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Barckmann B, El-Barouk M, Pélisson A, Mugat B, Li B, Franckhauser C, Fiston Lavier AS, Mirouze M, Fablet M, Chambeyron S. The somatic piRNA pathway controls germline transposition over generations. Nucleic Acids Res 2019; 46:9524-9536. [PMID: 30312469 PMCID: PMC6182186 DOI: 10.1093/nar/gky761] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/22/2018] [Indexed: 11/14/2022] Open
Abstract
Transposable elements (TEs) are parasitic DNA sequences that threaten genome integrity by replicative transposition in host gonads. The Piwi-interacting RNAs (piRNAs) pathway is assumed to maintain Drosophila genome homeostasis by downregulating transcriptional and post-transcriptional TE expression in the ovary. However, the bursts of transposition that are expected to follow transposome derepression after piRNA pathway impairment have not yet been reported. Here, we show, at a genome-wide level, that piRNA loss in the ovarian somatic cells boosts several families of the endogenous retroviral subclass of TEs, at various steps of their replication cycle, from somatic transcription to germinal genome invasion. For some of these TEs, the derepression caused by the loss of piRNAs is backed up by another small RNA pathway (siRNAs) operating in somatic tissues at the post transcriptional level. Derepressed transposition during 70 successive generations of piRNA loss exponentially increases the genomic copy number by up to 10-fold.
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Affiliation(s)
| | - Marianne El-Barouk
- IGH, CNRS, Univ. Montpellier, Montpellier, France.,Institut Cochin, Paris, France
| | | | - Bruno Mugat
- IGH, CNRS, Univ. Montpellier, Montpellier, France
| | - Blaise Li
- IGH, CNRS, Univ. Montpellier, Montpellier, France.,Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756, IP CNRS, Paris France
| | | | | | - Marie Mirouze
- LGPD, CNRS, Univ Perpignan Via Domitia, Perpignan, France
| | - Marie Fablet
- Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Laboratoire de Biométrie et Biologie Evolutive. 43 Boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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2
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Cosacak MI, Yiğit H, Kizil C, Akgül B. Re-Arrangements in the Cytoplasmic Distribution of Small RNAs Following the Maternal-to-Zygotic Transition in Drosophila Embryos. Genes (Basel) 2018; 9:genes9020082. [PMID: 29439397 PMCID: PMC5852578 DOI: 10.3390/genes9020082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 01/13/2023] Open
Abstract
Small ribonucleic acids (RNAs) are known to regulate gene expression during early development. However, the dynamics of interaction between small RNAs and polysomes during this process is largely unknown. To investigate this phenomenon, 0–1 h and 7–8 h Drosophila melanogaster embryos were fractionated on sucrose density gradients into four fractions based on A254 reading (1) translationally inactive messenger ribonucleoprotein (mRNP), (2) 60S, (3) monosome, and (4) polysome. Comparative analysis of deep-sequencing reads from fractionated and un-fractionated 0–1 h and 7–8 h embryos revealed development-specific co-sedimentation pattern of small RNAs with the cellular translation machinery. Although most micro RNAs (miRNAs) did not have a specific preference for any state of the translational machinery, we detected fraction-specific enrichment of a few miRNAs such as dme-miR-1-3p, -184-3p, 5-5p and 263-5p. More interestingly, we observed changes in the subcellular location of a subset of miRNAs in fractionated embryos despite no measurable difference in their amount in unfractionated embryos. Transposon-derived endo small interfering RNAs (siRNAs) were over-expressed in 7–8 h embryos and associated mainly with the mRNP fraction. In contrast, transposon-derived PIWI-interacting RNAs (piRNA), which were more abundant in 0–1 h embryos, co-sedimented primarily with the polysome fractions. These results suggest that there appears to be a complex interplay among the small RNAs with respect to their polysome-cosedimentation pattern during early development in Drosophila melanogaster.
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Affiliation(s)
- Mehmet Ilyas Cosacak
- Department of Molecular Biology and Genetics, İzmir Institute of Technology, Gülbahçeköyü, 35430 İzmir, Turkey.
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Arnoldstr. 18, 01307 Dresden, Germany.
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany.
| | - Hatice Yiğit
- Department of Molecular Biology and Genetics, İzmir Institute of Technology, Gülbahçeköyü, 35430 İzmir, Turkey.
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Arnoldstr. 18, 01307 Dresden, Germany.
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany.
| | - Bünyamin Akgül
- Department of Molecular Biology and Genetics, İzmir Institute of Technology, Gülbahçeköyü, 35430 İzmir, Turkey.
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Fedoseeva DM, Kretova OV, Gorbacheva MA, Tchurikov NA. Individual effects of the copia and gypsy enhancer and insulator on chromatin marks, eRNA synthesis, and binding of insulator proteins in transfected genetic constructs. Gene 2018; 641:151-160. [PMID: 29045822 DOI: 10.1016/j.gene.2017.10.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 07/10/2017] [Accepted: 10/11/2017] [Indexed: 12/28/2022]
Abstract
Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer. Insertion of the insulator between the enhancer and the promoter reduced these effects. We also observed the binding of dCTCF to the enhancer and to gypsy insulator. Our data indicate that a single gypsy insulator interacts with both the enhancer and the promoter, while two copies of the gypsy insulator preferentially interact with each other. Our results suggest the formation of chromatin loops that are shaped by the enhancer and the insulator.
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Affiliation(s)
| | - Olga V Kretova
- Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
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4
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Six Highly Conserved Targets of RNAi Revealed in HIV-1-Infected Patients from Russia Are Also Present in Many HIV-1 Strains Worldwide. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:330-344. [PMID: 28918033 PMCID: PMC5537207 DOI: 10.1016/j.omtn.2017.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 12/26/2022]
Abstract
RNAi has been suggested for use in gene therapy of HIV/AIDS, but the main problem is that HIV-1 is highly variable and could escape attack from the small interfering RNAs (siRNAs) due to even single nucleotide substitutions in the potential targets. To exhaustively check the variability in selected RNA targets of HIV-1, we used ultra-deep sequencing of six regions of HIV-1 from the plasma of two independent cohorts of patients from Russia. Six RNAi targets were found that are invariable in 82%-97% of viruses in both cohorts and are located inside the domains specifying reverse transcriptase (RT), integrase, vpu, gp120, and p17. The analysis of mutation frequencies and their characteristics inside the targets suggests a likely role for APOBEC3G (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G, A3G) in G-to-A mutations and a predominant effect of RT biases in the detected variability of the virus. The lowest frequency of mutations was detected in the central part of all six targets. We also discovered that the identical RNAi targets are present in many HIV-1 strains from many countries and from all continents. The data are important for both the understanding of the patterns of HIV-1 mutability and properties of RT and for the development of gene therapy approaches using RNAi for the treatment of HIV/AIDS.
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Tchurikov NA, Fedoseeva DM, Gashnikova NM, Sosin DV, Gorbacheva MA, Alembekov IR, Chechetkin VR, Kravatsky YV, Kretova OV. Conserved sequences in the current strains of HIV-1 subtype A in Russia are effectively targeted by artificial RNAi in vitro. Gene 2016; 583:78-83. [PMID: 26947394 DOI: 10.1016/j.gene.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 10/25/2022]
Abstract
Highly active antiretroviral therapy has greatly reduced the morbidity and mortality of AIDS. However, many of the antiretroviral drugs are toxic with long-term use, and all currently used anti-HIV agents generate drug-resistant mutants. Therefore, there is a great need for new approaches to AIDS therapy. RNAi is a powerful means of inhibiting HIV-1 production in human cells. We propose to use RNAi for gene therapy of HIV/AIDS. Previously we identified a number of new biologically active siRNAs targeting several moderately conserved regions in HIV-1 transcripts. Here we analyze the heterogeneity of nucleotide sequences in three RNAi targets in sequences encoding the reverse transcriptase and integrase domains of current isolates of HIV-1 subtype A in Russia. These data were used to generate genetic constructs expressing short hairpin RNAs 28-30-bp in length that could be processed in cells into siRNAs. After transfection of the constructs we observed siRNAs that efficiently attacked the selected targets. We expect that targeting several viral genes important for HIV-1 reproduction will help overcome the problem of viral adaptation and will prevent the appearance of RNAi escape mutants in current virus strains, an important feature of gene therapy of HIV/AIDS.
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Affiliation(s)
| | | | | | - Dmitri V Sosin
- Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
| | | | | | | | - Yuri V Kravatsky
- Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
| | - Olga V Kretova
- Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
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6
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Zenina OS, Fedoseeva DM, Kretova OV, Tchurikov NA. Molecular analysis of transcription start sites of separate copies of the suffix short retroelement in genome of Drosophila. DOKL BIOCHEM BIOPHYS 2013; 449:112-5. [PMID: 23657661 DOI: 10.1134/s1607672913020063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Indexed: 11/23/2022]
Abstract
In order to study TSS in the suffix element, we used total RNA isolated from ovaries of Drosophila melanogaster. Using a 5'-RACE System (Invitrogen) and 454 sequencing, we found the full-length suffix sense transcripts. However, most 5'-RACE reads (>70%) correspond to 5'-truncated transcripts lacking the first 33-39 nucleotides. The data may indicate that these RNAs are products of the RNAi-related silencing mech-anism producing small RNAs that are larger than piRNAs. The full-length suffix transcripts could arise either from the F element or from active separate copies of suffix.
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Affiliation(s)
- O S Zenina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, str. Vavilov 32, Moscow, 119991 Russia
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Mitkevich VA, Kretova OV, Petrushanko IY, Burnysheva KM, Sosin DV, Simonenko OV, Ilinskaya ON, Tchurikov NA, Makarov AA. Ribonuclease binase apoptotic signature in leukemic Kasumi-1 cells. Biochimie 2013; 95:1344-9. [PMID: 23499289 DOI: 10.1016/j.biochi.2013.02.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/26/2013] [Indexed: 10/27/2022]
Abstract
Cytotoxic exogenous RNases triggering apoptotic response in malignant cells have potential as anticancer drugs; surprisingly, detailed characterization of the RNase-induced apoptosis has not been conducted so far. Here we show that a cytotoxic RNase from Bacillus intermedius (binase) induces extrinsic and intrinsic apoptotic pathways in leukemic Kasumi-1 cells. The experiments were performed using TaqMan Array Human Apoptosis 96-well Plate for gene expression analysis, and flow cytometry. Cytometric studies demonstrated dissipation of the mitochondrial membrane potential, opening of mitochondrial permeability transition pores, activation of caspases, increase of intracellular Ca(2+) and decrease of reactive oxygen species levels. We found that expression of 62 apoptotic genes is up-regulated, including 16 genes that are highly up-regulated, and only one gene was found to be down-regulated. The highest, 16 fold increase of the expression level was observed for TNF gene. Highly up-regulated genes also include the non-canonical NF-κB signaling pathway and inflammatory caspases 1,4. The obtained results suggest that binase induces evolutionary acquired cellular response to a microbial agent and triggers unusual apoptosis pathway.
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Affiliation(s)
- Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str 32, 119991 Moscow, Russia
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Dicer-2- and Piwi-mediated RNA interference in Rift Valley fever virus-infected mosquito cells. J Virol 2012; 87:1631-48. [PMID: 23175368 DOI: 10.1128/jvi.02795-12] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a Phlebovirus (Bunyaviridae family) transmitted by mosquitoes. It infects humans and ruminants, causing dramatic epidemics and epizootics in Africa, Yemen, and Saudi Arabia. While recent studies demonstrated the importance of the nonstructural protein NSs as a major component of virulence in vertebrates, little is known about infection of mosquito vectors. Here we studied RVFV infection in three different mosquito cell lines, Aag2 cells from Aedes aegypti and U4.4 and C6/36 cells from Aedes albopictus. In contrast with mammalian cells, where NSs forms nuclear filaments, U4.4 and Aag2 cells downregulated NSs expression such that NSs filaments were never formed in nuclei of U4.4 cells and disappeared at an early time postinfection in the case of Aag2 cells. On the contrary, in C6/36 cells, NSs nuclear filaments were visible during the entire time course of infection. Analysis of virus-derived small interfering RNAs (viRNAs) by deep sequencing indicated that production of viRNAs was very low in C6/36 cells, which are known to be Dicer-2 deficient but expressed some viRNAs presenting a Piwi signature. In contrast, Aag2 and U4.4 cells produced large amounts of viRNAs predominantly matching the S segment and displaying Dicer-2 and Piwi signatures. Whereas 21-nucleotide (nt) Dicer-2 viRNAs were prominent during early infection, the population of 24- to 27-nt Piwi RNAs (piRNAs) increased progressively and became predominant later during the acute infection and during persistence. In Aag2 and U4.4 cells, the combined actions of the Dicer-2 and Piwi pathways triggered an efficient antiviral response permitting, among other actions, suppression of NSs filament formation and allowing establishment of persistence. In C6/36 cells, Piwi-mediated RNA interference (RNAi) appeared to be sufficient to mount an antiviral response against a secondary infection with a superinfecting virus. This study provides new insights into the role of Dicer and Piwi in mosquito antiviral defense and the development of the antiviral response in mosquitoes.
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Klase Z, Houzet L, Jeang KT. MicroRNAs and HIV-1: complex interactions. J Biol Chem 2012; 287:40884-90. [PMID: 23043098 DOI: 10.1074/jbc.r112.415448] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNAi plays important roles in many biological processes, including cellular defense against viral infection. Components of the RNAi machinery are widely conserved in plants and animals. In mammals, microRNAs (miRNAs) represent an abundant class of cell encoded small noncoding RNAs that participate in RNAi-mediated gene silencing. Here, findings that HIV-1 replication in cells can be regulated by miRNAs and that HIV-1 infection of cells can alter cellular miRNA expression are reviewed. Lessons learned from and questions outstanding about the complex interactions between HIV-1 and cellular miRNAs are discussed.
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Affiliation(s)
- Zachary Klase
- Molecular Virology Section, Laboratory of Molecular Microbiology, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
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Generation of genetic constructs that simultaneously express several shRNAs. Biotechniques 2012; 52:000113880. [DOI: 10.2144/000113880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 05/08/2012] [Indexed: 11/23/2022] Open
Abstract
RNAi has potential as an antiviral gene therapy strategy. Cassette constructs simultaneously expressing several siRNAs could prove to be the most efficient technique in developing gene therapy approaches for highly mutable viruses such as HIV-1. Here we describe a rapid and cost-saving protocol to generate cassettes that simultaneously express three siRNAs for repression of HIV-1 and CCR5 transcripts. siRNA biological activity was tested in a non-viral system, and exhibited both efficiency and specificity. Our results suggest this protocol can be used to rapidly generate cassette constructs for antiviral gene therapy applications.
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