Yuangui Zhang
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
| | - Bin Deng
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
| | - Shanyan Wei
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
| | - Weiwei Zhang
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
| | - Fengxia Lin
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
| | - Yinzhi Song
- Cardiology Department, Bao'an TCM Hospital Group, Shenzhen, China
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Wang Z, Jiang Y, Wu H, Xie X, Huang B. Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs Involved in the Heat Stress Response in Metarhizium robertsii. Front Microbiol 2019; 10:2336. [PMID: 31649657 PMCID: PMC6794563 DOI: 10.3389/fmicb.2019.02336] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play a significant role in stress responses. To date, only a few studies have reported the role of lncRNAs in insect-pathogenic fungi. Here, we report a genome-wide transcriptional analysis of lncRNAs produced in response to heat stress in Metarhizium robertsii, a model insect-pathogenic fungus, using strand-specific RNA sequencing. A total of 1655 lncRNAs with 1742 isoforms were identified, of which 1081 differentially expressed (DE) lncRNAs were characterized as being heat responsive. By characterizing their genomic structures and expression patterns, we found that the lncRNAs possessed shorter transcripts, fewer exons, and lower expression levels than the protein-coding genes in M. robertsii. Furthermore, target prediction analysis of the lncRNAs revealed thousands of potential DE lncRNA–messenger RNA (mRNA) pairs, among which 5381 pairs function in the cis-regulatory mode. Further pathway enrichment analysis of the corresponding cis-regulated target genes showed that the targets were significantly enriched in the following biological pathways: the Hippo signaling pathway and cell cycle. This finding suggested that these DE lncRNAs control the expression of their corresponding neighboring genes primarily through environmental information processing and cellular processes. Moreover, only 26 trans-regulated lncRNA–mRNA pairs were determined. In addition, among the targets of heat-responsive lncRNAs, two classic genes that may be involved in the response to heat stress were also identified, including hsp70 (XM_007821830 and XM_007825705). These findings expand our knowledge of lncRNAs as important regulators of the response to heat stress in filamentous fungi, including M. robertsii.
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Affiliation(s)
- Zhangxun Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China.,School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yuanyuan Jiang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China.,School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Hao Wu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Xiangyun Xie
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
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Ray M, Singh G, Lakhotia SC. Altered levels of hsromega lncRNAs further enhance Ras signaling during ectopically activated Ras induced R7 differentiation in Drosophila. Gene Expr Patterns 2019; 33:20-36. [DOI: 10.1016/j.gep.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/07/2019] [Indexed: 12/15/2022]
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25
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Pirogov SA, Gvozdev VA, Klenov MS. Long Noncoding RNAs and Stress Response in the Nucleolus. Cells 2019; 8:cells8070668. [PMID: 31269716 PMCID: PMC6678565 DOI: 10.3390/cells8070668] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) perform diverse functions in the regulation of cellular processes. Here we consider a variety of lncRNAs found in the ribosome production center, the nucleolus, and focus on their role in the response to environmental stressors. Nucleolar lncRNAs ensure stress adaptation by cessation of resource-intensive ribosomal RNA (rRNA) synthesis and by inducing the massive sequestration of proteins within the nucleolus. Different cell states like quiescence and cancer are also controlled by specific lncRNAs in the nucleolus. Taken together, recent findings allow us to consider lncRNAs as multifunctional regulators of nucleolar activities, which are responsive to various physiological conditions.
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Affiliation(s)
- Sergei A Pirogov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Vladimir A Gvozdev
- 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.
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26
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Gonçalves AT, Núñez-Acuña G, Détrée C, Gallardo-Escárate C. Coding/non-coding cross-talk in intestinal epithelium transcriptome gives insights on how fish respond to stocking density. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:14-23. [DOI: 10.1016/j.cbd.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 02/04/2023]
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27
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Xu C, Zhou J, Wang Y, Wang A, Su L, Liu S, Kang X. Inhibition of malignant human bladder cancer phenotypes through the down-regulation of the long non-coding RNA SNHG7. J Cancer 2019; 10:539-546. [PMID: 30719150 PMCID: PMC6360294 DOI: 10.7150/jca.25507] [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: 02/12/2018] [Accepted: 10/16/2018] [Indexed: 12/29/2022] Open
Abstract
There is abundant evidence that long non-coding RNAs play important roles in the development of tumors. In the present study, our main aim was to explore the relationship between lncRNA SNHG7 and human bladder cancer cells, thus finding a novel target for bladder cancer therapy and diagnosis. Expression of lncRNA SNHG7 was evaluated using real-time quantitative polymerase chain reaction in bladder tumor tissues and paired adjacent normal tissues from 72 patients diagnosed with urothelial bladder carcinoma. We analyzed the differences in expression according to grading and staging. Human bladder cancer cell lines UMUC, 5637, T24 and SW780 were transiently transfected with lncRNA SNHG7-specific siRNA and negative control siRNA. The changes in malignant phenotypes in transfected bladder cancer cells were determined using CCK-8 assay, wound-healing assay and ELISA. We found that lncRNA SNHG7 was correlated with human bladder cancer. lncRNA SNHG7 was overexpressed in bladder cancer tissues compared to paired normal tissues and expression of SNHG7 was higher in high-grade than low-grade tumors. The malignant phenotypes were significantly inhibited when we inhibited expression of lncRNA SNHG7 in several bladder cell lines. SNHG7 plays an oncogenic role in human bladder cancer and may be a potential novel therapeutic target for treating bladder cancer.
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Affiliation(s)
- Congjie Xu
- Hainan General Hospital, Haikou 570311, China
| | | | - Yang Wang
- Hainan General Hospital, Haikou 570311, China
| | - Anfang Wang
- Hainan General Hospital, Haikou 570311, China
| | - Liangju Su
- Hainan General Hospital, Haikou 570311, China
| | - Shuan Liu
- Hainan General Hospital, Haikou 570311, China
| | - Xinli Kang
- Hainan General Hospital, Haikou 570311, China
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28
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Verheyden Y, Goedert L, Leucci E. Control of nucleolar stress and translational reprogramming by lncRNAs. Cell Stress 2018; 3:19-26. [PMID: 31225496 PMCID: PMC6551676 DOI: 10.15698/cst2019.01.172] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Under adverse environmental conditions, cells activate stress re-sponses that favour adaptation or, in case of irreversible damage, induce cell death. Multiple stress response pathways converge to downregulate ribo-some biogenesis and translation since these are the most energy consuming processes in the cell. This adaptive response allows preserving genomic stabil-ity and saving energy for the recovery. It follows that the nucleolus is a major sensor and integrator of stress responses that are then transmitted to the translation machinery through an intricate series of conserved events. Long non-coding RNAs (lncRNAs) are emerging as important regulators of stress-induced cascades, for their ability to mediate post-transcriptional responses. Consistently, many of them are specifically expressed under stress conditions and a few have been already functionally linked to these processes, thus fur-ther supporting a role in stress management. In this review we survey differ-ent archetypes of lncRNAs specifically implicated in the regulation of nucleo-lar functions and translation reprogramming during stress responses.
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Affiliation(s)
- Yvessa Verheyden
- Laboratory of RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, 3000 Leuven, Belgium
| | - Lucas Goedert
- Laboratory of RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, 3000 Leuven, Belgium.,Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Eleonora Leucci
- Laboratory of RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, 3000 Leuven, Belgium
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29
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Gooding AJ, Zhang B, Gunawardane L, Beard A, Valadkhan S, Schiemann WP. The lncRNA BORG facilitates the survival and chemoresistance of triple-negative breast cancers. Oncogene 2018; 38:2020-2041. [PMID: 30467380 DOI: 10.1038/s41388-018-0586-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/10/2018] [Accepted: 10/12/2018] [Indexed: 12/31/2022]
Abstract
Disseminated breast cancer cells employ adaptive molecular responses following cytotoxic therapeutic insult which promotes their survival and subsequent outgrowth. Here we demonstrate that expression of the pro-metastatic lncRNA BORG (BMP/OP-Responsive Gene) is greatly induced within triple-negative breast cancer (TNBC) cells subjected to environmental and chemotherapeutic stresses commonly faced by TNBC cells throughout the metastatic cascade. This stress-mediated induction of BORG expression fosters the survival of TNBC cells and renders them resistant to the cytotoxic effects of doxorubicin both in vitro and in vivo. The chemoresistant traits of BORG depend upon its robust activation of the NF-κB signaling axis via a novel BORG-mediated feed-forward signaling loop, and via its ability to bind and activate RPA1. Indeed, genetic and pharmacologic inhibition of NF-κB signaling or the DNA-binding activity of RPA1 abrogates the pro-survival features of BORG and renders BORG-expressing TNBCs sensitive to doxorubicin-induced cytotoxicity. These findings suggest that therapeutic targeting of BORG or its downstream molecular effectors may provide a novel means to alleviate TNBC recurrence.
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Affiliation(s)
- Alex J Gooding
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Bing Zhang
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Lalith Gunawardane
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Abigail Beard
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - William P Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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30
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Sun X, Zheng G, Li C, Liu C. Long non‑coding RNA Fer‑1‑like family member 4 suppresses hepatocellular carcinoma cell proliferation by regulating PTEN in vitro and in vivo. Mol Med Rep 2018; 19:685-692. [PMID: 30431133 DOI: 10.3892/mmr.2018.9629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 06/22/2018] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to investigate the potential role of long non‑coding RNA Fer‑1‑like family member 4 (FER1L4) in the proliferation of hepatocellular carcinoma (HCC) through the regulation of phosphatase and tensin homolog (PTEN) expression. Reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) was used to detect the expression levels of FER1L4 and PTEN mRNA in HCC tissues, and western blotting was performed to measure the protein expression level of PTEN; MTT and colony formation assays were performed to detect the cell proliferative ability. Furthermore, nude mice were injected with transfected HCC cells and the tumor volume and weight were measured. The results indicated that FER1L4 was expressed at a low level in human HCC tissues compared with adjacent normal tissues. Functional studies indicated that FER1L4 may inhibit the proliferative ability of HCC cells. In addition, PTEN was highly expressed in HCC tissues compared with normal adjacent tissues and was positively associated with FER1L4. In addition, it was demonstrated that FER1L4 inhibited the proliferative ability of HCC cells in vitro, and silencing FER1L4 expression by small interfering RNAs promoted the growth of HCC tumors in vivo. Therefore, FER1L4 may be a potent therapeutic target for HCC.
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Affiliation(s)
- Xinyi Sun
- Department of Gastroenterology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Guoqi Zheng
- Department of Gastroenterology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Chunying Li
- Department of Gastroenterology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Chendi Liu
- Department of Gastroenterology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
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Schroeder M, Jakovcevski M, Polacheck T, Drori Y, Ben-Dor S, Röh S, Chen A. Sex dependent impact of gestational stress on predisposition to eating disorders and metabolic disease. Mol Metab 2018; 17:1-16. [PMID: 30174229 PMCID: PMC6197785 DOI: 10.1016/j.molmet.2018.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/08/2018] [Accepted: 08/14/2018] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Vulnerability to eating disorders (EDs) is broadly assumed to be associated with early life stress. However, a careful examination of the literature shows that susceptibility to EDs may depend on the type, severity and timing of the stressor and the sex of the individual. We aimed at exploring the link between chronic prenatal stress and predisposition to EDs and metabolic disease. METHODS We used a chronic variable stress protocol during gestation to explore the metabolic response of male and female offspring to food restriction (FR), activity-based anorexia (ABA), binge eating (BE) and exposure to high fat (HF) diet. RESULTS Contrary to controls, prenatally stressed (PNS) female offspring showed resistance to ABA and BE and displayed a lower metabolic rate leading to hyperadiposity and obesity on HF diet. Male PNS offspring showed healthy responses to FR and ABA, increased propensity to binge and improved coping with HF compared to controls. We found that long-lasting abnormal responses to metabolic challenge are linked to fetal programming and adult hypothalamic dysregulation in PNS females, resulting from sexually dimorphic adaptations in placental methylation and gene expression. CONCLUSIONS Our results show that maternal stress may have variable and even opposing effects on ED risk, depending on the ED and the sex of the offspring.
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Affiliation(s)
- Mariana Schroeder
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel; Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany.
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany
| | - Tamar Polacheck
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yonat Drori
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, Biological Services, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, 80804, Germany
| | - Alon Chen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel; Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany.
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32
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Zhou Q, Chen F, Zhao J, Li B, Liang Y, Pan W, Zhang S, Wang X, Zheng D. Long non-coding RNA PVT1 promotes osteosarcoma development by acting as a molecular sponge to regulate miR-195. Oncotarget 2018; 7:82620-82633. [PMID: 27813492 PMCID: PMC5347719 DOI: 10.18632/oncotarget.13012] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/29/2016] [Indexed: 12/29/2022] Open
Abstract
A growing body of evidence has indicated that long non-coding RNAs (lncRNAs) serve as competing endogenous RNAs (ceRNAs) during oncogenesis. In this study, the qRT-PCR results indicated that the lncRNA PVT1 is overexpressed in osteosarcoma and decreased the survival rate of osteosarcoma patients. MTT and clonal colony formation assays were used to detect the effect of PVT1 on proliferation, and flow cytometry was performed to assess apoptosis and the cell cycle. A Transwell assay was used to analyze migration and invasion. The results revealed that silencing PVT1 by siRNA inhibited proliferation, migration and invasion and promoted apoptosis and cell cycle arrest in osteosarcoma cells. Furthermore, a gene microarray was used to screen differentially expressed miRNAs associated with PVT1. The interaction between PVT1 and miRNAs was then analyzed by qRT-PCR and luciferase reporter gene assay. We found that PVT1 negatively regulated miR-195 in osteosarcoma cells. Simultaneously, we found that silencing PVT1 by siRNA suppressed proliferation, migration and invasion and promoted cell cycle arrest and apoptosis via miR-195 in osteosarcoma cells. Moreover, silencing PVT1 by siRNA inhibited BCL2, CCND1, and FASN protein expression via miR-195 in osteosarcoma cells, and BCL2 inhibited the si-PVT1#1-induced apoptosis of U2OS cells. CCND1 inhibited the cell cycle arrest of U2OS cells induced by si-PVT1#1. FASN promoted the invasiveness U2OS cells, which was inhibited by si-PVT1#1. Therefore, our study demonstrated that PVT1 may be a therapeutic target for treatment of osteosarcoma.
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Affiliation(s)
- Quan Zhou
- Department of Orthopaedics, Huai'an Hospital Affiliated of Xuzhou Medical University and Huai'an Second Hospital, Huai'an 223002, Jiangsu, China
| | - Fengli Chen
- Department of Central Laboratory, Huai'an First People's Hospital, Nanjing Medical University, Huai'an 223002, Jiangsu, China
| | - Jiali Zhao
- Department of Orthopaedics, Huai'an Hospital Affiliated of Xuzhou Medical University and Huai'an Second Hospital, Huai'an 223002, Jiangsu, China
| | - Baojun Li
- Department of Joint Surgery, Second People's Hospital of Hunan Province, Changsha 410007, Hunan, China
| | - Yong Liang
- Department of Central Laboratory and Department of Nephrology, Huai'an Hospital Affiliated of Xuzhou Medical University and Huai'an Second Hospital, Huai'an 223002, Jiangsu, China
| | - Wei Pan
- Department of Orthopaedics, Huai'an Hospital Affiliated of Xuzhou Medical University and Huai'an Second Hospital, Huai'an 223002, Jiangsu, China
| | - Shaoxian Zhang
- Department of Orthopaedics, Huai'an Hospital Affiliated of Xuzhou Medical University and Huai'an Second Hospital, Huai'an 223002, Jiangsu, China
| | - Xinhong Wang
- Department of Orthopaedics, Huai'an Hospital Affiliated of Xuzhou Medical University and Huai'an Second Hospital, Huai'an 223002, Jiangsu, China
| | - Donghui Zheng
- Department of Central Laboratory and Department of Nephrology, Huai'an Hospital Affiliated of Xuzhou Medical University and Huai'an Second Hospital, Huai'an 223002, Jiangsu, China
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Qiao M, Li R, Zhao X, Yan J, Sun Q. Up-regulated lncRNA-MSX2P1 promotes the growth of IL-22-stimulated keratinocytes by inhibiting miR-6731-5p and activating S100A7. Exp Cell Res 2018; 363:243-254. [PMID: 29339075 DOI: 10.1016/j.yexcr.2018.01.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/06/2018] [Accepted: 01/12/2018] [Indexed: 12/20/2022]
Abstract
Competitive endogenous RNAs (ceRNAs) regulate RNA transcripts by competing for shared miRNAs and play critical roles in disease development. Psoriasis is a long-lasting, recurring chronic inflammatory skin disease characterized by hyperproliferation of keratinocytes. The keratinocyte response is triggered by the activation of inflammatory cytokines, like interleukin-22 (IL-22). We used lncRNA array analysis to detect differentially expressed lncRNAs in skin (HaCaT) cells treated with or without IL-22. We used hematoxylin and eosin (H&E) staining to determine the pathological changes in skin cells and immunohistochemistry to evaluate the expression of S100A7. We used qRT-PCR and Western blotting to detect the expression levels of MSX2P1 and S100A7. We down-regulated the expression of MSX2P1 by infecting with lentiviral-vector shRNA. We measured cell proliferation, cell cycle status, and apoptosis by the CCK-8 assay, flow cytometry, and Annexin Ⅴ-FITC/PI staining, respectively. In addition, we used the luciferase reporter gene assay to determine the relationships between MSX2P1 or miR-6731-5p and S100A7, respectively. LncRNA array analysis revealed that 103 lncRNAs were up-regulated and 51 were down-regulated. Furthermore, qRT-PCR showed that the mRNAs levels of MSX2P1 was significantly altered in HaCaT cells treated with IL-22, compared with control cells; and MSX2P1 was mainly in the cytoplasm. Based on the IL-22-stimulated lncRNA-associated ceRNA network, we selected MSX2P1-miR-6731-5p-S100A7 for further study. H&E staining exhibited characteristic features specific to psoriatic lesions. Immunohistochemistry demonstrated significantly increased expression levels of S100A7 in psoriatic lesions, compared with normal skin tissue. We observed a positive correlation between lncRNA-MSX2P1 expression and S100A7 expression. In addition, miR-6731-5p suppressed proliferation, accelerated apoptosis in IL-22-stimulated keratinocytes, and decreased the expressions of S100A7, IL-12β, IL-23, HLA-C, CCHCR1, TNF-α, and NF-κB proteins. Our data demonstrated that MSX2P1 facilitate the progression and growth of IL-22-stimulated keratinocytes by inhibiting miR-6731-5p and activating S100A7. We speculate that the biological network of MSX2P1-miR-6731-5p-S100A7 is a potential novel therapeutic target for the future treatment of psoriasis.
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Affiliation(s)
- Meng Qiao
- Department of Dermatology, Qilu Hospital of Shandong University, Jinan 250012, Shandong, PR China
| | - Ronghua Li
- Department of Dermatology, Qilu Hospital of Shandong University, Jinan 250012, Shandong, PR China
| | - Xintong Zhao
- Department of Dermatology, Qilu Hospital of Shandong University, Jinan 250012, Shandong, PR China
| | - Jianjun Yan
- Department of Dermatology, Qilu Hospital of Shandong University, Jinan 250012, Shandong, PR China
| | - Qing Sun
- Department of Dermatology, Qilu Hospital of Shandong University, Jinan 250012, Shandong, PR China.
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Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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LncRNA NEAT1 enhances the radio-resistance of cervical cancer via miR-193b-3p/CCND1 axis. Oncotarget 2017; 9:2395-2409. [PMID: 29416780 PMCID: PMC5788648 DOI: 10.18632/oncotarget.23416] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/04/2017] [Indexed: 12/18/2022] Open
Abstract
LncRNAs have become a hot topic in various cancer-related researches. Radio-resistance is a great threat for cancer therapy. However, how lncRNAs affect the radio-resistance in cervical cancer is masked. As for our paper, it was discovered that NEAT1 was highly expressed in cervical cancer tissues and non-sensitive tissues as well as radio-resistant cell lines. And the overexpression of NEAT1 accelerated proliferation, while the knockdown of NEAT1 had the opposite result. The effect of NEAT1 on cell proliferation was dependent on the dose of ionizing radiation. And the silence of NEAT1 also caused cell cycle arrest in G0/G1 phase, and triggered more apoptosis, indicating the oncogenic role of NEAT1 in cervical cancer. Next, mechanistic assays affirmed that NEAT1 could function as a ceRNA to regulate cyclin D1 through sponging miR-193b-3p in cervical cancer. Rescue assays were employed to validate that miR-193b-3p and cyclin D1 could inhibit NEAT1-mediated suppressive effect on proliferation, and its stimulative effect on cell cycle arrest and apoptosis. In general, this article disclosed that NEAT1 could facilitate the radio-resistance of cervical cancer via competitively binding miR-193b-3p to up-regulate the expression of cyclin D1.
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Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection. mSphere 2017; 2:mSphere00456-17. [PMID: 29202041 PMCID: PMC5700376 DOI: 10.1128/msphere.00456-17] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/27/2017] [Indexed: 01/28/2023] Open
Abstract
Vector-borne viruses pose great risks to human health. Zika virus has recently emerged as a global threat, rapidly expanding its distribution. Understanding the interactions of the virus with mosquito vectors at the molecular level is vital for devising new approaches in inhibiting virus transmission. In this study, we embarked on analyzing the transcriptional response of Aedes aegypti mosquitoes to Zika virus infection. Results showed large changes in both coding and long noncoding RNAs. Analysis of these genes showed similarities with other flaviviruses, including dengue virus, which is transmitted by the same mosquito vector. The outcomes provide a global picture of changes in the mosquito vector in response to Zika virus infection. Zika virus (ZIKV) of the Flaviviridae family is a recently emerged mosquito-borne virus that has been implicated in the surge of the number of microcephaly instances in South America. The recent rapid spread of the virus led to its declaration as a global health emergency by the World Health Organization. The virus is transmitted mainly by the mosquito Aedes aegypti, which is also the vector of dengue virus; however, little is known about the interactions of the virus with the mosquito vector. In this study, we investigated the transcriptome profiles of whole A. aegypti mosquitoes in response to ZIKV infection at 2, 7, and 14 days postinfection using transcriptome sequencing. Results showed changes in the abundance of a large number of transcripts at each time point following infection, with 18 transcripts commonly changed among the three time points. Gene ontology analysis revealed that most of the altered genes are involved in metabolic processes, cellular processes, and proteolysis. In addition, 486 long intergenic noncoding RNAs that were altered upon ZIKV infection were identified. Further, we found changes of a number of potential mRNA target genes correlating with those of altered host microRNAs. The outcomes provide a basic understanding of A. aegypti responses to ZIKV and help to determine host factors involved in replication or mosquito host antiviral response against the virus. IMPORTANCE Vector-borne viruses pose great risks to human health. Zika virus has recently emerged as a global threat, rapidly expanding its distribution. Understanding the interactions of the virus with mosquito vectors at the molecular level is vital for devising new approaches in inhibiting virus transmission. In this study, we embarked on analyzing the transcriptional response of Aedes aegypti mosquitoes to Zika virus infection. Results showed large changes in both coding and long noncoding RNAs. Analysis of these genes showed similarities with other flaviviruses, including dengue virus, which is transmitted by the same mosquito vector. The outcomes provide a global picture of changes in the mosquito vector in response to Zika virus infection.
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Wang S, Hou Y, Chen W, Wang J, Xie W, Zhang X, Zeng L. KIF9‑AS1, LINC01272 and DIO3OS lncRNAs as novel biomarkers for inflammatory bowel disease. Mol Med Rep 2017; 17:2195-2202. [PMID: 29207070 PMCID: PMC5783463 DOI: 10.3892/mmr.2017.8118] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 09/18/2017] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a novel group of non-coding RNAs that are associated with inflammation and tumorigenesis. At present, the diagnostic efficacy of lncRNAs in inflammatory bowel disease (IBD) is unclear. The present study aimed to identify lncRNAs that may be used as potential biomarkers for IBD. The mRNA expression levels of various lncRNAs (KIF9-AS1, LINC01272 and DIO3OS) were detected in tissue and plasma samples from patients with IBD by reverse transcription-quantitative polymerase chain reaction. The results indicated that the mRNA expression levels of KIF9-AS1 and LINC01272 were significantly upregulated in tissue and plasma samples from patients with IBD compared with in the healthy controls; conversely, the mRNA expression levels of DIO3OS were significantly downregulated in tissue and plasma samples from patients with IBD compared with in the healthy controls. Subsequently, the specificity and sensitivity of KIF9-AS1, LINC01272 and DIO3OS were determined using a receiver operating characteristic (ROC) curve analysis. The results indicated that KIF9-AS1, LINC01272 and DIO3OS had potential diagnostic value for the detection of IBD. Furthermore, there were significantly positive correlations in KIF9-AS1, LINC01272 and DIO3OS expression between IBD tissue and plasma samples. Therefore, the present study indicated that KIF9-AS1, LINC01272 and DIO3OS may be potential diagnostic biomarkers for IBD.
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Affiliation(s)
- Sen Wang
- The First Clinical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
| | - Yong Hou
- Department of Surgery, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui 230031, P.R. China
| | - Weiping Chen
- The College of Basic Science, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
| | - Jianmin Wang
- The First Clinical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
| | - Weihua Xie
- The First Clinical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
| | - Xiaoping Zhang
- Graduate Department, Anhui University of Traditional Chinese Medicine, Hefei, Anhui 230012, P.R. China
| | - Li Zeng
- The First Clinical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
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38
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Lakhotia SC. Non-coding RNAs demystify constitutive heterochromatin as essential modulator of epigenotype. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0221-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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39
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Lu Q, Yu T, Ou X, Cao D, Xie T, Chen X. Potential lncRNA diagnostic biomarkers for early gastric cancer. Mol Med Rep 2017; 16:9545-9552. [PMID: 29039538 DOI: 10.3892/mmr.2017.7770] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 04/19/2017] [Indexed: 11/06/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) serve important functions in many crucial biological processes; however, the effects of lncRNAs in early gastric cancer (EGC) are not entirely clear. The present study aimed to demonstrate the potential of lncRNAs to be used as biomarkers in EGC. Reverse transcription‑quantitative polymerase chain reaction was used to measure the expression levels of lncRNAs, including X inactive‑specific transcript (XIST), Yiya, brain cytoplasmic RNA 1 (BCYRN1), ribosomal RNA processing 1B (RRP1B), KCNQ1 opposite transcript 1 (KCNQ1OT1) and testes development related 1 (TDRG1), in EGC tissues compared with normal adjacent tissues (NATs). XIST, BCYRN1, RRP1B and TDRG1 were identified as differentially expressed in EGC tissues compared with NATs. The specificity and sensitivity of XIST, BCYRN1, RRP1B and TDRG1 were determined by receiver operating characteristic curve analysis. In addition, RRP1B expression was revealed to be significantly correlated with distal metastasis (P=0.020) and tumor‑node‑metastasis staging (P=0.018), and TDRG1 expression was significantly correlated with lymph node metastasis (P=0.001). Furthermore, BCYRN1, RRP1B and TDRG1 expression levels were compared between EGC tissues and plasma, and the results indicated that there were significant positive correlations of XIST, BCYRN1, RRP1B and TDRG1 expression levels between the EGC tissues and plasma. Therefore, the present study suggested that XIST, BCYRN1, RRP1B and TDRG1 may be served as potential diagnostic biomarkers for EGC.
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Affiliation(s)
- Qin Lu
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Ting Yu
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Xilong Ou
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Dazhong Cao
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Ting Xie
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Xia Chen
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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Abstract
The importance of noncoding genome has become more evident in recent years. Before genome sequencing, the most well studied portion of our genome was protein coding genes. Interestingly, this coding portion accounted only for 1.5% of the genome, the rest being the noncoding sequences. Noncoding RNAs (ncRNAs) are involved in normal cell physiology, stress, and disease states. A class of small ncRNAs and miRNAs has gained much importance because of its involvement in human diseases such as cancer. Involvement of long ncRNAs have also been acknowledged in other human diseases, especially in neurodegenerative diseases. Neurodegenerative diseases are characterized by the presence of abnormally folded proteins that are toxic to the cell. Several studies from model organisms suggest upregulation of pathways that clear this toxic protein may provide protection against neurodegeneration. In this review, I summarize the importance of ncRNAs in protein quality control system of cell that is implicated in this fatal group of neurodegenerative diseases.
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Affiliation(s)
- Sonali Sengupta
- Division of Biomolecules and Genetics, School of Biosciences and Technology, VIT University, Vellore 632 014, India.
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41
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Détrée C, Núñez-Acuña G, Tapia F, Gallardo-Escárate C. Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra. Mar Genomics 2017; 33:39-45. [DOI: 10.1016/j.margen.2017.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/27/2016] [Accepted: 01/07/2017] [Indexed: 01/05/2023]
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Jin X, Chen X, Hu Y, Ying F, Zou R, Lin F, Shi Z, Zhu X, Yan X, Li S, Zhu H. LncRNA-TCONS_00026907 is involved in the progression and prognosis of cervical cancer through inhibiting miR-143-5p. Cancer Med 2017; 6:1409-1423. [PMID: 28544557 PMCID: PMC5463062 DOI: 10.1002/cam4.1084] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 12/19/2022] Open
Abstract
Our previous long noncoding RNA (lncRNA) microarray revealed that lncRNA-TCONS_00026907 is aberrantly expressed between cervical cancer tissues and adjacent tissues. This study aims to explore the potential role of TCONS_00026907 in the development of cervical cancer. The expression levels of TCONS_00026907 in cervical cancer tissues and adjacent tissues from 83 patients of cervical cancer were detected by quantitative real-time polymerase chain reaction and the survival rate was analyzed. In vitro, HeLa and SiHa cells were transfected with small hairpin RNA (shRNA)-TCONS_00026907, then cell proliferation, cycle distribution, apoptosis, migration and invasion were measured. To confirm TCONS_00026907 regulates expression of ELK1 through inhibiting miR-143-5p, overexpression of miR-143-5p and silencing of ELK1 were, respectively, performed in HeLa and SiHa cells. Results showed that TCONS_00026907 level was significantly higher in cervical cancer tissues compared to noncancerous tissues and the survival rate was lower in the high expression group. Silencing of TCONS_00026907, overexpression of miR-143-5p and silencing of ELK1 inhibited cervical cell cycle, proliferation, migration, and invasion, but promoted apoptosis, respectively. Furthermore, silencing of TCONS_00026907 suppressed the growth of cervical tumors and altered the expression of ELK1, p-ELK1, C-fos, Cyclin D1 and Bcl-2 in vivo. Our study identifies TCONS_00026907 as a potent proto-oncogene and indicates that TCONS_00026907/miR143-5p/ELK1 regulatory pathway plays an important role in cervical cancer.
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Affiliation(s)
- Xuejing Jin
- Department of Obstetrics and GynecologyWenzhou Hospital of Integrated Traditional Chinese and Western MedicineAffiliated Hospital of Zhejiang Chinese Medical UniversityWenzhouZhejiangChina
| | - Xiangjian Chen
- Department of General SurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Yan Hu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Furong Ying
- Department of medicine laboratory centerThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Ruanmin Zou
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Feng Lin
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Zhengzheng Shi
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Xuejie Zhu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Xiaojian Yan
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Shi Li
- Department of UrologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Hua Zhu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
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Etebari K, Asad S, Zhang G, Asgari S. Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection. PLoS Negl Trop Dis 2016; 10:e0005069. [PMID: 27760142 PMCID: PMC5070814 DOI: 10.1371/journal.pntd.0005069] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/23/2016] [Indexed: 12/13/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are appearing as an important class of regulatory RNAs with a variety of biological functions. The aim of this study was to identify the lincRNA profile in the dengue vector Aedes aegypti and evaluate their potential role in host-pathogen interaction. The majority of previous RNA-Seq transcriptome studies in Ae. aegypti have focused on the expression pattern of annotated protein coding genes under different biological conditions. Here, we used 35 publically available RNA-Seq datasets with relatively high depth to screen the Ae. aegypti genome for lincRNA discovery. This led to the identification of 3,482 putative lincRNAs. These lincRNA genes displayed a slightly lower GC content and shorter transcript lengths compared to protein-encoding genes. Ae. aegypti lincRNAs also demonstrate low evolutionary sequence conservation even among closely related species such as Culex quinquefasciatus and Anopheles gambiae. We examined their expression in dengue virus serotype 2 (DENV-2) and Wolbachia infected and non-infected adult mosquitoes and Aa20 cells. The results revealed that DENV-2 infection increased the abundance of a number of host lincRNAs, from which some suppress viral replication in mosquito cells. RNAi-mediated silencing of lincRNA_1317 led to enhancement in viral replication, which possibly indicates its potential involvement in the host anti-viral defense. A number of lincRNAs were also differentially expressed in Wolbachia-infected mosquitoes. The results will facilitate future studies to unravel the function of lncRNAs in insects and may prove to be beneficial in developing new ways to control vectors or inhibit replication of viruses in them.
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Affiliation(s)
- Kayvan Etebari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Sultan Asad
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Guangmei Zhang
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
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She K, Huang J, Zhou H, Huang T, Chen G, He J. lncRNA-SNHG7 promotes the proliferation, migration and invasion and inhibits apoptosis of lung cancer cells by enhancing the FAIM2 expression. Oncol Rep 2016; 36:2673-2680. [PMID: 27666964 DOI: 10.3892/or.2016.5105] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/11/2016] [Indexed: 11/06/2022] Open
Abstract
There is growing evidence that long non-coding RNAs (lncRNAs) are related to cancer development. In the present study, we found that the expression levels of lncRNA-SNHG7 mRNA and protein obviously increased in lung cancer tissues compared to adjacent non-cancerous tissues. Simultaneously, the expression levels of Fas apoptotic inhibitory molecule 2 (FAIM2) also increased in lung cancer tissues. In addition, lncRNA-SNHG7 was of positive relevance with FAIM2 in human lung cancer tissues. Silence of lncRNA‑SNHG7 by siRNA repressed the level of FAIM2 protein and suppressed cell proliferation, migration and invasion and accelerated apoptosis of A594 cells in vitro. Furthermore, silence of FAIM2 by siRNA generated a phenotype similar to silence of lncRNA-SNHG7 by siRNA. Therefore, our research showed that lncRNA-SNHG7 promotes the proliferation, migration and invasion, and inhibits apoptosis of lung cancer cells by enhancing the FAIM2 expression, suggesting that lncRNA-SNHG7 as a key regulator of gene expression, may be a promising therapeutic strategy for the treatment of lung cancer. It may improve the understanding of their biogenesis and function of lung cancer and further provide the theoretical fundamental basis for cancer pathogenesis and treatment.
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Affiliation(s)
- Kelin She
- Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jun Huang
- State Key Laboratory of Respiratory Disease, Guangzhou, Guangdong, P.R. China
| | - Huaping Zhou
- Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Tonghai Huang
- Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Guojun Chen
- Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jianxing He
- Southern Medical University, Guangzhou, Guangdong, P.R. China
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Magistri M, Velmeshev D, Makhmutova M, Faghihi MA. Transcriptomics Profiling of Alzheimer's Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs. J Alzheimers Dis 2016; 48:647-65. [PMID: 26402107 PMCID: PMC4698155 DOI: 10.3233/jad-150398] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The underlying genetic variations of late-onset Alzheimer's disease (LOAD) cases remain largely unknown. A combination of genetic variations with variable penetrance and lifetime epigenetic factors may converge on transcriptomic alterations that drive LOAD pathological process. Transcriptome profiling using deep sequencing technology offers insight into common altered pathways regardless of underpinning genetic or epigenetic factors and thus represents an ideal tool to investigate molecular mechanisms related to the pathophysiology of LOAD. We performed directional RNA sequencing on high quality RNA samples extracted from hippocampi of LOAD and age-matched controls. We further validated our data using qRT-PCR on a larger set of postmortem brain tissues, confirming downregulation of the gene encoding substance P (TAC1) and upregulation of the gene encoding the plasminogen activator inhibitor-1 (SERPINE1). Pathway analysis indicates dysregulation in neural communication, cerebral vasculature, and amyloid-β clearance. Beside protein coding genes, we identified several annotated and non-annotated long noncoding RNAs that are differentially expressed in LOAD brain tissues, three of them are activity-dependent regulated and one is induced by Aβ(1-42) exposure of human neural cells. Our data provide a comprehensive list of transcriptomics alterations in LOAD hippocampi and warrant holistic approach including both coding and non-coding RNAs in functional studies aimed to understand the pathophysiology of LOAD.
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Affiliation(s)
| | | | | | - Mohammad Ali Faghihi
- Correspondence to: Dr. Mohammad A. Faghihi, Center for Therapeutic Innovation & Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, BRB 508, Miami, FL 33136, USA.
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Serum stress responsive gene EhslncRNA of Entamoeba histolytica is a novel long noncoding RNA. Sci Rep 2016; 6:27476. [PMID: 27273618 PMCID: PMC4895391 DOI: 10.1038/srep27476] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/19/2016] [Indexed: 12/15/2022] Open
Abstract
Non coding RNAs are known to play important roles in regulating gene expression at the transcriptional and posttranscriptional levels in metazoans. There is very little information available about non coding RNAs in protists such as Entamoeba histolytica. Antisense and micro RNAs have been reported in E. histolytica, however no long non coding RNAs has been reported yet. Here, we report our findings on an in vitro serum stress-inducible gene EhslncRNA, a member of B1 transmembrane kinase family of E. histolytica. EhslncRNA encodes a transcript of 2.6 kb and sequence analysis revealed that there is no ORF >150 bp within this transcript. The transcript was found to be polyadenylated and mainly associated with monosomes in the cytoplasm under serum starvation. In normal proliferating cells this RNA is mainly present in the nucleus. The promoter element was mapped between 437 to 346 nucleotides upstream of transcriptional start site and has both positive and negative regulatory elements. Deletion of the negative element converted the promoter to serum inducible type. Oxygen and heat stress also increased expression levels of EhslncRNA. These observations suggest that EhslncRNA may be a long non coding RNA and likely to help cells withstand stressful conditions in the host.
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Singh AK, Lakhotia SC. Expression of hsrω-RNAi transgene prior to heat shock specifically compromises accumulation of heat shock-induced Hsp70 in Drosophila melanogaster. Cell Stress Chaperones 2016; 21:105-120. [PMID: 26386576 PMCID: PMC4679734 DOI: 10.1007/s12192-015-0644-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 09/03/2015] [Accepted: 09/08/2015] [Indexed: 02/02/2023] Open
Abstract
A delayed organismic lethality was reported in Drosophila following heat shock when developmentally active and stress-inducible noncoding hsrω-n transcripts were down-regulated during heat shock through hs-GAL4-driven expression of the hsrω-RNAi transgene, despite the characteristic elevation of all heat shock proteins (Hsp), including Hsp70. Here, we show that hsrω-RNAi transgene expression prior to heat shock singularly prevents accumulation of Hsp70 in all larval tissues without affecting transcriptional induction of hsp70 genes and stability of their transcripts. Absence of the stress-induced Hsp70 accumulation was not due to higher levels of Hsc70 in hsrω-RNAi transgene-expressing tissues. Inhibition of proteasomal activity during heat shock restored high levels of the induced Hsp70, suggesting very rapid degradation of the Hsp70 even during the stress when hsrω-RNAi transgene was expressed ahead of heat shock. Unexpectedly, while complete absence of hsrω transcripts in hsrω (66) homozygotes (hsrω-null) did not prevent high accumulation of heat shock-induced Hsp70, hsrω-RNAi transgene expression in hsrω-null background blocked Hsp70 accumulation. Nonspecific RNAi transgene expression did not affect Hsp70 induction. These observations reveal that, under certain conditions, the stress-induced Hsp70 can be selectively and rapidly targeted for proteasomal degradation even during heat shock. In the present case, the selective degradation of Hsp70 does not appear to be due to down-regulation of the hsrω-n transcripts per se; rather, this may be an indirect effect of the expression of hsrω-RNAi transgene whose RNA products may titrate away some RNA-binding proteins which may also be essential for stability of the induced Hsp70.
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Affiliation(s)
- Anand K Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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Hauser MA, Aboobakar IF, Liu Y, Miura S, Whigham BT, Challa P, Wheeler J, Williams A, Santiago-Turla C, Qin X, Rautenbach RM, Ziskind A, Ramsay M, Uebe S, Song L, Safi A, Vithana EN, Mizoguchi T, Nakano S, Kubota T, Hayashi K, Manabe SI, Kazama S, Mori Y, Miyata K, Yoshimura N, Reis A, Crawford GE, Pasutto F, Carmichael TR, Williams SEI, Ozaki M, Aung T, Khor CC, Stamer WD, Ashley-Koch AE, Allingham RR. Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus. Hum Mol Genet 2015; 24:6552-63. [PMID: 26307087 PMCID: PMC4614704 DOI: 10.1093/hmg/ddv347] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/04/2015] [Accepted: 08/19/2015] [Indexed: 12/31/2022] Open
Abstract
Exfoliation syndrome (XFS) is a common, age-related, systemic fibrillinopathy. It greatly increases risk of exfoliation glaucoma (XFG), a major worldwide cause of irreversible blindness. Coding variants in the lysyl oxidase-like 1 (LOXL1) gene are strongly associated with XFS in all studied populations, but a functional role for these variants has not been established. To identify additional candidate functional variants, we sequenced the entire LOXL1 genomic locus (∼40 kb) in 50 indigenous, black South African XFS cases and 50 matched controls. The variants with the strongest evidence of association were located in a well-defined 7-kb region bounded by the 3'-end of exon 1 and the adjacent region of intron 1 of LOXL1. We replicated this finding in US Caucasian (91 cases/1031 controls), German (771 cases/1365 controls) and Japanese (1484 cases/1188 controls) populations. The region of peak association lies upstream of LOXL1-AS1, a long non-coding RNA (lncRNA) encoded on the opposite strand of LOXL1. We show that this region contains a promoter and, importantly, that the strongly associated XFS risk alleles in the South African population are functional variants that significantly modulate the activity of this promoter. LOXL1-AS1 expression is also significantly altered in response to oxidative stress in human lens epithelial cells and in response to cyclic mechanical stress in human Schlemm's canal endothelial cells. Taken together, these findings support a functional role for the LOXL1-AS1 lncRNA in cellular stress response and suggest that dysregulation of its expression by genetic risk variants plays a key role in XFS pathogenesis.
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Affiliation(s)
- Michael A Hauser
- Department of Medicine, Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA, Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore, Duke, National University of Singapore, Singapore, Singapore,
| | - Inas F Aboobakar
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, GA, USA
| | | | | | - Pratap Challa
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | | | - Andrew Williams
- Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | | | | | - Robyn M Rautenbach
- Division of Ophthalmology, Department of Surgical Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Ari Ziskind
- Division of Ophthalmology, Department of Surgical Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, NHLS and School of Pathology and Sydney Brenner Institute for Molecular Bioscience, University of Witwatersrand, Johannesburg, South Africa
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lingyun Song
- Center for Genomic and Computational Biology and Department of Pediatrics, Duke University, Durham, NC, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology and Department of Pediatrics, Duke University, Durham, NC, USA
| | - Eranga N Vithana
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Takanori Mizoguchi
- Mizoguchi Eye Hospital, 6-13 Tawara-machi, Sasebo, Nagasaki 857-0016, Japan
| | - Satoko Nakano
- Department of Ophthalmology, Oita University Faculty of Medicine, Oita, Japan
| | - Toshiaki Kubota
- Department of Ophthalmology, Oita University Faculty of Medicine, Oita, Japan
| | - Ken Hayashi
- Hayashi Eye Hospital, 23-35, Hakataekimae-4, Hakata-ku, Fukuoka, Japan
| | - Shin-ichi Manabe
- Hayashi Eye Hospital, 23-35, Hakataekimae-4, Hakata-ku, Fukuoka, Japan
| | - Shigeyasu Kazama
- Shinjo Eye Clinic, 889-1, Mego, Simokitakatamachi, Miyazaki-shi, Miyazaki 880-0035, Japan
| | - Yosai Mori
- Miyata Eye Hospital, 6-3, Kurahara, Miyakonojo, Miyazaki 885-0051, Japan
| | - Kazunori Miyata
- Miyata Eye Hospital, 6-3, Kurahara, Miyakonojo, Miyazaki 885-0051, Japan, University of Miyazaki, Miyazaki, Japan
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Andre Reis
- Institute of Human Genetics, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gregory E Crawford
- Center for Genomic and Computational Biology and Department of Pediatrics, Duke University, Durham, NC, USA
| | - Francesca Pasutto
- Institute of Human Genetics, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Trevor R Carmichael
- Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa and
| | - Susan E I Williams
- Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa and
| | - Mineo Ozaki
- Ozaki Eye Hospital, 1-15, Kamezaki, Hyuga, Miyazaki 883-0066, Japan
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Chiea-Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - W Daniel Stamer
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | | | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA, Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore, Duke, National University of Singapore, Singapore, Singapore
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LAKHOTIA SUBHASHC. Divergent actions of long noncoding RNAs on X-chromosome remodelling in mammals and Drosophila achieve the same end result: dosage compensation. J Genet 2015; 94:575-84. [DOI: 10.1007/s12041-015-0566-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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50
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Etebari K, Furlong MJ, Asgari S. Genome wide discovery of long intergenic non-coding RNAs in Diamondback moth (Plutella xylostella) and their expression in insecticide resistant strains. Sci Rep 2015; 5:14642. [PMID: 26411386 PMCID: PMC4585956 DOI: 10.1038/srep14642] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/02/2015] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in genomic imprinting, cancer, differentiation and regulation of gene expression. Here, we identified 3844 long intergenic ncRNAs (lincRNA) in Plutella xylostella, which is a notorious pest of cruciferous plants that has developed field resistance to all classes of insecticides, including Bacillus thuringiensis (Bt) endotoxins. Further, we found that some of those lincRNAs may potentially serve as precursors for the production of small ncRNAs. We found 280 and 350 lincRNAs that are differentially expressed in Chlorpyrifos and Fipronil resistant larvae. A survey on P. xylostella midgut transcriptome data from Bt-resistant populations revealed 59 altered lincRNA in two resistant strains compared with the susceptible population. We validated the transcript levels of a number of putative lincRNAs in deltamethrin-resistant larvae that were exposed to deltamethrin, which indicated that this group of lincRNAs might be involved in the response to xenobiotics in this insect. To functionally characterize DBM lincRNAs, gene ontology (GO) enrichment of their associated protein-coding genes was extracted and showed over representation of protein, DNA and RNA binding GO terms. The data presented here will facilitate future studies to unravel the function of lincRNAs in insecticide resistance or the response to xenobiotics of eukaryotic cells.
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Affiliation(s)
- Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
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