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Epigenetic Requirements for Triggering Heterochromatinization and Piwi-Interacting RNA Production from Transgenes in the Drosophila Germline. Cells 2020; 9:cells9040922. [PMID: 32290057 PMCID: PMC7226800 DOI: 10.3390/cells9040922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/26/2022] Open
Abstract
Transgenes containing a fragment of the I retrotransposon represent a powerful model of piRNA cluster de novo formation in the Drosophila germline. We revealed that the same transgenes located at different genomic loci form piRNA clusters with various capacity of small RNA production. Transgenic piRNA clusters are not established in piRNA pathway mutants. However, in the wild-type context, the endogenous ancestral I-related piRNAs heterochromatinize and convert the I-containing transgenes into piRNA-producing loci. Here, we address how the quantitative level of piRNAs influences the heterochromatinization and piRNA production. We show that a minimal amount of maternal piRNAs from ancestral I-elements is sufficient to form the transgenic piRNA clusters. Supplemental piRNAs stemming from active I-element copies do not stimulate additional chromatin changes or piRNA production from transgenes. Therefore, chromatin changes and piRNA production are initiated by a minimum threshold level of complementary piRNAs, suggesting a selective advantage of prompt cell response to the lowest level of piRNAs. It is noteworthy that the weak piRNA clusters do not transform into strong ones after being targeted by abundant I-specific piRNAs, indicating the importance of the genomic context for piRNA cluster establishment. Analysis of ovarian transcription profiles suggests that regions facilitating convergent transcription favor the formation of transgenic piRNA clusters.
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2
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Akulenko N, Ryazansky S, Morgunova V, Komarov PA, Olovnikov I, Vaury C, Jensen S, Kalmykova A. Transcriptional and chromatin changes accompanying de novo formation of transgenic piRNA clusters. RNA (NEW YORK, N.Y.) 2018; 24:574-584. [PMID: 29358235 PMCID: PMC5855956 DOI: 10.1261/rna.062851.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 01/09/2018] [Indexed: 05/31/2023]
Abstract
Expression of transposable elements in the germline is controlled by Piwi-interacting (pi) RNAs produced by genomic loci termed piRNA clusters and associated with Rhino, a heterochromatin protein 1 (HP1) homolog. Previously, we have shown that transgenes containing a fragment of the I retrotransposon form de novo piRNA clusters in the Drosophila germline providing suppression of I-element activity. We noted that identical transgenes located in different genomic sites vary considerably in piRNA production and classified them as "strong" and "weak" piRNA clusters. Here, we investigated what chromatin and transcriptional changes occur at the transgene insertion sites after their conversion into piRNA clusters. We found that the formation of a transgenic piRNA cluster is accompanied by activation of transcription from both genomic strands that likely initiates at multiple random sites. The chromatin of all transgene-associated piRNA clusters contain high levels of trimethylated lysine 9 of histone H3 (H3K9me3) and HP1a, whereas Rhino binding is considerably higher at the strong clusters. None of these chromatin marks was revealed at the "empty" sites before transgene insertion. Finally, we have shown that in the nucleus of polyploid nurse cells, the formation of a piRNA cluster at a given transgenic genomic copy works according to an "all-or-nothing" model: either there is high Rhino enrichment or there is no association with Rhino at all. As a result, genomic copies of a weak piRNA transgenic cluster show a mosaic association with Rhino foci, while the majority of strong transgene copies associate with Rhino and are hence involved in piRNA production.
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Affiliation(s)
- Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Valeriya Morgunova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Pavel A Komarov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, F-63001 Clermont-Ferrand, France
| | - Silke Jensen
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, F-63001 Clermont-Ferrand, France
| | - Alla Kalmykova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
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3
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Ryazansky S, Radion E, Mironova A, Akulenko N, Abramov Y, Morgunova V, Kordyukova MY, Olovnikov I, Kalmykova A. Natural variation of piRNA expression affects immunity to transposable elements. PLoS Genet 2017; 13:e1006731. [PMID: 28448516 PMCID: PMC5407775 DOI: 10.1371/journal.pgen.1006731] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/31/2017] [Indexed: 11/25/2022] Open
Abstract
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements. The permissivity to I-element activity of R females, called reactivity, varies considerably in natural R populations, indicating the existence of a strong natural polymorphism in defense systems targeting transposons. To reveal the nature of such polymorphisms, we compared ovarian small RNAs between R strains with low and high reactivity and show that reactivity negatively correlates with the ancestral I-element-specific piRNA content. Analysis of piRNA clusters containing remnants of I-elements shows increased expression of the piRNA precursors and enrichment by the Heterochromatin Protein 1 homolog, Rhino, in weak R strains, which is in accordance with stronger piRNA expression by these regions. To explore the nature of the differences in piRNA production, we focused on two R strains, weak and strong, and showed that the efficiency of maternal inheritance of piRNAs as well as the I-element copy number are very similar in both strains. At the same time, germline and somatic uni-strand piRNA clusters generate more piRNAs in strains with low reactivity, suggesting the relationship between the efficiency of primary piRNA production and variable response to TE invasions. The strength of adaptive genome defense is likely driven by naturally occurring polymorphisms in the rapidly evolving piRNA pathway proteins. We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric retrotransposon HeT-A, which we have observed in one particular transposon-resistant R strain. Transposon activity in the germline is suppressed by the PIWI-interacting RNA (piRNA) pathway. The resistance of natural Drosophila strains to transposon invasion varies considerably, but the nature of this variability is unknown. We discovered that natural variation in the efficiency of primary piRNA production in the germline causes dramatic differences in the susceptibility to expansion of a newly invaded transposon. A high level of piRNA production in the germline is achieved by increased expression of piRNA precursors. In one of the most transposon-resistant strains, increased content of primary piRNA is observed in both the germline and ovarian somatic cells. We suggest that polymorphisms in piRNA pathway factors are responsible for increased piRNA production. piRNA pathway proteins have been shown to be evolving rapidly under selective pressure. Our data are the first to describe a phenotype that might be caused by this kind of polymorphism. We also demonstrate a likely explanation as to why an overly active piRNA pathway can cause more harm than good in Drosophila: Highly efficient piRNA processing leads to elimination of domesticated telomeric retrotransposons essential for telomere elongation, an effect which has been observed in a natural strain that is extremely resistant to transposon invasion.
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Affiliation(s)
- Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elizaveta Radion
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia Mironova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Yuri Abramov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Valeriya Morgunova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria Y. Kordyukova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ivan Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alla Kalmykova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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4
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Pisanu A, Lecca D, Valentini V, Bahi A, Dreyer JL, Cacciapaglia F, Scifo A, Piras G, Cadoni C, Di Chiara G. Impairment of acquisition of intravenous cocaine self-administration by RNA-interference of dopamine D1-receptors in the nucleus accumbens shell. Neuropharmacology 2015; 89:398-411. [PMID: 25446574 DOI: 10.1016/j.neuropharm.2014.10.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 01/17/2023]
Abstract
Microdialysis during i.v. drug self-administration (SA) have implicated nucleus accumbens (NAc) shell DA in cocaine and heroin reinforcement. However, this correlative evidence has not been yet substantiated by experimental evidence obtained by studying the effect of selective manipulation of NAc shell DA transmission on cocaine and heroin SA. In order to investigate this issue, DA D1a receptor (D1aR) expression was impaired in the NAc shell and core by locally infusing lentiviral vectors (LV) expressing specific D1aR-siRNAs (LV-siRNAs). Control rats were infused in the same areas with LV expressing GFP. Fifteen days later, rats were trained to acquire i.v. cocaine or heroin self-administration (SA). At the end of behavioral experiments, in order to evaluate the effect of LV-siRNA on D1aR expression, rats were challenged with amphetamine and the brains were processed for immunohistochemical detection of c-Fos and D1aR. Control rats acquired i.v. cocaine and heroin SA. Infusion of LV-siRNAs in the medial NAc shell reduced D1aR density and the number of c-Fos positive nuclei in the NAc shell, while sparing the core, and prevented the acquisition of cocaine, but not heroin SA. In turn, LV-siRNAs infusion in the core reduced D1aR density and the number of c-Fos positive nuclei in the same area, while sparing the shell, and failed to affect acquisition of cocaine. The differential effect of LV impairment of NAc shell D1aR on cocaine and heroin SA indicates that NAc shell DA acting on D1aR specifically mediates cocaine reinforcement.
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Affiliation(s)
- Augusta Pisanu
- Institute of Neuroscience, National Research Council of Italy, 09124 Cagliari, Italy
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Olovnikov I, Ryazansky S, Shpiz S, Lavrov S, Abramov Y, Vaury C, Jensen S, Kalmykova A. De novo piRNA cluster formation in the Drosophila germ line triggered by transgenes containing a transcribed transposon fragment. Nucleic Acids Res 2013; 41:5757-68. [PMID: 23620285 PMCID: PMC3675497 DOI: 10.1093/nar/gkt310] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) provide defence against transposable element (TE) expansion in the germ line of metazoans. piRNAs are processed from the transcripts encoded by specialized heterochromatic clusters enriched in damaged copies of transposons. How these regions are recognized as a source of piRNAs is still elusive. The aim of this study is to determine how transgenes that contain a fragment of the Long Interspersed Nuclear Elements (LINE)-like I transposon lead to an acquired TE resistance in Drosophila. We show that such transgenes, being inserted in unique euchromatic regions that normally do not produce small RNAs, become de novo bidirectional piRNA clusters that silence I-element activity in the germ line. Strikingly, small RNAs of both polarities are generated from the entire transgene and flanking genomic sequences—not only from the transposon fragment. Chromatin immunoprecipitation analysis shows that in ovaries, the trimethylated histone 3 lysine 9 (H3K9me3) mark associates with transgenes producing piRNAs. We show that transgene-derived hsp70 piRNAs stimulate in trans cleavage of cognate endogenous transcripts with subsequent processing of the non-homologous parts of these transcripts into piRNAs.
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Affiliation(s)
- Ivan Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
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Horman SR, Svoboda P, Luning Prak ET. The potential regulation of L1 mobility by RNA interference. J Biomed Biotechnol 2010; 2006:32713. [PMID: 16877813 PMCID: PMC1559915 DOI: 10.1155/jbb/2006/32713] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The hypothesis that RNA interference constrains L1 mobility seems
inherently reasonable: L1 mobility can be dangerous and L1 RNA,
the presumed target of RNAi, serves as a critical
retrotransposition intermediate. Despite its plausibility, proof
for this hypothesis has been difficult to obtain. Studies
attempting to link the L1 retrotransposition frequency to
alterations in RNAi activity have been hampered by the long times
required to measure retrotransposition frequency, the pleiotropic
and toxic effects of altering RNAi over similar time periods, and
the possibility that other cellular machinery may contribute to
the regulation of L1s. Another problem is that the commonly used
L1 reporter cassette may serve as a substrate for RNAi. Here we
review the L1-RNAi hypothesis and describe a genetic assay with a
modified reporter cassette that detects approximately 4 times more
L1 insertions than the conventional retrotransposition assay.
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Affiliation(s)
- Shane R. Horman
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia,
PA 19104-6055, USA
| | - Petr Svoboda
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia,
PA 19104-6055, USA
- *Eline T. Luning Prak:
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7
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Jia J, Xue Q. Codon usage biases of transposable elements and host nuclear genes in Arabidopsis thaliana and Oryza sativa. GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 7:175-84. [PMID: 20172490 PMCID: PMC5054417 DOI: 10.1016/s1672-0229(08)60047-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Transposable elements (TEs) are mobile genetic entities ubiquitously distributed in nearly all genomes. High frequency of codons ending in A/T in TEs has been previously observed in some species. In this study, the biases in nucleotide composition and codon usage of TE transposases and host nuclear genes were investigated in the AT-rich genome of Arabidopsis thaliana and the GC-rich genome of Oryza sativa. Codons ending in A/T are more frequently used by TEs compared with their host nuclear genes. A remarkable positive correlation between highly expressed nuclear genes and C/G-ending codons were detected in O. sativa (r=0.944 and 0.839, respectively, P<0.0001) but not in A. thaliana, indicating a close association between the GC content and gene expression level in monocot species. In both species, TE codon usage biases are similar to that of weakly expressed genes. The expression and activity of TEs may be strictly controlled in plant genomes. Mutation bias and selection pressure have simultaneously acted on the TE evolution in A. thaliana and O. sativa. The consistently observed biases of nucleotide composition and codon usage of TEs may also provide a useful clue to accurately detect TE sequences in different species.
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Affiliation(s)
- Jia Jia
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
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8
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Blauth ML, Bruno RV, Abdelhay E, Loreto ELS, Valente VLS. Detection of P element transcripts in embryos of Drosophila melanogaster and D. willistoni. AN ACAD BRAS CIENC 2009; 81:679-89. [PMID: 19893894 DOI: 10.1590/s0001-37652009000400007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 03/11/2009] [Indexed: 11/22/2022] Open
Abstract
The P element is one of the most thoroughly studied transposable elements (TE). Its mobilization causes the hybrid dysgenesis that was first described in Drosophila melanogaster. While studies of the P element have mainly been done in D. melanogaster, it is believed that Drosophila willistoni was the original host species of this TE and that P was transposed to the D. melanogaster genome by horizontal transfer. Our study sought to compare the transcriptional behavior of the P element in embryos of D. melanogaster, which is a recent host, with embryos of two strains of D. willistoni, a species that has contained the P element for a longer time. In both species, potential transcripts of transposase, the enzyme responsible for the TE mobilization, were detected, as were transcripts of the 66-kDa repressor, truncated and antisense sequences, which can have the ability to prevent TEs mobilization. The truncated transcripts reveal the truncated P elements present in the genome strains and whose number seems to be related to the invasion time of the genome by the TE. No qualitative differences in antisense transcripts were observed among the strains, even in the D. willistoni strain with the highest frequency of heterochromatic P elements.
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Affiliation(s)
- Monica L Blauth
- Departamento de Ciências Biológicas, Universidade do Estado de Mato Grosso, Tangará da Serra, MT, Brasil
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9
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Hartig JV, Esslinger S, Böttcher R, Saito K, Förstemann K. Endo-siRNAs depend on a new isoform of loquacious and target artificially introduced, high-copy sequences. EMBO J 2009; 28:2932-44. [PMID: 19644447 DOI: 10.1038/emboj.2009.220] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 07/09/2009] [Indexed: 12/20/2022] Open
Abstract
Colonization of genomes by a new selfish genetic element is detrimental to the host species and must lead to an efficient, repressive response. In vertebrates as well as in Drosophila, piRNAs repress transposons in the germ line, whereas endogenous siRNAs take on this role in somatic cells. We show that their biogenesis depends on a new isoform of the Drosophila TRBP homologue loquacious, which arises by alternative polyadenylation and is distinct from the one that functions during the biogenesis of miRNAs. For endo-siRNAs and piRNAs, it is unclear how an efficient response can be initiated de novo. Our experiments establish that the endo-siRNA pathway will target artificially introduced sequences without the need for a pre-existing template in the genome. This response is also triggered in transiently transfected cells, thus genomic integration is not essential. Deep sequencing showed that corresponding endo-siRNAs are generated throughout the sequence, but preferentially from transcribed regions. One strand of the dsRNA precursor can come from spliced mRNA, whereas the opposite strand derives from independent transcripts in antisense orientation.
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Affiliation(s)
- Julia Verena Hartig
- Department of Chemistry and Biochemistry, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
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10
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Abstract
In Drosophila, small RNAs bound to Piwi proteins are epigenetic factors transmitted from the mother to the progeny germline. This ensures 'immunization' of progeny against transposable elements.
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Affiliation(s)
- Sergey Shpiz
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia
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11
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Chen S, Li X. Molecular characterization of the first intact Transib transposon from Helicoverpa zea. Gene 2008; 408:51-63. [DOI: 10.1016/j.gene.2007.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/06/2007] [Accepted: 10/12/2007] [Indexed: 01/10/2023]
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12
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Kavi HH, Fernandez H, Xie W, Birchler JA. Genetics and biochemistry of RNAi in Drosophila. Curr Top Microbiol Immunol 2008; 320:37-75. [PMID: 18268839 DOI: 10.1007/978-3-540-75157-1_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RNA interference (RNAi) is the technique employing double-stranded RNA to target the destruction of homologous messenger RNAs. It has gained wide usage in genetics. While having the potential for many practical applications, it is a reflection of a much broader spectrum of small RNA-mediated processes in the cell. The RNAi machinery was originally perceived as a defense mechanism against viruses and transposons. While this is certainly true, small RNAs have now been implicated in many other aspects of cell biology. Here we review the current knowledge of the biochemistry of RNAi in Drosophila and the involvement of small RNAs in RNAi, transposon silencing, virus defense, transgene silencing, pairing-sensitive silencing, telomere function, chromatin insulator activity, nucleolar stability, and heterochromatin formation. The discovery of the role of RNA molecules in the degradation of mRNA transcripts leading to decreased gene expression resulted in a paradigm shift in the field of molecular biology. Transgene silencing was first discovered in plant cells (Matzke et al. 1989; van der Krol et al. 1990; Napoli et al. 1990) and can occur on both the transcriptional and posttranscriptional levels, but both involve short RNA moieties in their mechanism. RNA interference (RNAi) is a type of gene silencing mechanism in which a double-stranded RNA (dsRNA) molecule directs the specific degradation of the corresponding mRNA (target RNA). The technique of RNAi was first discovered in Caenorhabditis elegans in 1994 (Guo and Kemphues 1994). Later the active component was found to be a dsRNA (Fire et al. 1998). In subsequent years, it has been found to occur in diverse eukaryotes
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Affiliation(s)
- Harsh H Kavi
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
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13
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Dramard X, Heidmann T, Jensen S. Natural epigenetic protection against the I-factor, a Drosophila LINE retrotransposon, by remnants of ancestral invasions. PLoS One 2007; 2:e304. [PMID: 17375190 PMCID: PMC1810428 DOI: 10.1371/journal.pone.0000304] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 02/19/2007] [Indexed: 11/23/2022] Open
Abstract
Transposable elements are major components of most eukaryotic genomes. Such sequences are generally defective for transposition and have little or no coding capacity. Because transposition can be highly mutagenic, mobile elements that remain functional are tightly repressed in all living species. Drosophila pericentromeric heterochromatin naturally contains transposition-defective, non-coding derivatives of a LINE retrotransposon related to the I-factor. The I-factor is a good model to study the regulation of transposition in vivo because, under specific conditions, current functional copies of this mobile element can transpose at high frequency, specifically in female germ cells, with deleterious effects including female sterility. However, this high transpositional activity becomes spontaneously repressed upon ageing or heat treatment, by a maternally transmitted, transgenerational epigenetic mechanism of unknown nature. We have analyzed, by quantitative real time RT-PCR, the RNA profile of the transposition-defective I-related sequences, in the Drosophila ovary during ageing and upon heat treatment, and also in female somatic tissues and in males, which are not permissive for I-factor transposition. We found evidence for a role of transcripts from these ancestral remnants in the natural epigenetic protection of the Drosophila melanogaster genome against the deleterious effects of new invasions by functional I-factors. These results provide a molecular basis for a probably widespread natural protection against transposable elements by persisting vestiges of ancient invasions.
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Affiliation(s)
- Xavier Dramard
- Unité des Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs Centre National de la Recherche Scientifique (CNRS) UMR 8122, Institut Gustave Roussy, Villejuif, France
| | - Thierry Heidmann
- Unité des Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs Centre National de la Recherche Scientifique (CNRS) UMR 8122, Institut Gustave Roussy, Villejuif, France
| | - Silke Jensen
- Unité des Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs Centre National de la Recherche Scientifique (CNRS) UMR 8122, Institut Gustave Roussy, Villejuif, France
- * To whom correspondence should be addressed. E-mail:
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14
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Bergman CM, Quesneville H, Anxolabéhère D, Ashburner M. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biol 2007; 7:R112. [PMID: 17134480 PMCID: PMC1794594 DOI: 10.1186/gb-2006-7-11-r112] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 11/13/2006] [Accepted: 11/29/2006] [Indexed: 11/10/2022] Open
Abstract
An analysis of high-resolution transposable element annotations in Drosophila melanogaster suggests the existence of a global surveillance system against the majority of transposable elements families in the fly. Background The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the contribution of TEs to genomes sequences. Results Using a high-resolution annotation of TEs in Release 4 genome sequence, we revise estimates of TE abundance in Drosophila melanogaster. We show that TEs are non-randomly distributed within regions of high and low TE abundance, and that pericentromeric regions with high TE abundance are mosaics of distinct regions of extreme and normal TE density. Comparative analysis revealed that this punctate pattern evolves jointly by transposition and duplication, but not by inversion of TE-rich regions from unsequenced heterochromatin. Analysis of genome-wide patterns of TE nesting revealed a 'nesting network' that includes virtually all of the known TE families in the genome. Numerous directed cycles exist among TE families in the nesting network, implying concurrent or overlapping periods of transpositional activity. Conclusion Rapid restructuring of the genomic landscape by transposition and duplication has recently added hundreds of kilobases of TE sequence to pericentromeric regions in D. melanogaster. These events create ragged transitions between unique and repetitive sequences in the zone between euchromatic and beta-heterochromatic regions. Complex relationships of TE nesting in beta-heterochromatic regions raise the possibility of a co-suppression network that may act as a global surveillance system against the majority of TE families in D. melanogaster.
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Affiliation(s)
- Casey M Bergman
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Hadi Quesneville
- Laboratoire de Bioinformatique et Génomique, Institut Jacques Monod, place Jussieu, 75251 Paris cedex 05, France
| | - Dominique Anxolabéhère
- Laboratoire Dynamique du Génome et Évolution, Institut Jacques Monod, place Jussieu, 75251 Paris cedex 05, France
| | - Michael Ashburner
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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15
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McDonald JF, Matzke MA, Matzke AJ. Host defenses to transposable elements and the evolution of genomic imprinting. Cytogenet Genome Res 2005; 110:242-9. [PMID: 16093678 DOI: 10.1159/000084958] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2003] [Accepted: 04/14/2004] [Indexed: 12/18/2022] Open
Abstract
Genomic imprinting is the differential expression of maternally and paternally inherited alleles of specific genes. Several organismic level hypotheses have been offered to explain the evolution of genomic imprinting. We argue that evolutionary explanations of the origin of imprinting that focus exclusively on the organismic level are incomplete. We propose that the complex molecular mechanisms that underlie genomic imprinting originally evolved as an adaptive response to the mutagenic potential of transposable elements (TEs). We also present a model of how these mechanisms may have been co-opted by natural selection to evolve molecular features characteristic of genomic imprinting.
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Affiliation(s)
- J F McDonald
- Department of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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16
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Kavi HH, Fernandez HR, Xie W, Birchler JA. RNA silencing inDrosophila. FEBS Lett 2005; 579:5940-9. [PMID: 16198344 DOI: 10.1016/j.febslet.2005.08.069] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 08/26/2005] [Accepted: 08/28/2005] [Indexed: 11/18/2022]
Abstract
Knowledge of the role of RNA in affecting gene expression has expanded in the past several years. Small RNAs serve as homology guides to target messenger RNAs for destruction at the post-transcriptional level in the experimental technique known as RNA interference and in the silencing of some transgenes. These small RNAs are also involved in sequence-specific targeting of chromatin modifications for transcriptional silencing of transgenes, transposable elements, heterochromatin and some cases of Polycomb-mediated gene silencing. RNA silencing processes in Drosophila are described.
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Affiliation(s)
- Harsh H Kavi
- Division of Biological Sciences, University of Missouri, 117 Tucker Hall, Columbia, MO 65211, USA
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17
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Chambeyron S, Bucheton A. I elements in Drosophila: in vivo retrotransposition and regulation. Cytogenet Genome Res 2005; 110:215-22. [PMID: 16093675 DOI: 10.1159/000084955] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2004] [Accepted: 07/19/2004] [Indexed: 11/19/2022] Open
Affiliation(s)
- S Chambeyron
- Institut de Génétique Humaine, CNRS, Montpellier, France
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18
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Reiss D, Josse T, Anxolabéhère D, Ronsseray S. aubergine mutations in Drosophila melanogaster impair P cytotype determination by telomeric P elements inserted in heterochromatin. Mol Genet Genomics 2004; 272:336-43. [PMID: 15372228 DOI: 10.1007/s00438-004-1061-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2004] [Accepted: 08/20/2004] [Indexed: 11/30/2022]
Abstract
Transposable P elements inserted in the heterochromatic Telomeric Associated Sequences on the X chromosome (1A site) of Drosophila melanogaster have a very strong capacity to elicit the P cytotype, a maternally transmitted condition which represses P element transposition and P-induced hybrid dysgenesis. This repressive capacity has previously been shown to be sensitive to mutant alleles of the gene Su(var)205, which encodes HP1 (Heterochromatin Protein 1), thus suggesting a role for chromatin structure in repression. Since an interaction between heterochromatin formation and RNA interference has been reported in various organisms, we tested the effect of mutant alleles of aubergine, a gene that has been shown to play a role in RNA interference in Drosophila, on the repressive properties of telomeric P elements. Seven out of the eight mutant alleles tested clearly impaired the repressive capacities of the two independent telomeric P insertions at 1A analyzed. P repression by P strains whose repressive capacities are not linked to the presence of P copies at 1A were previously found to be insensitive to Su(var)205; here, we show that they are also insensitive to aubergine mutations. These results strongly suggest that both RNA interference and heterochromatin structure are involved in the establishment of the P cytotype elicited by telomeric P elements, and reinforce the hypothesis that different mechanisms for repression of P elements exist which depend on the chromosomal location of the regulatory copies of P.
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Affiliation(s)
- D Reiss
- Laboratoire Dynamique du Génome et Evolution, Institut Jacques Monod, UMR7592, CNRS-Universités Paris 6 et 7, 2 Place Jussieu, 75251, Paris 05, France
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19
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Neafsey DE, Blumenstiel JP, Hartl DL. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies. Mol Biol Evol 2004; 21:2310-8. [PMID: 15342795 DOI: 10.1093/molbev/msh243] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Comparative analysis of recently sequenced eukaryotic genomes has uncovered extensive variation in transposable element (TE) abundance, diversity, and distribution. The TE profile in the sequenced pufferfish genomes is more similar to that of Drosophila melanogaster than to human or mouse, in that pufferfish TEs exhibit low overall abundance, high family diversity, and localization in the heterochromatin. It has been suggested that selection against the deleterious effects of ectopic recombination between TEs has structured the TE profile in Drosophila and pufferfish but not in humans. We test this hypothesis by measuring the sample frequency of 48 euchromatic TE insertions in the genome of the green spotted pufferfish (Tetraodon nigroviridis). We estimate the strength of selection acting on recent insertions by analyzing the site frequency spectrum using a maximum-likelihood approach. We show that in contrast to Drosophila, euchromatic TE insertions in Tetraodon are selectively neutral and that the low copy number and compartmentalized distribution of TEs in the Tetraodon genome must be caused by regulation by means other than purifying selection acting on recent insertions. Inference of regulatory processes governing TE profiles should take into account factors such as effective population size, incidence of inbreeding/outcrossing, and other species-specific traits.
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Affiliation(s)
- Daniel E Neafsey
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
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20
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Walter MF, Biessmann H. Expression of the telomeric retrotransposon HeT-A in Drosophila melanogaster is correlated with cell proliferation. Dev Genes Evol 2004; 214:211-9. [PMID: 15069641 DOI: 10.1007/s00427-004-0400-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Accepted: 02/29/2004] [Indexed: 10/26/2022]
Abstract
Drosophila melanogaster extends its telomeres by transposition of two non-LTR retrotransposons, HeT-A and TART, to chromosome ends. We have determined the tissue-specific expression of these two elements by whole-mount in situ hybridization with digoxigenin-labeled RNA sense and antisense probes in the germ line and in a variety of larval tissues during normal development in the wild type and in tissues of mutants that cause overproliferation. Our results indicate that transcript levels, which are a key component in the process of telomere elongation in D. melanogaster, are correlated with cell proliferation in normal tissues and that RNA levels are elevated in growth-stimulated tissues.
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Affiliation(s)
- Marika F Walter
- Developmental Biology Center, University of California, Irvine 92697, USA
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21
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Handler AM. Understanding and improving transgene stability and expression in insects for SIT and conditional lethal release programs. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2004; 34:121-130. [PMID: 14871608 DOI: 10.1016/j.ibmb.2003.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2002] [Revised: 03/19/2003] [Accepted: 08/07/2003] [Indexed: 05/24/2023]
Abstract
Genetically transformed insect pests provide significant opportunities to create strains for improved sterile insect technique and new strategies based on conditional lethality. A major concern for programs that rely on the release of transgenic insects is the stability of the transgene, and maintenance of consistent expression of genes of interest within the transgene. Transgene instability would influence the integrity of the transformant strain upon which the effectiveness of the biological control program depends. Loss or intra-genomic transgene movement would result in strain attributes important to the program being lost or diminished, and the mass-release of such insects could significantly exacerbate the insect pest problem. Instability resulting in intra-genomic movement may also be a prelude to inter-genomic transgene movement between species resulting in ecological risks. This is less of a concern for short-term releases, where transgenic insects are not expected to survive in the environment beyond two or three generations. Transgene movement may occur, however, into infectious agents during mass-rearing, and the potential for movement after release is a possibility for programs using many millions of insects. The primary methods of addressing potential transgene instability relate to an understanding of the vector system used for gene transfer, the potential for its mobilization by the same or a related vector system, and methods required to identify transformants and determine if unexpected transgene movement has occurred. Methods also exist for preventing transposon-mediated mobilization, by deleting or rearranging vector sequences required for transposition using recombination systems. Stability of transgene expression is also a critical concern, especially in terms of potential epigenetic interactions with host genomes resulting in gene silencing that have been observed in plants and fungi, and it must be determined if this or related phenomena can occur in insects.
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Affiliation(s)
- Alfred M Handler
- Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, U.S. Department of Agriculture, 1700 S.W. 23rd Drive, Gainesville, FL 32608, USA.
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22
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Kim SH, Walbot V. Deletion derivatives of the MuDR regulatory transposon of maize encode antisense transcripts but are not dominant-negative regulators of mutator activities. THE PLANT CELL 2003; 15:2430-47. [PMID: 14508005 PMCID: PMC197307 DOI: 10.1105/tpc.014605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2003] [Accepted: 08/13/2003] [Indexed: 05/18/2023]
Abstract
The maize MuDR/Mu transposable elements are highly aggressive, and their activities are held in check by host developmental and epigenetic mechanisms. The Mutator regulatory element, MuDR, produces both sense and antisense transcripts. We have investigated the impact of the presence of antisense transcripts on the abundance of the corresponding sense messages and on the regulation of Mutator activities. We report that internal deletions in MuDR arise frequently in somatic tissues; preferential loss of the 3' untranslated region of mudrA and/or mudrB containing the intergenic region is correlated with chimeric sense mudrA/antisense mudrB and sense mudrB/antisense mudrA transcripts. Heritable internal deletions are extremely frequent (>10(-2) per element), and the resulting defective MuDR elements also encode antisense transcripts. Expression of endogenous or additional transgene-encoded antisense transcripts neither decreases sense transcript levels nor inhibits Mutator excision activity over the three generations examined. We propose that antisense transcripts produced by MuDR deletions are not dominant-negative regulators of Mutator activities.
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Affiliation(s)
- Soo-Hwan Kim
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.
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23
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Wickstead B, Ersfeld K, Gull K. Repetitive elements in genomes of parasitic protozoa. Microbiol Mol Biol Rev 2003; 67:360-75, table of contents. [PMID: 12966140 PMCID: PMC193867 DOI: 10.1128/mmbr.67.3.360-375.2003] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five medically important species with ongoing or completed genome sequencing projects: Plasmodium falciparum, Leishmania major, Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia. These organisms are used to illustrate five thematic classes of repeats with different structures and genomic locations. We discuss how these repeat classes may interact with parasitic life-style and also how they can be used as experimental tools. The story which emerges is one of opportunism and upheaval which have been employed to add genetic diversity and genomic flexibility.
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Affiliation(s)
- Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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24
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Robin S, Chambeyron S, Bucheton A, Busseau I. Gene silencing triggered by non-LTR retrotransposons in the female germline of Drosophila melanogaster. Genetics 2003; 164:521-31. [PMID: 12807773 PMCID: PMC1462600 DOI: 10.1093/genetics/164.2.521] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several studies have recently shown that the activity of some eukaryotic transposable elements is sensitive to the presence of homologous transgenes, suggesting the involvement of homology-dependent gene-silencing mechanisms in their regulation. Here we provide data indicating that two non-LTR retrotransposons of Drosophila melanogaster are themselves natural triggers of homology-dependent gene silencing. We show that, in the female germline of D. melanogaster, fragments from the R1 or from the I retrotransposons can mediate silencing of chimeric transcription units into which they are inserted. This silencing is probably mediated by sequence identity with endogenous copies of the retrotransposons because it does not occur with a fragment from the divergent R1 elements of Bombyx mori, and, when a fragment of I is used, it occurs only in females containing functional copies of the I element. This silencing is not accompanied by cosuppression of the endogenous gene homologous to the chimeric transcription unit, which contrasts to some other silencing mechanisms in Drosophila. These observations suggest that in the female germline of D. melanogaster the R1 and I retrotransposons may self-regulate their own activity and their copy number by triggering homology-dependent gene silencing.
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Affiliation(s)
- Stéphanie Robin
- Institut de Génétique Humaine, CNRS, 34396 Montpellier, Cedex 5, France
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25
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Affiliation(s)
- Joanna B Grabarek
- Polgen/Cyclacel, Ltd, Babraham Bioincubators, Babraham, CB2 4AT, UK.
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26
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Jensen S, Gassama MP, Dramard X, Heidmann T. Regulation of I-transposon activity in Drosophila: evidence for cosuppression of nonhomologous transgenes and possible role of ancestral I-related pericentromeric elements. Genetics 2002; 162:1197-209. [PMID: 12454066 PMCID: PMC1462345 DOI: 10.1093/genetics/162.3.1197] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have previously shown that the activity of functional I retrotransposons (I factors) introduced into Drosophila devoid of such elements can be repressed by transgenes containing an internal fragment of the I factor itself and that this repressing effect presents the characteristic features of homology-dependent gene silencing or cosuppression. Here we show that the same transgenes can induce silencing of a nonhomologous reporter gene containing as the sole I-factor sequence its 100-bp promoter fragment. Silencing of the nonhomologous reporter gene shows strong similarities to I-factor cosuppression: It does not require any translation product from the regulating transgenes, sense and antisense constructs are equally potent, and the silencing effect is only maternally transmitted and fully reversible. A search for genomic I-like sequences containing domains with similarities to those of both the regulating and the reporter transgenes led to the identification of four such elements, which therefore could act as intermediates-or relays-in the cosuppression machinery. These results strongly suggest that ancestral transposition-defective I-related elements, which are naturally present in the Drosophila genome, may participate per se in the natural conditions of I-factor silencing.
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Affiliation(s)
- Silke Jensen
- CNRS UMR 1573, Institut Gustave Roussy, 94805 Villejuif Cedex, France
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27
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Abstract
SINEs and LINEs are short and long interspersed retrotransposable elements, respectively, that invade new genomic sites using RNA intermediates. SINEs and LINEs are found in almost all eukaryotes (although not in Saccharomyces cerevisiae) and together account for at least 34% of the human genome. The noncoding SINEs depend on reverse transcriptase and endonuclease functions encoded by partner LINEs. With the completion of many genome sequences, including our own, the database of SINEs and LINEs has taken a great leap forward. The new data pose new questions that can only be answered by detailed studies of the mechanism of retroposition. Current work ranges from the biochemistry of reverse transcription and integration invitro, target site selection in vivo, nucleocytoplasmic transport of the RNA and ribonucleoprotein intermediates, and mechanisms of genomic turnover. Two particularly exciting new ideas are that SINEs may help cells survive physiological stress, and that the evolution of SINEs and LINEs has been shaped by the forces of RNA interference. Taken together, these studies promise to explain the birth and death of SINEs and LINEs, and the contribution of these repetitive sequence families to the evolution of genomes.
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Affiliation(s)
- Alan M Weiner
- Department of Biochemistry, HSB J417, University of Washington, Box 357350, Seattle, WA 98195-7350, USA.
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28
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Opsahl ML, McClenaghan M, Springbett A, Reid S, Lathe R, Colman A, Whitelaw CBA. Multiple effects of genetic background on variegated transgene expression in mice. Genetics 2002; 160:1107-12. [PMID: 11901126 PMCID: PMC1462007 DOI: 10.1093/genetics/160.3.1107] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BLG/7 transgenic mice express an ovine beta-lactoglobulin transgene during lactation. Unusually, transgene expression levels in milk differ between siblings. This variable expression is due to variegated transgene expression in the mammary gland and is reminiscent of position-effect variegation. The BLG/7 line was created and maintained on a mixed CBA x C57BL/6 background. We have investigated the effect on transgene expression of backcrossing for 13 generations into these backgrounds. Variable transgene expression was observed in all populations examined, confirming that it is an inherent property of the transgene array at its site of integration. There were also strain-specific effects on transgene expression that appear to be independent of the inherent variegation. The transgene, compared to endogenous milk protein genes, is specifically susceptible to inbreeding depression. Outcrossing restored transgene expression levels to that of the parental population; thus suppression was not inherited. Finally, no generation-dependent decrease in mean expression levels was observed in the parental population. Thus, although the BLG/7 transgene is expressed in a variegated manner, there was no generation-associated accumulated silencing of transgene expression.
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Affiliation(s)
- Margaret L Opsahl
- Roslin Institute (Edinburgh), Division of Molecular Biology, Roslin, Midlothian, EH25 9PS, United Kingdom
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29
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Ronsseray S, Boivin A, Anxolabéhère D. P-Element repression in Drosophila melanogaster by variegating clusters of P-lacZ-white transgenes. Genetics 2001; 159:1631-42. [PMID: 11779802 PMCID: PMC1461890 DOI: 10.1093/genetics/159.4.1631] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Drosophila, clusters of P transgenes (P-lac-w) display a variegating phenotype for the w marker. In addition, X-ray-induced rearrangements of chromosomes bearing such clusters may lead to enhancement of the variegated phenotype. Since P-lacZ transgenes in subtelomeric heterochromatin have some P-element repression abilities, we tested whether P-lac-w clusters also have the capacity to repress P-element activity in the germline. One cluster (T-1), located on a rearranged chromosome (T2;3) and derived from a line bearing a variegating tandem array of seven P-lac-w elements, partially represses the dysgenic sterility (GD sterility) induced by P elements. This cluster also strongly represses in trans the expression of P-lacZ elements in the germline. This latter suppression shows a maternal effect. Finally, the combination of variegating P-lac-w clusters and a single P-lacZ reporter inserted in subtelomeric heterochromatic sequences at the X chromosome telomere (cytological site 1A) leads to strong repression of dysgenic sterility. These results show that repression of P-induced dysgenic sterility can be elicited in the absence of P elements encoding a polypeptide repressor and that a transgene cluster can repress the expression of a single homologous transgene at a nonallelic position. Implications for models of transposable element silencing are discussed.
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Affiliation(s)
- S Ronsseray
- Laboratoire Dynamique du Génome et Evolution, Institut Jacques Monod, UMR7592, CNRS-Universités Paris 6 et 7, 75251 Paris Cedex 05, France.
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30
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Nykänen A, Haley B, Zamore PD. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 2001; 107:309-21. [PMID: 11701122 DOI: 10.1016/s0092-8674(01)00547-5] [Citation(s) in RCA: 745] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We examined the role of ATP in the RNA interference (RNAi) pathway. Our data reveal two ATP-dependent steps and suggest that the RNAi reaction comprises at least four sequential steps: ATP-dependent processing of double-stranded RNA into small interfering RNAs (siRNAs), incorporation of siRNAs into an inactive approximately 360 kDa protein/RNA complex, ATP-dependent unwinding of the siRNA duplex to generate an active complex, and ATP-independent recognition and cleavage of the RNA target. Furthermore, ATP is used to maintain 5' phosphates on siRNAs. A 5' phosphate on the target-complementary strand of the siRNA duplex is required for siRNA function, suggesting that cells check the authenticity of siRNAs and license only bona fide siRNAs to direct target RNA destruction.
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Affiliation(s)
- A Nykänen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
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31
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Aravin AA, Naumova NM, Tulin AV, Vagin VV, Rozovsky YM, Gvozdev VA. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr Biol 2001; 11:1017-27. [PMID: 11470406 DOI: 10.1016/s0960-9822(01)00299-8] [Citation(s) in RCA: 540] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The injection of double-stranded RNA (dsRNA) has been shown to induce a potent sequence-specific inhibition of gene function in diverse invertebrate and vertebrate species. The homology-dependent posttranscriptional gene silencing (PTGS) caused by the introduction of transgenes in plants may be mediated by dsRNA. The analysis of Caenorhabditis elegans mutants impaired with dsRNA-mediated silencing and studies in plants implicate a biological role of dsRNA-mediated silencing as a transposon-repression and antiviral mechanism. RESULTS We investigated the silencing of testis-expressed Stellate genes by paralogous Su(Ste) tandem repeats, which are known to be involved in the maintenance of male fertility in Drosophila melanogaster. We found that both strands of repressor Su(Ste) repeats are transcribed, producing sense and antisense RNA. The Stellate silencing is associated with the presence of short Su(Ste) RNAs. Cotransfection experiments revealed that Su(Ste) dsRNA can target and eliminate Stellate transcripts in Drosophila cell culture. The short fragment of Stellate gene that is homologous to Su(Ste) was shown to be sufficient to confer Su(Ste)-dependent silencing of a reporter construct in testes. We demonstrated that Su(Ste) dsRNA-mediated silencing affects not only Stellate expression but also the level of sense Su(Ste) RNA providing a negative autogenous regulation of Su(Ste) expression. Mutation in the spindle-E gene relieving Stellate silencing also leads to a derepression of the other genomic tandem repeats and retrotransposons in the germline. CONCLUSIONS Homology-dependent gene silencing was shown to be used to inhibit Stellate gene expression in the D. melanogaster germline, ensuring male fertility. dsRNA-mediated silencing may provide a basis for negative autogenous control of gene expression. The related surveillance system is implicated to control expression of retrotransposons in the germline.
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Affiliation(s)
- A A Aravin
- Department of Animal Molecular Genetics, Institute of Molecular Genetics, 123182, Moscow, Russia
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32
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Affiliation(s)
- T Tuschl
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany.
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33
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Abstract
Eukaryotes silence gene expression in the presence of double-stranded RNA homologous to the silenced gene. Silencing occurs by the targeted degradation of mRNA. Biochemical reactions that recapitulate this phenomenon generate RNA fragments of 21--23 nucleotides from the double-stranded RNA. These stably associate with an RNA endonuclease and probably serve as a discriminator to select mRNAs. Once selected, mRNAs are cleaved at sites 21--23 nucleotides apart. This mechanism, termed RNAi, has functional links to viral defense and silencing phenomena, such as cosuppression. It also functions to repress the hopping of transposable elements.
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Affiliation(s)
- R W Carthew
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA. carthew+@pitt.edu
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34
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35
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Hammond SM, Caudy AA, Hannon GJ. Post-transcriptional gene silencing by double-stranded RNA. Nat Rev Genet 2001; 2:110-9. [PMID: 11253050 DOI: 10.1038/35052556] [Citation(s) in RCA: 532] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Imagine being able to knock out your favourite gene with only a day's work. Not just in one model system, but in virtually any organism: plants, flies, mice or cultured cells. This sort of experimental dream might one day become reality as we learn to harness the power of RNA interference, the process by which double-stranded RNA induces the silencing of homologous endogenous genes. How this phenomenon works is slowly becoming clear, and might help us to develop an effortless tool to probe gene function in cells and animals.
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Affiliation(s)
- S M Hammond
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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36
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Azou Y, Bregliano JC. I-R system of hybrid dysgenesis in Drosophila melanogaster: analysis of the mitochondrial DNA in reactive strains exhibiting different potentials for I factor transposition. Heredity (Edinb) 2001; 86:110-6. [PMID: 11298822 DOI: 10.1046/j.1365-2540.2001.00814.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the I-R hybrid dysgenesis system, Drosophila melanogaster strains fall into two categories denoted inducer (I) and reactive (R). Among the reactive strains we can distinguish strains with weak, medium or strong reactivity levels. These levels are inherited in a complex way involving both chromosomal and nonchromosomal determinants, the nonchromosomal determinant being mainly maternally inherited. We were interested in determining the molecular basis of this maternal transmission. In this article we analyse the possible implication of the mitochondrial DNA in the determination of the reactivity levels. The mtDNA was analysed in lines with very different reactivity levels with the aim of correlating sequence differences with reactivity levels. The mtDNA was analysed by sequencing and restriction fragment length. No correlation was established between reactivity level and mtDNA sequence. This may favour the hypothesis that epigenetic changes would be responsible for the different reactivity levels and their transgenerational transmission.
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Affiliation(s)
- Y Azou
- Laboratoire de Génétique et Physiologie du Développement, IBDM, CNRS/INSERM, Université de la Méditerranée, AP de Marseille, Parc Scientifique de Luminy, Case 907, 13288, Marseille Cedex 9, France.
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37
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Gauthier E, Tatout C, Pinon H. Artificial and epigenetic regulation of the I factor, a nonviral retrotransposon of Drosophila melanogaster. Genetics 2000; 156:1867-78. [PMID: 11102380 PMCID: PMC1461392 DOI: 10.1093/genetics/156.4.1867] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The I factor (IF) is a LINE-like transposable element from Drosophila melanogaster. IF is silenced in most strains, but under special circumstances its transposition can be induced and correlates with the appearance of a syndrome of female sterility called hybrid dysgenesis. To elucidate the relationship between IF expression and female sterility, different transgenic antisense and/or sense RNAs homologous to the IF ORF1 have been expressed. Increasing the transgene copy number decreases both the expression of an IF-lacZ fusion and the intensity of the female sterile phenotype, demonstrating that IF expression is correlated with sterility. Some transgenes, however, exert their repressive abilities not only through a copy number-dependent zygotic effect, but also through additional maternal and paternal effects that may be induced at the DNA and/or RNA level. Properties of the maternal effect have been detailed: (1) it represses hybrid dysgenesis more efficiently than does the paternal effect; (2) its efficacy increases with both the transgene copy number and the aging of sterile females; (3) it accumulates slowly over generations after the transgene has been established; and (4) it is maintained for at least two generations after transgene removal. Conversely, the paternal effect increases only with female aging. The last two properties of the maternal effect and the genuine existence of a paternal effect argue for the occurrence, in the IF regulation pathway, of a cellular memory transmitted through mitosis, as well as through male and female meiosis, and akin to epigenetic phenomena.
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Affiliation(s)
- E Gauthier
- Centre de Génétique Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard, F-69622 Villeurbanne Cedex, France
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Malinsky S, Bucheton A, Busseau I. New insights on homology-dependent silencing of I factor activity by transgenes containing ORF1 in Drosophila melanogaster. Genetics 2000; 156:1147-55. [PMID: 11063690 PMCID: PMC1461323 DOI: 10.1093/genetics/156.3.1147] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
I factors in Drosophila melanogaster are non-LTR retrotransposons that transpose at very high frequencies in the germ line of females resulting from crosses between reactive females (devoid of active I factors) and inducer males (containing active I factors). Constructs containing I factor ORF1 under the control of the hsp70 promoter repress I factor activity. This repressor effect is maternally transmitted and increases with the transgene copy number. It is irrespective of either frame integrity or transcriptional orientation of ORF1, suggesting the involvement of a homology-dependent trans-silencing mechanism. A promoterless transgene displays no repression. The effect of constructs in which ORF1 is controlled by the hsp70 promoter does not depend upon heat-shock treatments. No effect of ORF1 is detected when it is controlled by the I factor promoter. We discuss the relevance of the described regulation to the repression of I factors in I strains.
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Affiliation(s)
- S Malinsky
- Institut de Génétique Humaine, CNRS, 34396 Montpellier Cedex 05, France
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Abstract
For 50 years now, one of the enigmas of molecular evolution has been the C-value paradox, which refers to the often massive, counterintuitive and seemingly arbitrary differences in genome size observed among eukaryotic organisms. For example, the genome of the fruitfly Drosophila melanogaster is 180 megabases (Mb), whereas that of the European brown grasshopper Podisma pedestris is 18,000 Mb. The difference in genome size of a factor of 100 is difficult to explain in view of the apparently similar levels of evolutionary, developmental and behavioural complexity of these organisms.
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Affiliation(s)
- D L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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Abstract
About two years ago, it was recognized that introduction of double-stranded RNA (dsRNA) had a potent effect on gene expression, in particular on mRNA stability. Since then, this process has been found to occur in many different organisms, and to bear a strong resemblance to a previously recognized process in plants, called cosuppression. Both genetic and biochemical studies have started to unravel the mysteries of RNA interference: genes involved in this process are being identified and in vitro studies are giving the first hints of what is happening to both the dsRNA and the affected mRNA molecules after the introduction of the dsRNA.
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Affiliation(s)
- R H Plasterk
- Hubrecht Laboratory, Uppsalalaan 8, 3584 CT, The, Utrecht, Netherlands.
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Marin L, Lehmann M, Nouaud D, Izaabel H, Anxolabéhère D, Ronsseray S. P-Element repression in Drosophila melanogaster by a naturally occurring defective telomeric P copy. Genetics 2000; 155:1841-54. [PMID: 10924479 PMCID: PMC1461209 DOI: 10.1093/genetics/155.4.1841] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In Drosophila melanogaster, hybrid dysgenesis occurs in progeny from crosses between females lacking P elements and males carrying P elements scattered throughout the genome. We have genetically isolated a naturally occurring P insertion at cytological location 1A, from a Tunisian population. The Nasr'Allah-P(1A) element [NA-P(1A)] has a deletion of the first 871 bp including the P promoter. It is flanked at the 3' end by telomeric associated sequences and at the 5' end by a HeT-A element sequence. The NA-P(1A) element strongly represses dysgenic sterility and P transposition. However, when testing P-promoter repression, NA-P(1A) was unable to repress a germinally expressed P-lacZ construct bearing no 5'-homology with it. Conversely, a second P-lacZ construct, in which the fusion with lacZ takes place in exon 3 of P, was successfully repressed by NA-P(1A). This suggests that NA-P(1A) repression involves a homology-dependent component.
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Affiliation(s)
- L Marin
- Département Dynamique du Génome et Evolution, Institut Jacques Monod, 75251 Paris Cedex 05, France
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Matzke MA, Mette MF, Matzke AJ. Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates. PLANT MOLECULAR BIOLOGY 2000; 43:401-15. [PMID: 10999419 DOI: 10.1023/a:1006484806925] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Increasing evidence supports the idea that various transgene silencing phenomena reflect the activity of diverse host defense responses that act ordinarily on natural foreign or parasitic sequences such as transposable elements, viroids, RNA and DNA viruses, and bacterial DNA. Transgenes or their transcripts can resemble these cellular invaders in a number of ways, thus making them targets of host protective reactions. At least two distinct host defense systems operate to silence transgenes. One acts at the genome level and is associated with de novo DNA methylation. A second line of defense operates post-transcriptionally and involves sequence-specific RNA degradation in the cytoplasm. Transgenes that are silenced as a consequence of the genome defense are revealing that de novo methylation can be cued by DNA-DNA or RNA-DNA interactions. These methylation signals can be interpreted in the context of transposable elements or their transcripts. During evolution, as transposable elements accumulated in plant and vertebrate genomes and as they invaded flanking regions of genes, the genome defense was possibly recruited to establish global epigenetic mechanisms to regulate gene expression. Transposons integrated into promoters of host genes could conceivably change expression patterns and attract methylation, thus imposing on endogenous genes the type of epigenetic regulation associated with the genome defense. This recruitment process might have been particularly effective in the polyploid genomes of plants and early vertebrates. Duplication of the entire genome in polyploids buffers against insertional mutagenesis by transposable elements and permits their infiltration into individual copies of duplicated genes.
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Affiliation(s)
- M A Matzke
- Institute of Molecular Biology, Austrian Academy of Sciences, Salzburg.
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