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Wu B, Huang L, Qiu W, Liu X, Shen Y, Lu Y, Yang Z, Li X, Cui B, Xu S, Qiao H, Qiu R, Yao L, Kan Y, Li D. Small nucleolar RNA Sf-15 regulates proliferation and apoptosis of Spodoptera frugiperda Sf9 cells. BMC Mol Biol 2019; 20:12. [PMID: 30971200 PMCID: PMC6458620 DOI: 10.1186/s12867-019-0128-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small nucleolar RNAs (snoRNAs) function in guiding 2'-O-methylation and pseudouridylation of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). In recent years, more and more snoRNAs have been found to play novel roles in mRNA regulation, such as pre-mRNA splicing or RNA editing. In our previous study, we found a silkworm C/D box snoRNA Bm-15 can interact with Notch receptor gene in vitro. To further study the function of Bm-15, we cloned its homolog Sf-15 from Spodoptera frugiperda and investigate the function of Sf-15 in Sf9 cells. RESULTS We showed that knocking down of Sf-15 can inhibit the proliferation, then induce apoptosis of insect S. frugiperda Sf9 cells, but the results were reversed when Sf-15 was overexpressed. De novo sequencing of transcriptome of Sf9 cells showed that the expression of 21 apoptosis-related genes were increased upon Sf-15 repression. Further analysis showed that a Ca2+-induced cell death pathway gene Cn (PPP3C, the serine/threonine-protein phosphatase 2B catalytic subunit), was significantly increased upon Sf-15 depression but decreased when Sf-15 was overexpressed, which indicated that Cn might be a potential target of Sf-15. CONCLUSIONS We conclude that C/D box snoRNA Sf-15 can participate in apoptosis through regulating the expression of Ca2+-induced cell death pathway gene Cn in Sf9 cells. This is the first time that we found snoRNAs exhibiting dual functions in insect, which reveals a novel layer of ncRNA modulation in cell growth and death.
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Affiliation(s)
- Bo Wu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Lei Huang
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Wujie Qiu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Xiao Liu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yawen Shen
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yiping Lu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Zonglin Yang
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Xinmei Li
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Bin Cui
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Shidong Xu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Huili Qiao
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Reng Qiu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
| | - Dandan Li
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
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Cao T, Rajasingh S, Samanta S, Dawn B, Bittel DC, Rajasingh J. Biology and clinical relevance of noncoding sno/scaRNAs. Trends Cardiovasc Med 2017; 28:81-90. [PMID: 28869095 DOI: 10.1016/j.tcm.2017.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/18/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are a group of noncoding RNAs that perform various biological functions, including biochemical modifications of other RNAs, precursors of miRNA, splicing, and telomerase activity. The small Cajal body-associated RNAs (scaRNAs) are a subset of the snoRNA family and collect in the Cajal body where they perform their canonical function to biochemically modify spliceosomal RNAs prior to maturation. Failure of sno/scaRNAs have been implicated in pathology such as congenital heart anomalies, neuromuscular disorders, and various malignancies. Thus, understanding of sno/scaRNAs demonstrates the clinical value.
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Affiliation(s)
- Thuy Cao
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Sheeja Rajasingh
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Saheli Samanta
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Buddhadeb Dawn
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | | | - Johnson Rajasingh
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS.
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Agrisani A, Tafer H, Stadler PF, Furia M. Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster. Noncoding RNA 2015; 1:139-150. [PMID: 29861420 PMCID: PMC5932544 DOI: 10.3390/ncrna1020139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 12/12/2022] Open
Abstract
A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome.
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Affiliation(s)
- Alberto Agrisani
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, I-80126 Napoli, Italy.
| | - Hakim Tafer
- Institut für Biotechnologie, Universität für Bodenkultur, Muthgasse 18, A-1190 Wien, Austria.
| | - Peter F Stadler
- Bioinformatics Group, Department Computer Science, German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig; University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany.
- Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.
- Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.
| | - Maria Furia
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, I-80126 Napoli, Italy.
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Angrisani A, Tafer H, Stadler PF, Furia M. Developmentally regulated expression and expression strategies of Drosophila snoRNAs. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 61:69-78. [PMID: 25641266 DOI: 10.1016/j.ibmb.2015.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
Small nucleolar RNAs constitute a significant portion of the eukaryotic small ncRNA transcriptome and guide site-specific methylation or pseudouridylation of target RNAs. In addition, they can play diverse regulatory roles on gene expression, acting as precursors of smaller fragments able to modulate alternative splicing or operate as microRNAs. Defining their expression strategies and the full repertory of their biological functions is a critical, but still ongoing, process in most organisms. Considering that Drosophila melanogaster is one of the most advantageous model organism for genetic, functional and developmental studies, we analysed the whole genomic organization of its annotated snoRNAs - whose vast majority is known to be embedded in an intronic context - and show by GO term enrichment analysis that protein-coding genes involved in cell division and cytoskeleton organization are those mostly preferred as hosts. This finding was unexpected, and delineates an unpredicted link between snoRNA host genes and cell proliferation that might be of general relevance. We also defined by quantitative RT-PCR the expression of a representative subset of annotated specimens throughout the life cycle, providing a first overview on developmental profiling of the fly snoRNA transcriptome. We found that most of the tested specimens, rather than acting as housekeeping genes with uniform expression, exhibit dynamic developmental expression patterns; moreover, intronic snoRNAs harboured by the same host gene often exhibit distinct temporal profiles, indicating that they can be expressed uncoordinatedly. In addition to provide an updated outline of the fly snoRNA transcriptome, our data highlight that expression of these versatile ncRNAs can be finely regulated.
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Affiliation(s)
- Alberto Angrisani
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy
| | - Hakim Tafer
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Maria Furia
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy.
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Deryusheva S, Gall JG. Novel small Cajal-body-specific RNAs identified in Drosophila: probing guide RNA function. RNA (NEW YORK, N.Y.) 2013; 19:1802-14. [PMID: 24149844 PMCID: PMC3884663 DOI: 10.1261/rna.042028.113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 09/23/2013] [Indexed: 05/05/2023]
Abstract
The spliceosomal small nuclear RNAs (snRNAs) are modified post-transcriptionally by introduction of pseudouridines and 2'-O-methyl modifications, which are mediated by box H/ACA and box C/D guide RNAs, respectively. Because of their concentration in the nuclear Cajal body (CB), these guide RNAs are known as small CB-specific (sca) RNAs. In the cell, scaRNAs are associated with the WD-repeat protein WDR79. We used coimmunoprecipitation with WDR79 to recover seven new scaRNAs from Drosophila cell lysates. We demonstrated concentration of these new scaRNAs in the CB by in situ hybridization, and we verified experimentally that they can modify their putative target RNAs. Surprisingly, one of the new scaRNAs targets U6 snRNA, whose modification is generally assumed to occur in the nucleolus, not in the CB. Two other scaRNAs have dual guide functions, one for an snRNA and one for 28S rRNA. Again, the modification of 28S rRNA is assumed to take place in the nucleolus. These findings suggest that canonical scaRNAs may have functions in addition to their established role in modifying U1, U2, U4, and U5 snRNAs. We discuss the likelihood that processing by scaRNAs is not limited to the CB.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G. Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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Rajendra T, Praveen K, Matera AG. Genetic analysis of nuclear bodies: from nondeterministic chaos to deterministic order. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2011; 75:365-74. [PMID: 21467138 PMCID: PMC4062921 DOI: 10.1101/sqb.2010.75.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The eukaryotic nucleus is a congested place, and macromolecular crowding is thought to have an important role in increasing the relative concentrations of nuclear proteins, thereby accelerating the rates of biochemical reactions. Crowding is also thought to provide the environment needed for formation of nuclear bodies/subcompartments, such as the Cajal body (CB) and the histone locus body (HLB), via self-organization. In this chapter, we contrast the theories of stochastic self-organization and hierarchical self-organization in their application to nuclear body assembly, using CBs and HLBs as paradigms. Genetic ablation studies in Drosophila on components of CBs and HLBs have revealed an order to the assembly of these structures that is suggestive of a hierarchical model of self-organization. These studies also show that functions attributed to the nuclear bodies are largely unaffected in their absence, reinforcing an emerging theme in the field that the purpose of these subdomains may be to enhance the efficiency and specificity of reactions.
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Affiliation(s)
- T.K. Rajendra
- Departments of Biology and Genetics, Program in Molecular Biology & Biotechnology, Lineberger Comprehensive Cancer Center University of North Carolina, Chapel Hill, NC 27599
| | - Kavita Praveen
- Departments of Biology and Genetics, Program in Molecular Biology & Biotechnology, Lineberger Comprehensive Cancer Center University of North Carolina, Chapel Hill, NC 27599
| | - A. Gregory Matera
- Departments of Biology and Genetics, Program in Molecular Biology & Biotechnology, Lineberger Comprehensive Cancer Center University of North Carolina, Chapel Hill, NC 27599
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