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Sánchez-Luque F, López MC, Macias F, Alonso C, Thomas MC. Pr77 and L1TcRz: A dual system within the 5'-end of L1Tc retrotransposon, internal promoter and HDV-like ribozyme. Mob Genet Elements 2014; 2:1-7. [PMID: 22754746 PMCID: PMC3383444 DOI: 10.4161/mge.19233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The sequence corresponding to the first 77 nucleotides of the L1Tc and NARTc non-LTR retrotransposons from Trypanosoma cruzi is an internal promoter (Pr77) that generates abundant, although poorly translatable, un-spliced transcripts. It has been recently described that L1TcRz, an HDV-like ribozyme, resides within the 5'-end of the RNA from the L1Tc and NARTc retrotransposons. Remarkably, the same first 77 nucleotides of L1Tc/NARTc elements comprise both the Pr77 internal promoter and the HDV-like L1TcRz. The L1TcRz cleaves on the 5'-side of the +1 nucleotide of the L1Tc element insuring that the promoter and the ribozyme functions travel with the transposon during retrotransposition. The ribozyme activity would prevent the mobilization of upstream sequences and insure the individuality of the L1Tc/NARTc copies transcribed from associated tandems. The Pr77/L1TcRz sequence is also found in other trypanosomatid's non-LTR retrotransposons and degenerated retroposons. The possible conservation of the ribozyme activity in a widely degenerated retrotransposon, as the Leishmania SIDERs, could indicate that the presence of this element and the catalytic activity could play some favorable genetic regulation. The functional implications of the Pr77/L1TcRz dual system in the regulation of the L1Tc/NARTc retrotransposons and in the gene expression of trypanosomatids are also discussed in this paper.
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Sánchez-Luque FJ, López MC, Carreira PE, Alonso C, Thomas MC. The wide expansion of hepatitis delta virus-like ribozymes throughout trypanosomatid genomes is linked to the spreading of L1Tc/ingi clade mobile elements. BMC Genomics 2014; 15:340. [PMID: 24884364 PMCID: PMC4035085 DOI: 10.1186/1471-2164-15-340] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 04/24/2014] [Indexed: 01/03/2023] Open
Abstract
Background Hepatitis Delta Virus (HDV)-like ribozymes have recently been found in many mobile elements in which they take part in a mechanism that releases intermediate RNAs from cellular co-transcripts. L1Tc in Trypanosoma cruzi is one of the elements in which such a ribozyme is located. It lies in the so-called Pr77-hallmark, a conserved region shared by retrotransposons belonging to the trypanosomatid L1Tc/ingi clade. The wide distribution of the Pr77-hallmark detected in trypanosomatid retrotransposons renders the potential catalytic activity of these elements worthy of study: their distribution might contribute to host genetic regulation at the mRNA level. Indeed, in Leishmania spp, the pervasive presence of these HDV-like ribozyme-containing mobile elements in certain 3′-untranslated regions of protein-coding genes has been linked to mRNA downregulation. Results Intensive screening of publicly available trypanosomatid genomes, combined with manual folding analyses, allowed the isolation of putatively Pr77-hallmarks with HDV-like ribozyme activity. This work describes the conservation of an HDV-like ribozyme structure in the Pr77 sequence of retrotransposons in a wide range of trypanosomatids, the catalytic function of which is maintained in the majority. These results are consistent with the previously suggested common phylogenetic origin of the elements that belong to this clade, although in some cases loss of functionality appears to have occurred and/or perhaps molecular domestication by the host. Conclusions These HDV-like ribozymes are widely distributed within retrotransposons across trypanosomatid genomes. This type of ribozyme was once thought to be rare in nature, but in fact it would seem to be abundant in trypanosomatid transcripts. It can even form part of the pool of mRNA 3′-untranslated regions, particularly in Leishmania spp. Its putative regulatory role in host genetic expression is discussed. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-340) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Manuel Carlos López
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC, Parque Tecnológico de Ciencias de la Salud, Av, del Conocimiento s/n, 18016 Granada, Spain.
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Rebollo R, Romanish MT, Mager DL. Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet 2012; 46:21-42. [PMID: 22905872 DOI: 10.1146/annurev-genet-110711-155621] [Citation(s) in RCA: 365] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The fact that transposable elements (TEs) can influence host gene expression was first recognized more than 50 years ago. However, since that time, TEs have been widely regarded as harmful genetic parasites-selfish elements that are rarely co-opted by the genome to serve a beneficial role. Here, we survey recent findings that relate to TE impact on host genes and remind the reader that TEs, in contrast to other noncoding parts of the genome, are uniquely suited to gene regulatory functions. We review recent studies that demonstrate the role of TEs in establishing and rewiring gene regulatory networks and discuss the overall ubiquity of exaptation. We suggest that although individuals within a population can be harmed by the deleterious effects of new TE insertions, the presence of TE sequences in a genome is of overall benefit to the population.
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Affiliation(s)
- Rita Rebollo
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.
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Sánchez-Luque FJ, López MC, Macias F, Alonso C, Thomas MC. Identification of an hepatitis delta virus-like ribozyme at the mRNA 5'-end of the L1Tc retrotransposon from Trypanosoma cruzi. Nucleic Acids Res 2011; 39:8065-77. [PMID: 21724615 PMCID: PMC3185411 DOI: 10.1093/nar/gkr478] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
L1Tc is a non-LTR LINE element from Trypanosoma cruzi that encodes its transposition machinery and bears an internal promoter. Herewith, we report the identification of an in vitro active hepatitis delta virus-like ribozyme located in the first 77 nt at the 5′-end of the L1Tc mRNA (L1TcRz). The data presented show that L1TcRz has a co-transcriptional function. Using gel-purified uncleaved RNA transcripts, the data presented indicate that the kinetics of the self-cleaving, in a magnesium-dependent reaction, fits to a two-phase decay curve. The cleavage point identified by primer extension takes place at +1 position of the element. The hydroxyl nature of the 5′-end of the 3′-fragment generated by the cleavage activity of L1TcRz was confirmed. Since we have previously described that the 77-nt long fragment located at the 5′-end of L1Tc has promoter activity, the existence of a ribozyme in L1Tc makes this element to be the first described non-LTR retroelement that has an internal promoter–ribozyme dual function. The L1Tc nucleotides located downstream of the ribozyme catalytic motif appear to inhibit its activity. This inhibition may be influenced by the existence of a specific L1Tc RNA conformation that is recognized by RNase P.
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Affiliation(s)
- Francisco J Sánchez-Luque
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra-CSIC, Parque Tecnológico de Ciencias de Salud, Granada
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Shpiz S, Kwon D, Rozovsky Y, Kalmykova A. rasiRNA pathway controls antisense expression of Drosophila telomeric retrotransposons in the nucleus. Nucleic Acids Res 2008; 37:268-78. [PMID: 19036789 PMCID: PMC2615633 DOI: 10.1093/nar/gkn960] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Telomeres in Drosophila are maintained by the specialized telomeric retrotransposons HeT-A, TART and TAHRE. Sense transcripts of telomeric retroelements were shown to be the targets of a specialized RNA-interference mechanism, a repeat-associated short interfering (rasi)RNA-mediated system. Antisense rasiRNAs play a key role in this mechanism, highlighting the importance of antisense expression in retrotransposon silencing. Previously, bidirectional transcription was reported for the telomeric element TART. Here, we show that HeT-A is also bidirectionally transcribed, and HeT-A antisense transcription in ovaries is regulated by a promoter localized within its 3' untranslated region. A remarkable feature of noncoding HeT-A antisense transcripts is the presence of multiple introns. We demonstrate that sense and antisense HeT-A-specific rasiRNAs are present in the same tissue, indicating that transcripts of both directions may be considered as natural targets of the rasiRNA pathway. We found that the expression of antisense transcripts of telomeric elements is regulated by the RNA silencing machinery, suggesting rasiRNA-mediated interplay between sense and antisense transcripts in the cell. Finally, this regulation occurs in the nucleus since disruption of the rasiRNA pathway leads to an accumulation of TART and HeT-A transcripts in germ cell nuclei.
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Affiliation(s)
- Sergey Shpiz
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Schostak N, Pyatkov K, Zelentsova E, Arkhipova I, Shagin D, Shagina I, Mudrik E, Blintsov A, Clark I, Finnegan DJ, Evgen’ev M. Molecular dissection of Penelope transposable element regulatory machinery. Nucleic Acids Res 2008; 36:2522-9. [PMID: 18319284 PMCID: PMC2377424 DOI: 10.1093/nar/gkm1166] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2007] [Revised: 12/15/2007] [Accepted: 12/18/2007] [Indexed: 11/12/2022] Open
Abstract
Penelope-like elements (PLEs) represent a new class of retroelements identified in more than 80 species belonging to at least 10 animal phyla. Penelope isolated from Drosophila virilis is the only known transpositionally active representative of this class. Although the size and structure of the Penelope major transcript has been previously described in both D. virilis and D. melanogaster transgenic strains, the architecture of the Penelope regulatory region remains unknown. In order to determine the localization of presumptive Penelope promoter and enhancer-like elements, segments of the putative Penelope regulatory region were linked to a CAT reporter gene and introduced into D. melanogaster by P-element-mediated transformation. The results obtained using ELISA to measure CAT expression levels and RNA studies, including RT-PCR, suggest that the active Penelope transposon contains an internal promoter similar to the TATA-less promoters of LINEs. The results also suggest that some of the Penelope regulatory sequences control the preferential expression in the ovaries of the adult flies by enhancing expression in the ovary and reducing expression in the carcass. The possible significance of the intron within Penelope for the function and evolution of PLEs, and the effect of Penelope insertions on adjacent genes, are discussed.
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Affiliation(s)
- Nataliya Schostak
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Konstantin Pyatkov
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Elena Zelentsova
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Irina Arkhipova
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Dmitrii Shagin
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Irina Shagina
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Elena Mudrik
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Anatolii Blintsov
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Ivan Clark
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - David J. Finnegan
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
| | - Michael Evgen’ev
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia, California Institute of Technology, Pasadena, CA, Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Evrogen JSC, Moscow, Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region, Moscow State University, Moscow, Russia and Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK
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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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Maxwell PH, Belote JM, Levis RW. Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons. Nucleic Acids Res 2006; 34:5498-507. [PMID: 17020919 PMCID: PMC1636488 DOI: 10.1093/nar/gkl709] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Drosophila non-long terminal repeat (non-LTR) retrotransposons TART and HeT-A specifically retrotranspose to chromosome ends to maintain Drosophila telomeric DNA. Relatively little is known, though, about the regulation of their expression and their retrotransposition to telomeres. We have used rapid amplification of cDNA ends (RACE) to identify multiple transcription initiation and polyadenylation sites for sense and antisense transcripts of three subfamilies of TART elements in Drosophila melanogaster. These results are consistent with the production of an array of TART transcripts. In contrast to other Drosophila non-LTR elements, a major initiation site for sense transcripts was mapped near the 3′ end of the TART 5′-untranslated region (5′-UTR), rather than at the start of the 5′-UTR. A sequence overlapping this sense start site contains a good match to an initiator consensus for the transcription start sites of Drosophila LTR retrotransposons. Interestingly, analysis of 5′ RACE products for antisense transcripts and the GenBank EST database revealed that TART antisense transcripts contain multiple introns. Our results highlight differences between transcription of TART and of other Drosophila non-LTR elements and they provide a foundation for testing the relationship between exceptional aspects of TART transcription and TART's specialized role at telomeres.
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Affiliation(s)
- Patrick H Maxwell
- Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA.
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Bringaud F, Ghedin E, Blandin G, Bartholomeu DC, Caler E, Levin MJ, Baltz T, El-Sayed NM. Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements. Mol Biochem Parasitol 2005; 145:158-70. [PMID: 16257065 DOI: 10.1016/j.molbiopara.2005.09.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 09/25/2005] [Accepted: 09/27/2005] [Indexed: 11/22/2022]
Abstract
The ingi and L1Tc non-LTR retrotransposons--which constitute the ingi clade--are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5'-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.
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Affiliation(s)
- Frédéric Bringaud
- Laboratoire de Génomique Fonctionnelle Des Trypanosomatides, Université Victor Segalen Bordeaux 2, UMR-5162 CNRS, 146 Rue Léo Saignat, 33076 Bordeaux Cedex, France.
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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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Pardue ML, DeBaryshe PG. Retrotransposons provide an evolutionarily robust non-telomerase mechanism to maintain telomeres. Annu Rev Genet 2004; 37:485-511. [PMID: 14616071 DOI: 10.1146/annurev.genet.38.072902.093115] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Telomere molecular biology is far more complex than originally thought. Understanding biological systems is aided by study of evolutionary variants, and Drosophila telomeres are remarkable variants. Drosophila lack telomerase and the arrays of simple repeats generated by telomerase in almost all other organisms; instead, Drosophila telomeres are long tandem arrays of two non-LTR retrotransposons, HeT-A and TART. These are the first transposable elements found to have a bona fide role in cell structure, revealing an unexpected link between telomeres and what is generally considered to be parasitic DNA. In addition to providing insight into the cellular functions performed by telomeres, analysis of HeT-A and TART is providing insight into the evolution of chromosomes, retrotransposons, and retroviruses. Recent studies show that retrotransposon telomeres constitute a robust system for maintaining chromosome ends. These telomeres are now known to predate the separation of extant Drosophila species, allowing ample time for elements and hosts to coevolve interesting mechanisms.
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Affiliation(s)
- Mary-Lou Pardue
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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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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Mason JM, Konev AY, Golubovsky MD, Biessmann H. Cis- and trans-acting influences on telomeric position effect in Drosophila melanogaster detected with a subterminal transgene. Genetics 2003; 163:917-30. [PMID: 12663532 PMCID: PMC1462480 DOI: 10.1093/genetics/163.3.917] [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] [Indexed: 11/14/2022] Open
Abstract
One model of telomeric position effect (TPE) in Drosophila melanogaster proposes that reporter genes in the vicinity of telomeres are repressed by subterminal telomere-associated sequences (TAS) and that variegation of these genes is the result of competition between the repressive effects of TAS and the stimulating effects of promoters in the terminal HeT-A transposon array. The data presented here support this model, but also suggest that TPE is more complex. Activity of a telomeric white reporter gene increases in response to deletion of some or all of the TAS on the homolog. Only transgenes next to fairly long HeT-A arrays respond to this trans-interaction. HeT-A arrays of 6-18 kb respond by increasing the number of dark spots on the eye, while longer arrays increase the background eye color or increase the number of spots sufficiently to cause them to merge. Thus, expression of a subtelomeric reporter gene is influenced by the telomere structure in cis and trans. We propose that the forces involved in telomere length regulation in Drosophila are the underlying forces that manifest themselves as TPE. In the wild-type telomere TAS may play an important role in controlling telomere elongation by repressing HeT-A promoter activity. Modulation of this repression by the homolog may thus regulate telomere elongation.
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Affiliation(s)
- James M Mason
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709-2233, USA
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George JA, Pardue ML. The promoter of the heterochromatic Drosophila telomeric retrotransposon, HeT-A, is active when moved into euchromatic locations. Genetics 2003; 163:625-35. [PMID: 12618401 PMCID: PMC1462444 DOI: 10.1093/genetics/163.2.625] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Drosophila telomeric retrotransposon, HeT-A, is found only in heterochromatin; therefore, its promoter must function in this chromatin environment. Studies of position effect variegation suggest that promoters of heterochromatic genes are very different from euchromatic promoters, but this idea has not been tested with isolated promoter sequences. The HeT-A promoter is the first heterochromatin promoter to be isolated and it is of interest to investigate its activity when removed from telomeric heterochromatin. This promoter was initially characterized by testing reporter constructs in transient transfection of cultured cells, an environment that may approximate its endogenous heterochromatin. We now report P-element-mediated transpositions of these constructs, testing the function of different parts of the putative promoter in euchromatin. Expression of endogenous HeT-A RNA shows marked developmental regulation and accumulates preferentially in replicating diploid tissues. HeT-A promoter constructs are active in all euchromatic locations tested and some display aspects of endogenous HeT-A stage- and cell-type expression programs. The activity of each promoter construct in euchromatic locations is also generally consistent with its activity in the transient transfection tests; a possibly significant exception is one sequence segment that appreciably enhanced activity in transient transfection but repressed promoter activity in euchromatin.
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Affiliation(s)
- Janet A George
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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15
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Ohta Y, Noma K, Tsuchimoto S, Ohtsubo E, Ohtsubo H. Expression of Arabidopsis LINEs from two promoters. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 32:809-818. [PMID: 12472695 DOI: 10.1046/j.1365-313x.2002.01466.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Most Arabidopsis long interspersed elements (LINEs, called ATLNs) have two open reading frames, orf1 and orf2. In the 5' untranslated regions (UTRs) located upstream of orf1, the most proximal segments of tens of base pairs long are not homologous even in two ATLN members with almost identical sequences. In this study, we first show that RT-PCR products from ATLN39, a member of ATLN, can be detected only in total RNA from the hypomethylation mutant ddm1 or from suspension-cultured cells treated with a DNA methylation inhibitor 5-azacytidine, indicating that the expression of ATLN39 is negatively regulated by DNA methylation. We then show that orf1 fused in frame with the luciferase (luc) gene is expressed in suspension-cultured cells of A. thaliana when the 5' UTR is present in the region upstream of orf1. Analysis of deletion in the 5' UTR revealed that the 5' UTR has two promoters, designated here as P1 and P2. Analysis of transcripts by 5' RACE showed that their 5' ends were located at sites immediately upstream of the P1 region or at sites downstream of the P2 region. This observation and the fact that the P1 region contains no TATA sequence indicate that P1 is an internal promoter that initiates transcription from sites upstream of the promoter. A sequence containing GGCGA with a CpG methylatable site is conserved in the P1 regions in members closely related to ATLN39. The P2 region, however, contains the TATA sequence as well as another sequence with a CpG site. The TATA sequence is conserved in members closely related to ATLN39 but not in the other ATLN members, suggesting that P2 is the promoter uniquely present in the ATLN39-related members. Transcripts from promoter P1 can be used as templates to give new copies proficient in retroposition, but those from promoter P2 cannot because of the lack of the proximal half region of the 5' UTR sequence. Transcripts from promoter P2, as well as those from promoter P1 can, however, be used for the production of a sufficient amount of proteins for retroposition. Only a short sequence of the non-homologous region is present at the 5' ends of transcripts from promoter P1, thus suggesting that the non-homologous regions seen in the most proximal regions in ATLN elements are not generated in transcription.
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Affiliation(s)
- Yoshizu Ohta
- Institute of Molecular and Cellular Biosciences, the University of Tokyo, Bunkyo-ku, Japan
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16
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Chambeyron S, Bucheton A, Busseau I. Tandem UAA repeats at the 3'-end of the transcript are essential for the precise initiation of reverse transcription of the I factor in Drosophila melanogaster. J Biol Chem 2002; 277:17877-82. [PMID: 11882661 DOI: 10.1074/jbc.m200996200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Non-long terminal repeat retrotransposons, widespread among eukaryotic genomes, transpose by reverse transcription of an RNA intermediate. Some of them, like L1 in the human, terminate at the 3'-end with a poly(dA) stretch whereas others, like the I factor in Drosophila melanogaster, have instead a short sequence repeated in tandem. This suggests different requirements for the initiation of reverse transcription. Here, we have used an RNA circularization/reverse transcription-PCR technique to analyze the 5'- and 3'-ends of the full-length transcripts produced by the I factor at the time of active retrotransposition. These transcripts are capped and polyadenylated similar to conventional messenger RNAs. We have analyzed the 3'-ends of transcripts and transposed copies produced by I elements mutated at the 3'-ends. Transcripts devoid of tandem UAA repeats, although capable of building the components of the retrotransposition machinery, are inefficiently used as retrotransposition intermediates. Such transcripts produce rare new integrated copies issued from the inaccurate initiation of reverse transcription near the 3'-end of the element. The tandem UAA repeats at the 3'-end of the transcripts of I are required for the efficient and precise initiation of reverse transcription. This strong specificity of the I factor reverse transcriptase for its own transcript has implications for the impact of I factor retrotransposition on the host genome.
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Affiliation(s)
- Séverine Chambeyron
- Institut de Génétique Humaine, CNRS, 141 Rue de la Cardonille, 34396 Montpellier Cedex 5, France
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17
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Kubo Y, Okazaki S, Anzai T, Fujiwara H. Structural and phylogenetic analysis of TRAS, telomeric repeat-specific non-LTR retrotransposon families in Lepidopteran insects. Mol Biol Evol 2001; 18:848-57. [PMID: 11319268 DOI: 10.1093/oxfordjournals.molbev.a003866] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
TRAS1 is a non-LTR retrotransposon inserted specifically into the telomeric repeat (TTAGG)(n) in the silkworm, Bombyx mori. To characterize the evolutionary origin of TRAS-like elements, we identified seven TRAS families (TRAS3, TRAS4, TRAS5, TRAS6, TRASY, TRASZ, and TRASW) from B. mori and four elements from two Lepidoptera, Dictyoploca japonica (TRASDJ) and Samia cynthia ricini (TRASSC3, TRASSC4, and TRASSC9). More than 2,000 copies of various Bombyx TRAS elements accumulated within (TTAGG)(n) sequences as unusual but orderly tandem repeats. The 5' and 3' regions were highly conserved within each class of Bombyx TRAS elements without truncation. This suggests that distinct classes of TRAS have been maintained independently by retrotransposition into (TTAGG)(n). The phylogenetic tree of site-specific retroelements showed that nine TRAS families in Lepidoptera constitute a single phylogenetic group that is closely related to the R1 family that inserts specifically into arthropod 28S rDNA. The higher amino acid sequence identity from endonuclease (EN) to reverse transcriptase (RT) domains between TRAS groups (about 37%-70%) than among TRAS elements and R1Bm (about 25%-30%), may reflect the presence of some DNA structure responsible for their target specificity. Sequence comparison from EN to RT domains among non-LTR elements revealed several regions conserved only within TRAS elements. We found a highly conserved region that resembles the Myb-like DNA-binding structure, between the EN and RT domains. These regions may be involved in site-specific integration of TRAS elements into the (TTAGG)(n) telomeric repeats.
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Affiliation(s)
- Y Kubo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
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18
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Busseau I, Berezikov E, Bucheton A. Identification of Waldo-A and Waldo-B, two closely related non-LTR retrotransposons in Drosophila. Mol Biol Evol 2001; 18:196-205. [PMID: 11158378 DOI: 10.1093/oxfordjournals.molbev.a003793] [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
We have identified two novel, closely related subfamilies of non-long-terminal-repeat (non-LTR) retrotransposons in Drosophila melanogaster, the Waldo-A and Waldo-B subfamilies, that are in the same lineage as site-specific LTR retrotransposons of the R1 clade. Both contain potentially active copies with two large open reading frames, having coding capacities for a nucleoprotein as well as endonuclease and reverse transcriptase activities. Many copies are truncated at the 5' end, and most are surrounded by target site duplications of variable lengths. Elements of both subfamilies have a nonrandom distribution in the genome, often being inserted within or very close to (CA)(n) arrays. At the DNA level, the longest elements of Waldo-A and Waldo-B are 69% identical on their entire length, except for the 5' untranslated regions, which have a mosaic organization, suggesting that one arose from the other following new promoter acquisition. This event occurred before the speciation of the D. melanogaster subgroup of species, since both Waldo-A and Waldo-B coexist in other species of this subgroup.
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Affiliation(s)
- I Busseau
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, 141 rue de la Cardonille, 34396 Montpellier cedex 05, France.
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19
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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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20
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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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21
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22
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Takahashi H, Fujiwara H. Transcription analysis of the telomeric repeat-specific retrotransposons TRAS1 and SART1 of the silkworm Bombyx mori. Nucleic Acids Res 1999; 27:2015-21. [PMID: 10198435 PMCID: PMC148415 DOI: 10.1093/nar/27.9.2015] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The telomeres of the silkworm Bombyx mori consist of (TTAGG)n repeats and harbor a large number of sequence-specific non-LTR retrotransposons such as TRAS1 and SART1. In order to ascertain if TRAS1 and SART1 are transcribed in vivo and if there is a novel transcription mechanism peculiar to the sequence-specific retrotransposons, we studied their transcription. We detected transcripts of TRAS1 and SART1 by northern hybridization in many tissues and the BmN4 cell line of the silkworm. 5'-Rapid amplification of cDNA ends analysis showed that transcription of both elements was initiated precisely from their own 5'-ends and that most of their genomic copies contained these initiation sites. TRAS1 contained an internal promoter and positively regulating elements in the +1/+581 nucleotides in its 2432 bp 5'-untranslated region (UTR). We could not, however, detect any promoter activity in the SART1 5'-UTR. This difference may be related to the fact that only TRAS1 contained an initiator-like element at its 5'-end. Placing 1-52 units of the telomeric repeat (TTAGG)n upstream of TRAS1 reduced transcription 5-fold. The evidence suggests that most of the TRAS1 genomic copies within the telomeric repeats are weakly transcribed in vivo.
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Affiliation(s)
- H Takahashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,Tokyo 113-0033, Japan
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23
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Seleme MC, Busseau I, Malinsky S, Bucheton A, Teninges D. High-frequency retrotransposition of a marked I factor in Drosophila melanogaster correlates with a dynamic expression pattern of the ORF1 protein in the cytoplasm of oocytes. Genetics 1999; 151:761-71. [PMID: 9927467 PMCID: PMC1460479 DOI: 10.1093/genetics/151.2.761] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To study the expression of the I factor, a non-long-terminal-repeat retrotransposon responsible for I-R hybrid dysgenesis in Drosophila melanogaster, we have tagged the ORF1 protein (ORF1p) by inserting the HA epitope in its N-terminal region. In transgenic flies, this modification is compatible with a high rate of autonomous transposition and allows direct estimation of the transposition frequency. I factor transposes in the germline of females (SF) that are daughters from crosses between I strain males (which contain active copies of the I factor) and R strain females (which do not). We analyzed the expression pattern of ORF1p by indirect immunofluorescence. Its expression correlates with retrotransposition. During oogenesis ORF1p appears unexpectedly as a cytoplasmic product, which accumulates with a specific pattern into the oocyte. A comparison of the expression patterns under conditions that modify the transposing activity of the element clarifies some aspects of I-factor functioning in the transposition process.
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Affiliation(s)
- M C Seleme
- Centre de Génétique Moléculaire, CNRS, 91198 Gif sur Yvette Cedex, France
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24
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de La Roche Saint André C, Bregliano JC. Evidence for a multistep control in transposition of I factor in Drosophila melanogaster. Genetics 1998; 148:1875-84. [PMID: 9560401 PMCID: PMC1460065 DOI: 10.1093/genetics/148.4.1875] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Drosophila melanogaster strains belong to one of two interactive categories, inducer (I) or reactive (R), with respect to the I-R system of hybrid dysgenesis. The dysgenic interaction results from the presence of several transposition-competent copies of a LINE-like element, the I factor, only in the genome of I strains. When a cross is performed between I males and R females, I factor transposes at high frequency in the germ line of F1 daughters, known as SF females. This transposition burst results in the sterility of SF females. I factor transposes by reverse transcription of a full-length transcript. Specific RT-PCR experiments were done to compare the amount of I factor transcript in samples corresponding to various transposition frequencies. The sensitivity of the method allowed the ready detection of the I factor RNA in every tissue and genetic background examined. Comparison of amplification signals suggests that I factor activity in ovaries is regulated at different levels. First, the amount of I factor RNA subjected to negative and positive regulation. Whereas the negative control, which limits transposition in nonpermissive contexts, may be exerted by an I factor encoded repressor function, the positive control is linked to reactivity level, a cellular state maternally inherited from R mothers. Additionally, negative regulation is also exerted downstream of I factor RNA. This differs notably from previous conclusions in which transcription was envisaged as the main level of regulation of the I factor transposition.
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25
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Busseau I, Malinsky S, Balakireva M, Chaboissier MC, Teninges D, Bucheton A. A genetically marked I element in Drosophila melanogaster can be mobilized when ORF2 is provided in trans. Genetics 1998; 148:267-75. [PMID: 9475738 PMCID: PMC1459780 DOI: 10.1093/genetics/148.1.267] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
I factors in Drosophila melanogaster are non-LTR retrotransposons similar to mammalian LINEs. They transpose at very high frequencies in the germ line of SF females resulting from crosses between reactive females, devoid of active I factors, and inducer males, containing active I factors. The vermilion marked IviP2 element was designed to allow easy phenotypical screening for retrotransposition events. It is deleted in ORF2 and therefore cannot produce reverse transcriptase. IviP2 can be mobilized at very low frequencies by actively transposing I factors in the germ line of SF females. This paper shows that IviP2 can be mobilized more efficiently in the germ line of strongly reactive females in the absence of active I factors, when it is trans-complemented by the product of ORF2 synthesized from the hsp70 heat-shock promoter. This represents a promising step toward the use of marked I elements to study retrotransposition and as tools for mutagenesis.
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Affiliation(s)
- I Busseau
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France.
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26
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Laurençon A, Gay F, Ducau J, Bregliano JC. Evidence for an inducible repair-recombination system in the female germ line of Drosophila melanogaster. III. Correlation between reactivity levels, crossover frequency and repair efficiency. Genetics 1997; 146:1333-44. [PMID: 9258678 PMCID: PMC1208079 DOI: 10.1093/genetics/146.4.1333] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We previously reported evidence that the so-called reactivity level, a peculiar cellular state of oocytes that regulates the frequency of transposition of I factor, a LINE element-like retrotransposon, might be one manifestation of a DNA repair system. In this article, we report data showing that the reactivity level is correlated with the frequency of crossing over, at least on the X chromosome and on the pericentromeric region of the third chromosome. Moreover, a check for X-chromosome losses and recessive lethals produced after gamma irradiation in flies with different reactivity levels, but common genetic backgrounds, brings more precise evidence for the relationship between reactivity levels and DNA repair. Those results support the existence of a repair-recombination system whose efficiency is modulated by endogenous and environmental factors. The implications of this biological system in connecting genomic variability and environment may shed new lights on adaptative mechanisms. We propose to call it VAMOS for variability modulation system.
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Affiliation(s)
- A Laurençon
- Institut de Biologie du Developpement de Marseille, France
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27
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Minchiotti G, Di Nocera PP. Alternative activation of transcriptional initiators in Drosophila melanogaster LINE promoters. FEBS Lett 1997; 411:189-94. [PMID: 9271203 DOI: 10.1016/s0014-5793(97)00689-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the Drosophila I, F and Doc LINEs, basal transcription is ensured by the functional interaction of initiator sequences with intragenic regulatory segments (B regions) which comprise distinct functional modules. Removing the B regions, as changing their composition or location, allowed different activators to stimulate transcription from novel initiators both in Doc and F promoters. The use of distinct initiators plausibly reflects the assembly of transcriptional complexes in which TFIID assumes alternative spatial conformations. The response of I, F and Doc promoters to the same enhancer is significantly influenced by the number, position and type of core elements present.
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Affiliation(s)
- G Minchiotti
- Dipartimento di Biologia e Patologia Cellulare e Molecolare L. Califano, Universita degli Studi di Napoli Federico II, Naples, Italy
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28
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Minchiotti G, Contursi C, Di Nocera PP. Multiple downstream promoter modules regulate the transcription of the Drosophila melanogaster I, Doc and F elements. J Mol Biol 1997; 267:37-46. [PMID: 9096205 DOI: 10.1006/jmbi.1996.0860] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The basal promoters of three Drosophila long interspersed nuclear elements (LINEs), the I factor and the F and Doc elements, have the same architecture. In each, transcription is directed by an initiator which is faithfully and efficiently recognized only when flanked 3' by a DNA segment approximately 20 bp in length called the B region. The B regions of the three promoters are interchangeable and have a complex structure, comprising three functionally distinct elements: de1, de2 and de3. While de2 is relatively conserved, fitting the consensus RGACGTGY, de1 and de3 vary among the three promoters. At different levels, each downstream element is able to ensure accurate recognition of the initiator. The de2 domain stimulates transcription of the F, I and Doc promoters to the same extent. In contrast, the I de1 domain stimulates transcription much more efficiently than the corresponding domains of the F and Doc elements. The finding that de2 is selectively required in order to detect full activity of enhancer sequences found in the F element suggests that de1 and de2 interact with different proteins. The B regions can be replaced by and synergize with a TATA element, can functionally substitute for downstream promoter sequences in the Drosophila hsp70 gene, and significantly activate the mouse terminal deoxynucleotidyl transferase initiator. Our data suggest that the B regions stimulate transcription by providing sites of interaction for the TFIID complex. Sequences homologous to the del to de3 array are found downstream from the transcription start site(s) both in TATA-less and TATA-containing promoters.
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Affiliation(s)
- G Minchiotti
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, L. Califano, Università degli Studi di Napoli Federico II, Italy
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29
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Danilevskaya ON, Arkhipova IR, Traverse KL, Pardue ML. Promoting in tandem: the promoter for telomere transposon HeT-A and implications for the evolution of retroviral LTRs. Cell 1997; 88:647-55. [PMID: 9054504 DOI: 10.1016/s0092-8674(00)81907-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
HeT-A elements are non-long terminal repeat (non-LTR) retrotransposons found in head-to-tail arrays on Drosophila chromosome ends, where they form telomeres. We report that HeT-A promoter activity is located in the 3' end of the element, unlike the 5' location seen for other non-LTR retrotransposons. In HeT-A arrays the 3' sequence of one element directs transcription of its downstream neighbor. Because the upstream promoter has the same sequence as the 3' end of the transcribed element, the HeT-A promoter is effectively equivalent to a 5' LTR in both structure and function. Retroviruses and LTR retrotransposons have their promoters and transcription initiation sites in their 5' LTRs. Thus HeT-A appears to have the structure of an evolutionary intermediate between non-LTR and LTR retrotransposons.
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Affiliation(s)
- O N Danilevskaya
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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30
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Blinov AG, Sobanov YV, Scherbik SV, Aimanova KG. The Chironomus (Camptochironomus) tentans genome contains two non-LTR retrotransposons. Genome 1997; 40:143-50. [PMID: 9061921 DOI: 10.1139/g97-021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A cDNA library from salivary gland cells of Chironomus tentans was screened with a probe containing the NLRCth1 non-LTR (long terminal repeat) retrotransposon from Chironomus thummi. Several positive clones were obtained and one of them, p62, was characterized by in situ hybridization and sequencing. The sequencing analysis showed that this clone contained a 4607 bp nucleotide sequence of a new transposable element that hybridized in situ to more than 100 sites over all four C. tentans chromosomes. The detailed analysis of this sequence revealed the presence of the 3'-end of open reading frame 1 (ORF1), a complete ORF2, and a 1.3-kb 3'-end untranslated region (UTR). The new element has been designated NLRCt2 (non-LTR retrotransposon 2 from C. tentans). A comparison of the nucleotide sequences of NLRCth1 and NLRCt2 showed 30% similarity in the region of ORF1 and 70% similarity in the region of ORF2. Based on the results of Southern blot analysis, two transposable elements have been found in the C. tentans genome, one of which is identical to NLRCth1 from C. thummi. This may be explained by horizontal transmission. The second element, NLRCt2, has been found in two different forms in the C. tentans genome. These can be distinguished by the presence of the 1.3-kb 3'-end UTR in one of the forms. Since the cDNA clone investigated was isolated from a tissue-specific cDNA library, the data showed that NRLCt2 is expressed in somatic cells.
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Affiliation(s)
- A G Blinov
- Institute of Cytology and Genetics, Siberian Department of Russian Academy of Sciences, Novosibirsk, Russia.
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31
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Pardue ML, Danilevskaya ON, Traverse KL, Lowenhaupt K. Evolutionary links between telomeres and transposable elements. Genetica 1997. [PMID: 9440260 DOI: 10.1007/978-94-011-4898-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Transposable elements are abundant in the genomes of higher organisms but are usually thought to affect cells only incidentally, by transposing in or near a gene and influencing its expression. Telomeres of Drosophila chromosomes are maintained by two non-LTR retrotransposons, HeT-A and TART. These are the first transposable elements with identified roles in chromosome structure. We suggest that these elements may be evolutionarily related to telomerase; in both cases an enzyme extends the end of a chromosome by adding DNA copied from an RNA template. The evolution of transposable elements from chromosomal replication mechanisms may have occurred multiple times, although in other organisms the new products have not replaced the endogenous telomerase, as they have in Drosophila. This is somewhat reminiscent of the oncogenes that have arisen from cellular genes. Perhaps the viruses that carry oncogenes have also arisen from cellular genetic systems.
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Affiliation(s)
- M L Pardue
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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32
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Udomkit A, Forbes S, McLean C, Arkhipova I, Finnegan DJ. Control of expression of the I factor, a LINE-like transposable element in Drosophila melanogaster. EMBO J 1996; 15:3174-81. [PMID: 8670818 PMCID: PMC450260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
I factors are LINE-like transposable elements in the genome of Drosophila melanogaster. They normally transpose infrequently but are activated in the germline of female progeny of crosses between males of a strain that contains complete elements, an I or inducer strain and females of a strain that does not, an R or reactive strain. This causes a phenomenon known as I-R hybrid dysgenesis. We have previously shown that the I factor promoter lies between nucleotides 1 and 30. Here we demonstrate that expression of this promoter is regulated by nucleotides 41-186 of the I factor. This sequence can act as an enhancer as it stimulates expression of the hsp7O promoter in ovaries in the absence of heat-shock. Within this region there is a site that is required for promoter activity and that is recognized by a sequence-specific binding protein. We propose that this protein contributes to the enhancer activity of nucleotides 41-186 and that reduced I factor expression in inducer strains is due to titration of this protein or others that interact with it.
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Affiliation(s)
- A Udomkit
- Institute of Cell and Molecular Biology, University of Edinburgh, UK
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33
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Hochstenbach R, Harhangi H, Schouren K, Bindels P, Suijkerbuijk R, Hennig W. Transcription of gypsy elements in a Y-chromosome male fertility gene of Drosophila hydei. Genetics 1996; 142:437-46. [PMID: 8852843 PMCID: PMC1206978 DOI: 10.1093/genetics/142.2.437] [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: 02/02/2023] Open
Abstract
We have found that defective gypsy retrotransposons are a major constituent of the lampbrush loop pair Nooses in the short arm of the Y chromosome of Drosophila hydei. The loop pair is formed by male fertility gene Q during the primary spermatocyte stage of spermatogenesis, each loop being a single transcription unit with an estimated length of 260 kb. Using fluorescent in situ hybridization, we show that throughout the loop transcripts gypsy elements are interspersed with blocks of a tandemly repetitive Y-specific DNA sequence, ay1. Nooses transcripts containing both sequence types show a wide size range on Northern blots, do not migrate to the cytoplasm, and are degraded just before the first meiotic division. Only one strand of ay1 and only the coding strand of gypsy can be detected in the loop transcripts. However, as cloned genomic DNA fragments also display opposite orientations of ay1 and gypsy, such DNA sections cannot be part of the Nooses. Hence, they are most likely derived from the flanking heterochromatin. The direction of transcription of ay1 and gypsy thus appears to be of a functional significance.
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Affiliation(s)
- R Hochstenbach
- Department of Molecular and Developmental Genetics, Catholic University of Nijmegen, Netherlands
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34
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Contursi C, Minchiotti G, Di Nocera PP. Identification of sequences which regulate the expression of Drosophila melanogaster Doc elements. J Biol Chem 1995; 270:26570-6. [PMID: 7592878 DOI: 10.1074/jbc.270.44.26570] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Long interspersed nuclear elements (LINEs) are mobile DNA elements which propagate by reverse transcription of RNA intermediates. LINEs lack long terminal repeats, and their expression is controlled by promoters located inside to the transcribed region of unit-length DNA copies. Doc elements constitute one of the seven families of LINEs found in Drosophila melanogaster. Plasmids in which the chloramphenicol acetyltransferase (CAT) gene is preceded by DNA segments from different Doc family members were used as templates for transient expression assays in Drosophila S2 cells. Transcription is initiated at the 5' end of Doc elements within hexamers fitting the consensus (C/G)AYTCG and is regulated by a DNA region which is located approximately 20 base pairs (bp) downstream from the RNA start site(s). The region includes a sequence (RGACGTGY motif, or DE2) which stimulates transcription in other Drosophila LINEs, and two adjacent elements, DE1 and DE3. Moving the downstream region either 4 bp away from, or 5 bp closer to the RNA start site region inhibited transcription. Sequences located approximately 200 bp downstream from the Doc 5' end repressed CAT expression in an orientation- and position-dependent manner. The inhibition reflects impaired translation of the CAT gene possibly consequent to the interaction of specific Doc RNA sequences with a cellular component.
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Affiliation(s)
- C Contursi
- Dipartimento di Biologia e Patologie Cellulare e Molecolare L. Califano, Università degli Studi di Napoli Federico II, Italy
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35
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Bregliano JC, Laurençon A, Degroote F. Evidence for an inducible repair-recombination system in the female germ line of Drosophila melanogaster. I. Induction by inhibitors of nucleotide synthesis and by gamma rays. Genetics 1995; 141:571-8. [PMID: 8647393 PMCID: PMC1206756 DOI: 10.1093/genetics/141.2.571] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In the I-R system of hybrid dysgenesis in Drosophila melanogaster, the transposition frequency of I factor, a LINE element-like retrotransposon, is regulated by the reactivity level of the R mother. This reactivity is a cellular state maternally inherited but chromosomally determined, which has been shown to undergo heritable, cumulative and reversible changes with aging and some environmental conditions. We propose the hypothesis that this reactivity level is one manifestation of an inducible repair-recombination system whose biological role might be analogous to the SOS response in bacteria. In this paper, we show that inhibitors of DNA synthesis and gamma rays enhance the reactivity level in a very similar way. This enhancement is heritable, cumulative and reversible.
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Affiliation(s)
- J C Bregliano
- Laboratoire de Génétique et Physiologie du Developpement, Marseille-Luminy, France
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36
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Laurençon A, Bregliano JC. Evidence for an inducible repair-recombination system in the female germ line of Drosophila melanogaster. II. Differential sensitivity to gamma rays. Genetics 1995; 141:579-85. [PMID: 8647394 PMCID: PMC1206757 DOI: 10.1093/genetics/141.2.579] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In a previous paper, we reported that the reactivity level, which regulates the frequency of transposition of I factor, a LINE element-like retrotransposon, is enhanced by the same agents that induce the SOS response in Escherichia coli. In this report, we describe experimental evidence that, for identical genotypes, the reactivity levels correlate with the sensitivity of oogenesis to gamma rays, measured by the number of eggs laid and by frequency of dominant lethals. This strongly supports the hypothesis that the reactivity level is one manifestation of an inducible DNA repair system taking place in the female germ line of Drosophila melanogaster. The implications of this finding for the understanding of the regulation of I factor are discussed and some other possible biological roles of this system are outlined.
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Affiliation(s)
- A Laurençon
- Laboratoire de Génétique et Physiologie du Développement, Marseille-Luminy, France
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37
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Jensen S, Cavarec L, Gassama MP, Heidmann T. Defective I elements introduced into Drosophila as transgenes can regulate reactivity and prevent I-R hybrid dysgenesis. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:381-90. [PMID: 7565601 DOI: 10.1007/bf02191637] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The I-R hybrid dysgenesis syndrome is characterized by a high level of sterility and I element transposition, occurring in the female offspring of crosses between males of inducer (I) strains, which contain full-length transposable I elements, and females of reactive (R) strains, devoid of functional I elements. The intensity of the syndrome in the dysgenic cross is essentially dependent on the reactivity level of the R females, which is ultimately controlled by still unresolved polygenic chromosomal determinants. In the work reported here, we have introduced a transposition-defective I element with a 2.6 kb deletion within its second open reading frame into a highly reactive R strain, by P-mediated transgenesis. We demonstrate that this defective I element gradually alters the level of reactivity in the three independent transgenic lines that were obtained, over several generations. After > 15 generations, the transgenic Drosophila show strongly reduced reactivity, and finally become refractory to hybrid dysgenesis, without, however, acquiring the inducer phenotype. Induction of a low reactivity level is reversible--reactivity again increases upon transgene removal--and is maternally inherited, as observed for the control of reactivity in natural R strains. These results demonstrate that defective I elements introduced as single-copy transgenes can act as regulators of reactivity, and suggest that some of the ancestral defective pericentromeric I elements that can be found in all reactive strains could be the molecular determinants of reactivity.
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Affiliation(s)
- S Jensen
- Institut Gustave Roussy, CNRS URA147, Villejuif, France
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38
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Chaboissier MC, Bornecque C, Busseau I, Bucheton A. A genetically tagged, defective I element can be complemented by actively transposing I factors in the germline of I-R dysgenic females in Drosophila melanogaster. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:434-8. [PMID: 7565607 DOI: 10.1007/bf02191643] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Non-LTR retrotransposons, also known as LINEs, transpose by reverse transcription of an RNA intermediate. Their mechanism of transposition is apparently different from that of retrotransposons and similar to that of proviruses of retroviruses. The I factor is responsible for the I-R system of hybrid dysgenesis in Drosophila melanogaster. Inducer strains contain several functional I factors whereas reactive strains do not. Transposition of I factors can be experimentally induced: they are stable in inducer strains, but transpose at high frequency in the germline of females, known as SF females, produced by crossing reactive females and inducer males. We have constructed an I element, called IviP2, marked with the vermilion gene, the coding sequence of which was interrupted by an intron. Splicing of the intron can only occur in the transcript initiated from the I element promoter. Transposed copies expressing a wild-type vermilion phenotype were recovered in the germline of SF females in which I factors were actively transposing. This indicates that trans-complementation of a defective I element, deficient for the second open reading frame, by functional I factors can occur in the germline of dysgenic females.
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Affiliation(s)
- M C Chaboissier
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France
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39
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Abstract
Retroelements are genetic entities that exist in both DNA and RNA forms generated by cyclic alternation of transcription and reverse transcription. They have in common a genetic core (the gag-pol core), encoding conserved functions of a structural protein and a replicase. These are supplemented with a variety of cis-acting nucleic acid sequences controlling transcription and reverse transcription. Most retroelements have additional genes with regulatory or adaptive roles, both within the cell and for movement between cells and organisms. These features reflect the variety of mechanisms that have developed to ensure propagation of the elements and their ability to adapt to specific niches in their hosts with which they co-evolve.
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Affiliation(s)
- R Hull
- John Innes Centre, Colney, Norwich, UK
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40
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Chaboissier MC, Lemeunier F, Bucheton A. IR hybrid dysgenesis increases the frequency of recombination in Drosophila melanogaster. Genet Res (Camb) 1995; 65:167-74. [PMID: 7615258 DOI: 10.1017/s0016672300033255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The I factor is a LINE-like transposable element responsible for the I-R system of hybrid dysgenesis in Drosophila melanogaster. Inducer strains of this species contain several I factors whereas reactive strains do not. I factors are stable in inducer strains, but transpose at high frequency in the germ-line of females, known as SF females, produced by crossing reactive females and inducer males. Various abnormalities occur in SF females, most of which result from this high rate of transposition. We report here that recombination is increased in the germ-line of these females. This is a new characteristic of the I-R system of hybrid dysgenesis that might also be associated with transposition of the I factor.
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Affiliation(s)
- M C Chaboissier
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France
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41
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Abstract
A Drosophila Promoter Database containing 252 independent Drosophila melanogaster promoter entries has been compiled. The database and its subsets have been searched for overrepresented sequences. The analysis reveals that the proximal promoter region displays the most dramatic nucleotide sequence irregularities and exhibits a tripartite structure, consisting of TATA at -25/-30 bp, initiator (Inr) at +/- 5 bp and a novel class of downstream elements at +20/+30 bp from the RNA start site. These latter elements are also strand-specific. However, they differ from TATA and Inr in several aspects: (1) they are represented not by a single, but by multiple sequences, (2) they are shorter, (3) their position is less strictly fixed with respect to the RNA start site, (4) they emerge as a characteristic feature of Drosophila promoters and (5) some of them are strongly overrepresented in the TATA-less, but not TATA-containing, subset. About one-half of known Drosophila promoters can be classified as TATA-less. The overall sequence organization of the promoter region is characterized by an extended region with an increase in GC-content and a decrease in A, which contains a number of binding sites for Drosophila transcription factors.
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Affiliation(s)
- I R Arkhipova
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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42
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Minchiotti G, Contursi C, Graziani F, Gargiulo G, Di Nocera PP. Expression of Drosophila melanogaster F elements in vivo. MOLECULAR & GENERAL GENETICS : MGG 1994; 245:152-9. [PMID: 7816022 DOI: 10.1007/bf00283262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drosophila melanogaster F elements are mobile, oligo(A)-terminated DNA sequences that probably propagate by the retrotranscription of RNA intermediates. Polyadenylated transcripts corresponding in size to full-length (4.7 kb) family members were detected in the Drosophila melanogaster Canton-S strain from 2nd larval instar to the adult stage. RNA accumulation reached a maximum in pupae. In the adult, F elements are transcribed in both sexes. F expression is directed in vivo by the intragenic promoter (Fin) located at the 5' end of F. Whole-mount hybridizations were carried out to define the site of synthesis of full-length transcripts found in the ovary. Selective RNA accumulation was not detected in the cytoplasm of any specific cell type. Stained nuclear dots were observed in nurse cells from stage 2-3 to the end of oogenesis. RNase treatment of egg chambers prior to the addition of the probe led to disappearance of the nuclear dots and appearance of a cytoplasmic hybridization signal suggesting leakage of nuclear transcripts. Transgenic lines harbouring the chloramphenicol acetyltransferase (CAT) gene under the control of the Fin promoter were obtained. In independent lines, CAT enzyme levels mirror the ontogenetic profile of F expression drawn from Northern RNA blotting data. An antisense promoter (Fout) that is located downstream from the Fin promoter and transcribe too bords the 5' end of F seems to be constitutively expressed in the fly.
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Affiliation(s)
- G Minchiotti
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Facoltà di Medicina, Università degli Studi di Napoli Federico II, Italy
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43
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Ogura T, Okano K, Tsuchida K, Miyajima N, Tanaka H, Takada N, Izumi S, Tomino S, Maekawa H. A defective non-LTR retrotransposon is dispersed throughout the genome of the silkworm, Bombyx mori. Chromosoma 1994; 103:311-23. [PMID: 7821086 DOI: 10.1007/bf00417878] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The presence of long repetitive sequences is demonstrated in the genome of the silkworm, Bombyx mori. Members of this BMC1 family reveal several features typical of the L1 (long interspersed sequence one) family of mammals, except for species specific elements. The number of BMC1 elements is estimated to be approximately 3500 per haploid genome. Elements containing the full length unit of 5.1 kb are dispersed throughout the genome and their restriction sites are conserved, although most members are preferentially truncated to varying extents at their 5' ends. DNA sequencing indicates that this element contains six tandem repeats of 15 bp CpG-rich sequence in the 5' proximal region. It terminates with a 3' oligo(A) stretch, and is flanked at both ends by a 7-10 bp target sequence duplication. In addition, there is significant evidence for amino acid sequence homology with reverse transcriptase domains of other L1 families, especially F, Doc and Jockey of Drosophila melanogaster. No large open reading frame is present. The BMC1 element is suggested to be dispersed in the genome by a transposition mechanism involving RNA intermediates.
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Affiliation(s)
- T Ogura
- Department of Molecular Cell Biology, Kumamoto University School of Medicine, Japan
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44
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Abstract
Mobile elements known as LINEs are members of a superfamily of repeated DNA conserved from protozoa to man. These sequences propagate by the retrotranscription of RNA intermediates and differ in many respects from retroviruses. Whereas most eukaryotic genomes host a single LINE family, several families of LINE-like sequences or type II retrotransposons coexist in the fruit fly Drosophila melanogaster. Properties and features of these elements are discussed in this work.
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Affiliation(s)
- P P Di Nocera
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Facoltà di Medicina e Chirurgia, Università degli Studi di Napoli, Italy
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45
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Biessmann H, Kasravi B, Bui T, Fujiwara G, Champion LE, Mason JM. Comparison of two active HeT-A retroposons of Drosophila melanogaster. Chromosoma 1994; 103:90-8. [PMID: 8055715 DOI: 10.1007/bf00352317] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
HeT-A elements are Drosophila melanogaster LINE-like retroposons that transpose to broken chromosome ends by attaching themselves with an oligo(A) tail. Since this family of elements is believed to be involved in the vital function of telomere elongation in Drosophila, it is important to understand their transposition mechanism and the molecular aspects of activity. By comparison of several elements we have defined here the unit length of HeT-A elements to be approximately 6 kb. Also, we studied an active HeT-A element that had transposed very recently to the end of a terminally deleted X chromosome. The 12 kb of newly transposed DNA consisted of a tandem array of three different HeT-A elements joined by oligo(A) tails to each other and to the chromosome end broken in the yellow gene. Such an array may have transposed as a single unit or resulted from rapid successive transpositions of individual HeT-A elements. By sequence comparison with another recently transposed HeT-A element, conserved domains in the single open reading frame (ORF), encoding a gag-like polypeptide, of these elements were defined. We conclude that for transposition an intact ORF is required in cis, while the reverse transcriptase is not encoded on the HeT-A element but is provided in trans. This would make HeT-A elements dependent on an external reverse transcriptase for transposition and establish control of the genome over the activity of HeT-A elements. This distinguishes the Drosophila HeT-A element, which has been implicated in Drosophila telomere elongation, from the other, 'selfish' LINE-like elements.
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Affiliation(s)
- H Biessmann
- Developmental Biology Center, University of California, Irvine 92717
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46
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Abstract
Most of the transposons so far characterized from mosquito genomes are retroelements which seem to be distributed worldwide. The Juan transposons constitute a family of non-LTR retroelements, or LINE-retroposons, which are dispersed in the genomes of several mosquito species. Three different Juan subfamilies have been characterized, each being amplified in the genomes of many strains, if not all, of a given mosquito species. These subfamilies have been designated respectively Juan-C in Culex pipiens, Juan-Ct in Culex tarsalis and Juan-A in Aedes aegypti. A large number of the Juan retroposons which are amplified in the mosquito genomes are apparently full-length copies and potentially encode the enzymes necessary for their transposition, a nucleic acid binding protein and a reverse transcriptase. However, these complete Juan copies seem to be most frequently transcriptionally silent in insects reared under laboratory conditions. A few of them are transcribed in C. pipiens cells grown in vitro, but from an external promoter, the Juan-C specific RNA being fused to an upstream RNA sequence. Therefore, the transcription of Juan retroposons seems to depend on external promoters which are most frequently inactive. The occurrence and distribution of Juan retroposon subfamilies among mosquito species do not reflect the phylogeny of these species. Furthermore, complete Juan-C and Juan-A copies which are reiterated in strains collected from regions covering different continents are nearly identical. Juan-C copies belonging to geographically different C. pipiens strains display low levels of divergence between their nucleotide sequences and many of the mutations which have occurred among these copies do not alter their coding potential. These results indicate that the Juan retroposons occur as homogeneous subfamilies distributed worldwide and that selective constraints against amino acid change have been acting recently on these elements, despite the fact that they are now highly repeated through mosquito genomes. Therefore, Juan transposons have most probably been recently amplified in mosquito genomes. Each subfamily may have been amplified from one master element present in a unique population which has since spread worldwide. Alternatively, this amplification may have arisen in many mosquito populations, but from highly conserved master elements submitted to selection pressures. Horizontal transfers between species may also have contributed to the spread of these transposons.
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Affiliation(s)
- N Bensaadi-Merchermek
- Laboratoire d'Ecologie Moléculaire, Université de Pau et des Pays de l'Adour, France
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47
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Vaury C, Chaboissier MC, Drake ME, Lajoinie O, Dastugue B, Pélisson A. The Doc transposable element in Drosophila melanogaster and Drosophila simulans: genomic distribution and transcription. Genetica 1994; 93:117-24. [PMID: 7813908 DOI: 10.1007/bf01435244] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The mobile element Doc is similar in structure and coding potential to the LINE families found in various organisms. In this paper, we analyze the insertional and structural polymorphism of this element and show that it appears to have a long evolutionary history in the genome of D. melanogaster. Like the family of I elements, the Doc family seems to display three types of elements: full length elements, defective members that have recently transposed and long since immobilized members common to each D. melanogaster strain. These three classes of Doc elements seem to be present in D. simulans, a closely related species to D. melanogaster. Furthermore, we show that Doc is transcribed as a polyadenylated RNA of about 5 kb in length, presumed to be a full length RNA. This transcript is present in different tissues and at different stages of Drosophila development. These results are compared with previous records on the chromosomal distribution of LINEs or other transposable element families. Doc transcription is analyzed in an attempt to understand the link between Doc transcription and transposition.
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Affiliation(s)
- C Vaury
- INSERM unité 384, Faculté de Médecine, Clermont-Ferrand, France
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48
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Busseau I, Chaboissier MC, Pélisson A, Bucheton A. I factors in Drosophila melanogaster: transposition under control. Genetica 1994; 93:101-16. [PMID: 7813907 DOI: 10.1007/bf01435243] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
I factors are responsible for the I-R system of hybrid dysgenesis in Drosophila melanogaster. They belong to the LINE class of mobile elements, which transpose via reverse transcription of a full-length RNA intermediate. I factors are active members of the I element family, which also contains defective I elements that are immobilized within peri-centromeric heterochromatin and represent very old components of the genome. Active I factors have recently invaded natural populations of Drosophila melanogaster, giving rise to inducer strains. Reactive strains, devoid of active I factors, derive from old laboratory stocks established before the invasion. Transposition of I factors is activated at very high frequencies in the germline of hybrid females issued from crosses between females from reactive strains and males from inducer strains. It results in the production of high rates of mutations and chromosomal rearrangements as well as in a particular syndrome of sterility. The frequency of transposition of I factors is dependent on the amount of full-length RNA that is synthesized from an internal promoter. This full-length RNA serves both as an intermediate of transposition and presumably as a messenger for protein synthesis. Regulators of transposition apparently affect transcription initiation from the internal promoter. The data presented here lead to the proposal of a tentative model for transposition.
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Affiliation(s)
- I Busseau
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France
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