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Waymack R, Gad M, Wunderlich Z. Molecular competition can shape enhancer activity in the Drosophila embryo. iScience 2021; 24:103034. [PMID: 34568782 PMCID: PMC8449247 DOI: 10.1016/j.isci.2021.103034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/27/2021] [Accepted: 08/20/2021] [Indexed: 01/12/2023] Open
Abstract
Transgenic reporters allow the measurement of regulatory DNA activity in vivo and consequently have long been useful tools for studying enhancers. Despite their utility, few studies have investigated the effects these reporters may have on the expression of other genes. Understanding these effects is required to accurately interpret reporter data and characterize gene regulatory mechanisms. By measuring the expression of Kruppel (Kr) enhancer reporters in live Drosophila embryos, we find reporters inhibit one another’s expression and that of a nearby endogenous gene. Using synthetic transcription factor (TF) binding site arrays, we present evidence that competition for TFs is partially responsible for the observed transcriptional inhibition. We develop a simple thermodynamic model that predicts competition of the measured magnitude specifically when TF binding is restricted to distinct nuclear subregions. Our findings underline an unexpected role of the non-homogenous nature of the nucleus in regulating gene expression. Live tracking of transcription reveals competition between transgenic reporters Transgenic reporters can also depress the expression of a neighboring gene Expression inhibition is in part because of competition for transcription factors (TFs) Competition is predicted with a model that restricts TFs to sub-nuclear “hubs”
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Affiliation(s)
- Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Mario Gad
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA.,Department of Biology, Boston University, 610 Commonwealth Ave., Boston, MA 02215, USA.,Biological Design Center, Boston University, 610 Commonwealth Avenue, Boston, MA 02215, USA
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Birchler JA. Parallel Universes for Models of X Chromosome Dosage Compensation in Drosophila: A Review. Cytogenet Genome Res 2016; 148:52-67. [PMID: 27166165 DOI: 10.1159/000445924] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
Dosage compensation in Drosophila involves an approximately 2-fold increase in expression of the single X chromosome in males compared to the per gene expression in females with 2 X chromosomes. Two models have been considered for an explanation. One proposes that the male-specific lethal (MSL) complex that is associated with the male X chromosome brings histone modifiers to the sex chromosome to increase its expression. The other proposes that the inverse effect which results from genomic imbalance would tend to upregulate the genome approximately 2-fold, but the MSL complex sequesters histone modifiers from the autosomes to the X to mute this autosomal male-biased expression. On the X, the MSL complex must override the high level of resulting histone modifications to prevent overcompensation of the X chromosome. Each model is evaluated in terms of fitting classical genetic and recent molecular data. Potential paths toward resolving the models are suggested.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Mo., USA
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Omotezako T, Onuma TA, Nishida H. DNA interference: DNA-induced gene silencing in the appendicularian Oikopleura dioica. Proc Biol Sci 2016; 282:20150435. [PMID: 25904672 DOI: 10.1098/rspb.2015.0435] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA interference is widely employed as a gene-silencing system in eukaryotes for host defence against invading nucleic acids. In response to invading double-stranded RNA (dsRNA), mRNA is degraded in sequence-specific manner. So far, however, DNA interference (DNAi) has been reported only in plants, ciliates and archaea, and has not been explored in Metazoa. Here, we demonstrate that linear double-stranded DNA promotes both sequence-specific transcription blocking and mRNA degradation in developing embryos of the appendicularian Oikopleura dioica. Introduced polymerase chain reaction (PCR) products or linearized plasmids encoding Brachyury induced tail malformation and mRNA degradation. This malformation was also promoted by DNA fragments of the putative 5'-flanking region and intron without the coding region. PCR products encoding Zic-like1 and acetylcholine esterase also induced loss of sensory organ and muscle acetylcholinesterase activity, respectively. Co-injection of mRNA encoding EGFP and mCherry, and PCR products encoding these fluorescent proteins, induced sequence-specific decrease in the green or red fluorescence, respectively. These results suggest that O. dioica possesses a defence system against exogenous DNA and RNA, and that DNA fragment-induced gene silencing would be mediated through transcription blocking as well as mRNA degradation. This is the first report of DNAi in Metazoa.
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Affiliation(s)
- Tatsuya Omotezako
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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Abstract
SUMMARY The involvement of RNA interference (RNAi) in heterochromatin formation has become clear largely through studies in the fission yeast Schizosaccharomyces pombe and plants like Arabidopsis thaliana. This article discusses how heterochromatic small interfering RNAs are produced and how the RNAi machinery participates in the formation and function of heterochromatin.
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Affiliation(s)
| | - Danesh Moazed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115-5730
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Duan G, Saint RB, Helliwell CA, Behm CA, Wang MB, Waterhouse PM, Gordon KHJ. C. elegans RNA-dependent RNA polymerases rrf-1 and ego-1 silence Drosophila transgenes by differing mechanisms. Cell Mol Life Sci 2013; 70:1469-81. [PMID: 23224429 PMCID: PMC11113355 DOI: 10.1007/s00018-012-1218-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/19/2012] [Accepted: 11/22/2012] [Indexed: 10/27/2022]
Abstract
Drosophila possesses the core gene silencing machinery but, like all insects, lacks the canonical RNA-dependent RNA polymerases (RdRps) that in C. elegans either trigger or enhance two major small RNA-dependent gene silencing pathways. Introduction of two different nematode RdRps into Drosophila showed them to be functional, resulting in differing silencing activities. While RRF-1 enhanced transitive dsRNA-dependent silencing, EGO-1 triggered dsRNA-independent silencing, specifically of transgenes. The strain w; da-Gal4; UAST-ego-1, constitutively expressing ego-1, is capable of silencing transgene including dsRNA hairpin upon a single cross, which created a powerful tool for research in Drosophila. In C. elegans, EGO-1 is involved in transcriptional gene silencing (TGS) of chromosome regions that are unpaired during meiosis. There was no opportunity for meiotic interactions involving EGO-1 in Drosophila that would explain the observed transgene silencing. Transgene DNA is, however, unpaired during the pairing of chromosomes in embryonic mitosis that is an unusual characteristic of Diptera, suggesting that in Drosophila, EGO-1 triggers transcriptional silencing of unpaired DNA during embryonic mitosis.
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Affiliation(s)
- Guowen Duan
- CSIRO Ecosystem Sciences, Clunies Ross St., Canberra, ACT, 2601, Australia.
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6
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Pushpavalli SNCVL, Bag I, Pal-Bhadra M, Bhadra U. Drosophila Argonaute-1 is critical for transcriptional cosuppression and heterochromatin formation. Chromosome Res 2012; 20:333-51. [PMID: 22476395 PMCID: PMC3323821 DOI: 10.1007/s10577-012-9279-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 02/22/2012] [Accepted: 02/23/2012] [Indexed: 01/03/2023]
Abstract
Argonaute-1 (Ago-1) plays a crucial role in gene regulation and genome stability via biogenesis of small non-coding RNAs. Two "Argonaute" family genes, piwi and Ago-2 in Drosophila are involved in multiple silencing mechanisms in the nucleus, transgene cosuppression, long-distant chromosome interaction, nuclear organization and heterochromatin formation. To investigate whether Ago-1 also plays a similar role, we have generated a series of Ago-1 mutations by excising P element, inserted in the Ago-1 promoter (Ago-1k08121). AGO-1 protein is distributed uniformly in the nucleus and cytosol in early embryos but accumulated predominantly in the cytoplasm during the gastrulation stage. Repeat induced silencing produced by the mini-white (mw) array and transcriptional cosuppression of non-homologous transgenes Adh-w/w-Adh was disrupted by Ago-1 mutation. These effects of Ago-1 are distict from its role in microRNA processing because Dicer-1, a critical enzyme for miRNA biogenesis, has no role on the above silencing. Reduction of AGO-1 protein dislodged the POLYCOMB, EZ (enhancer of zeste) and H3me3K27 binding at the cosuppressed Adh-w transgene insertion sites suggesting its role in Polycomb dependent cosuppression. An overall reduction of methylated histone H3me2K9 and H3me3K27 from the polytene nuclei precisely from the mw promoters was also found that leads to concomitant changes in the chromatin structure. These results suggest a prominent role of Ago-1 in chromatin organization and transgene silencing and demonstrate a critical link between transcriptional transgene cosuppression, heterochromatin formation and chromatin organization. We propose Drosophila Ago-1 as a multifunctional RNAi component that interconnects at least two unrelated events, chromatin organization in the nucleus and microRNA processing in the cytoplasm, which may be extended to the other systems.
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Affiliation(s)
| | - Indira Bag
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Hyderabad, 500007 India
| | - Manika Pal-Bhadra
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Hyderabad, 500007 India
| | - Utpal Bhadra
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
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Pandya-Jones A. Pre-mRNA splicing during transcription in the mammalian system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:700-17. [PMID: 21823230 DOI: 10.1002/wrna.86] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Splicing of RNA polymerase II transcripts is a crucial step in gene expression and a key generator of mRNA diversity. Splicing and transcription have generally been studied in isolation, although in vivo pre-mRNA splicing occurs in concert with transcription. The two processes appear to be functionally connected because a number of variables that regulate transcription have been identified as also influencing splicing. However, the mechanisms that couple the two processes are largely unknown. This review highlights the observations that implicate splicing as occurring during transcription and describes the evidence supporting functional interactions between the two processes. I discuss postulated models of how splicing couples to transcription and consider the potential impact that such coupling might have on exon recognition. WIREs RNA 2011 2 700-717 DOI: 10.1002/wrna.86 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Amy Pandya-Jones
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles (UCLA), USA.
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8
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Kavi HH, Birchler JA. Interaction of RNA polymerase II and the small RNA machinery affects heterochromatic silencing in Drosophila. Epigenetics Chromatin 2009; 2:15. [PMID: 19917092 PMCID: PMC2785806 DOI: 10.1186/1756-8935-2-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 11/16/2009] [Indexed: 01/17/2023] Open
Abstract
Background Heterochromatin is the tightly packaged dynamic region of the eukaryotic chromosome that plays a vital role in cellular processes such as mitosis and meiotic recombination. Recent experiments in Schizosaccharomyces pombe have revealed the structure of centromeric heterochromatin is affected in RNAi pathway mutants. It has also been shown in fission yeast that the heterochromatin barrier is traversed by RNA Pol II and that the passage of RNA Pol II through heterochromatin is important for heterochromatin structure. Thus, an intricate interaction between the RNAi machinery and RNA Pol II affects heterochromatin structure. However, the role of the RNAi machinery and RNA Pol II on the metazoan heterochromatin landscape is not known. This study analyses the interaction of the small RNA machinery and RNA Pol II on Drosophila heterochromatin structure. Results The results in this paper show genetic and biochemical interaction between RNA Pol II (largest and second largest subunit) and small RNA silencing machinery components (dcr-2, ago1, ago2, piwi, Lip [D], aub and hls). Immunofluorescence analysis of polytene chromosomes from trans-heterozygotes of RNA Pol II and different mutations of the small RNA pathways show decreased H3K9me2 and mislocalization of Heterochromatin protein-1. A genetic analysis performed on these mutants showed a strong suppression of white-mottled4h position effect variegation. This was further corroborated by a western blot analysis and chromatin immunoprecipitation, which showed decreased H3K9me2 in trans-heterozygote mutants compared to wild type or single heterozygotes. Co-immunoprecipitation performed using Drosophila embryo extracts showed the RNA Pol II largest subunit interacting with Dcr-2 and dAGO1. Co-localization performed on polytene chromosomes showed RNA Pol II and dAGO1 overlapping at some sites. Conclusion Our experiments show a genetic and biochemical interaction between RNA Pol II (largest and second largest subunits) and the small RNA silencing machinery in Drosophila. The interaction has functional aspects in terms of determining H3K9me2 and HP-1 deposition at the chromocentric heterochromatin. Thus, RNA Pol II has an important role in establishing heterochromatin structure in Drosophila.
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Affiliation(s)
- Harsh H Kavi
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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9
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Ching B, Jamieson S, Heath JW, Heath DD, Hubberstey A. Transcriptional differences between triploid and diploid Chinook salmon (Oncorhynchus tshawytscha) during live Vibrio anguillarum challenge. Heredity (Edinb) 2009; 104:224-34. [DOI: 10.1038/hdy.2009.108] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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10
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Role of Small RNAs in Establishing Chromosomal Architecture in Drosophila. Epigenomics 2008. [DOI: 10.1007/978-1-4020-9187-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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11
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Bühler M. RNA turnover and chromatin-dependent gene silencing. Chromosoma 2008; 118:141-51. [DOI: 10.1007/s00412-008-0195-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 10/31/2008] [Accepted: 11/03/2008] [Indexed: 12/31/2022]
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12
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Kavi HH, Fernandez H, Xie W, Birchler JA. Genetics and biochemistry of RNAi in Drosophila. Curr Top Microbiol Immunol 2008; 320:37-75. [PMID: 18268839 DOI: 10.1007/978-3-540-75157-1_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RNA interference (RNAi) is the technique employing double-stranded RNA to target the destruction of homologous messenger RNAs. It has gained wide usage in genetics. While having the potential for many practical applications, it is a reflection of a much broader spectrum of small RNA-mediated processes in the cell. The RNAi machinery was originally perceived as a defense mechanism against viruses and transposons. While this is certainly true, small RNAs have now been implicated in many other aspects of cell biology. Here we review the current knowledge of the biochemistry of RNAi in Drosophila and the involvement of small RNAs in RNAi, transposon silencing, virus defense, transgene silencing, pairing-sensitive silencing, telomere function, chromatin insulator activity, nucleolar stability, and heterochromatin formation. The discovery of the role of RNA molecules in the degradation of mRNA transcripts leading to decreased gene expression resulted in a paradigm shift in the field of molecular biology. Transgene silencing was first discovered in plant cells (Matzke et al. 1989; van der Krol et al. 1990; Napoli et al. 1990) and can occur on both the transcriptional and posttranscriptional levels, but both involve short RNA moieties in their mechanism. RNA interference (RNAi) is a type of gene silencing mechanism in which a double-stranded RNA (dsRNA) molecule directs the specific degradation of the corresponding mRNA (target RNA). The technique of RNAi was first discovered in Caenorhabditis elegans in 1994 (Guo and Kemphues 1994). Later the active component was found to be a dsRNA (Fire et al. 1998). In subsequent years, it has been found to occur in diverse eukaryotes
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Affiliation(s)
- Harsh H Kavi
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
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13
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Bühler M, Moazed D. Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 2007; 14:1041-8. [DOI: 10.1038/nsmb1315] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Liu Y, Taverna SD, Muratore TL, Shabanowitz J, Hunt DF, Allis CD. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev 2007; 21:1530-45. [PMID: 17575054 PMCID: PMC1891430 DOI: 10.1101/gad.1544207] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 05/01/2007] [Indexed: 01/17/2023]
Abstract
Methylated H3K27 is an important mark for Polycomb group (PcG) protein-mediated transcriptional gene silencing (TGS) in multicellular eukaryotes. Here a Drosophila E(z) homolog, EZL1, is characterized in the ciliated protozoan Tetrahymena thermophila and is shown to be responsible for H3K27 methylation associated with developmentally regulated heterochromatin formation and DNA elimination. Importantly, Ezl1p-catalyzed H3K27 methylation occurs in an RNA interference (RNAi)-dependent manner. H3K27 methylation also regulates H3K9 methylation in these processes. Furthermore, an "effector" of programmed DNA elimination, the chromodomain protein Pdd1p, is shown to bind both K27- and K9-methylated H3. These studies provide a framework for an RNAi-dependent, Polycomb group protein-mediated heterochromatin formation pathway in Tetrahymena and underscore the connection between the two highly conserved machineries in eukaryotes.
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Affiliation(s)
- Yifan Liu
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | - Sean D. Taverna
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | - Tara L. Muratore
- Department of Chemistry, University of Virginia, Charlottesville, Virgina 22904, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virgina 22904, USA
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virgina 22904, USA
- Department of Pathology, Health Science Center, University of Virginia, Charlottesville, Virginia 22908, USA
| | - C. David Allis
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
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Grimaud C, Bantignies F, Pal-Bhadra M, Ghana P, Bhadra U, Cavalli G. RNAi Components Are Required for Nuclear Clustering of Polycomb Group Response Elements. Cell 2006; 124:957-71. [PMID: 16530043 DOI: 10.1016/j.cell.2006.01.036] [Citation(s) in RCA: 246] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 12/02/2005] [Accepted: 01/17/2006] [Indexed: 01/14/2023]
Abstract
Drosophila Polycomb group (PcG) proteins silence homeotic genes through binding to Polycomb group response elements (PREs). Fab-7 is a PRE-containing regulatory element from the homeotic gene Abdominal-B. When present in multiple copies in the genome, Fab-7 can induce long-distance gene contacts that enhance PcG-dependent silencing. We show here that components of the RNA interference (RNAi) machinery are involved in PcG-mediated silencing at Fab-7 and in the production of small RNAs at transgenic Fab-7 copies. In general, these mutations do not affect the recruitment of PcG components, but they are specifically required for the maintenance of long-range contacts between Fab-7 copies. Dicer-2, PIWI, and Argonaute1, three RNAi components, frequently colocalize with PcG bodies, and their mutation significantly reduces the frequency of PcG-dependent chromosomal associations of endogenous homeotic genes. This suggests a novel role for the RNAi machinery in regulating the nuclear organization of PcG chromatin targets.
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Affiliation(s)
- Charlotte Grimaud
- Institute of Human Genetics, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
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Edwards RG. Changing genetic world of IVF, stem cells and PGD. B. Polarities and gene expression in differentiating embryo cells and stem cells. Reprod Biomed Online 2006; 11:761-76. [PMID: 16417744 DOI: 10.1016/s1472-6483(10)61696-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Novel genetic techniques in the later twentieth century led to new analytical methods for assessing the growth of embryos and stem cells and improve preimplantation diagnosis. Increasing attention to the nature of polarities in mouse and human embryos revealed the existence of an animal-vegetal axis in human oocytes and embryos. Combinations of meridional and transverse cleavage divisions, the latter due to spindle rotation, determined the unequal division of ooplasm to embryonic blastomeres. Blastomeres with differing functions were accordingly formed in 4-cell embryos, including founders of inner cell mass and trophectoderm. New forms of gene analysis led to the polymerase chain reaction, while fluorescence in-situ hybridization revealed astonishingly high degrees of heteroploidy in human embryos. Developmental genetics gained immense analytical power as cDNA libraries, microarrays, transcriptomes RNAi and other methods clarified the roles of hundreds of genes in pre- and early post-implantation embryos and stem cells.
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Cernilogar FM, Orlando V. Epigenome programming by Polycomb and Trithorax proteins. Biochem Cell Biol 2005; 83:322-31. [PMID: 15959558 DOI: 10.1139/o05-040] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins work, respectively, to maintain repressed or active transcription states of developmentally regulated genes through cell division. Data accumulated in the recent years have increased our understanding of the mechanisms by which PcG and TrxG proteins regulate gene expression. The discovery that histone methylation can serve as a specific mark for PcG and TrxG complexes has provided new insight into the mechanistic function of this cell-memory system.
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Kavi HH, Fernandez HR, Xie W, Birchler JA. RNA silencing inDrosophila. FEBS Lett 2005; 579:5940-9. [PMID: 16198344 DOI: 10.1016/j.febslet.2005.08.069] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 08/26/2005] [Accepted: 08/28/2005] [Indexed: 11/18/2022]
Abstract
Knowledge of the role of RNA in affecting gene expression has expanded in the past several years. Small RNAs serve as homology guides to target messenger RNAs for destruction at the post-transcriptional level in the experimental technique known as RNA interference and in the silencing of some transgenes. These small RNAs are also involved in sequence-specific targeting of chromatin modifications for transcriptional silencing of transgenes, transposable elements, heterochromatin and some cases of Polycomb-mediated gene silencing. RNA silencing processes in Drosophila are described.
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Affiliation(s)
- Harsh H Kavi
- Division of Biological Sciences, University of Missouri, 117 Tucker Hall, Columbia, MO 65211, USA
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19
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Bhadra MP, Bhadra U, Kundu J, Birchler JA. Gene expression analysis of the function of the male-specific lethal complex in Drosophila. Genetics 2005; 169:2061-74. [PMID: 15716510 PMCID: PMC1449592 DOI: 10.1534/genetics.104.036020] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Accepted: 01/03/2005] [Indexed: 01/01/2023] Open
Abstract
Dosage compensation refers to the equal expression of X-linked genes despite the difference in copy number between the two sexes. The male-specific lethal (MSL) complex is concentrated on the X chromosome in males. A gene expression assay for embryos was developed to examine the function of this complex. In mutant male embryos without either the MSL complex or MOF histone acetylase, dosage compensation is retained but autosomal expression is increased. Dosage compensation is lost in the double-mutant embryos. In embryos in which the MSL complex and MOF are targeted to the X chromosomes in females, the results are consistent with previous surveys showing that in general the X expression remains unchanged, but autosomal expression is reduced. Mutations in the ISWI chromatin-remodeling component cause increases specifically of X-linked genes in males. Thus, the function of the MSL complex in conjunction with ISWI is postulated to override the effect on gene expression of high histone acetylation on the male X. The basic determinant of dosage compensation is suggested to be an inverse dosage effect produced by an imbalance of transcription factors on the X vs. the autosomes. The sequestration of the MSL complex to the male X may have evolved to counteract a similar effect on the autosomes and to prevent an overexpression of the X chromosome in males that would otherwise occur due to the high levels of histone acetylation.
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Affiliation(s)
- Manika Pal Bhadra
- Division of Biological Sciences, University of Missouri, Columbia, 65211, USA
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20
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Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM, Rajewsky K. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 2005; 19:489-501. [PMID: 15713842 PMCID: PMC548949 DOI: 10.1101/gad.1248505] [Citation(s) in RCA: 953] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dicer is the enzyme that cleaves double-stranded RNA (dsRNA) into 21-25-nt-long species responsible for sequence-specific RNA-induced gene silencing at the transcriptional, post-transcriptional, or translational level. We disrupted the dicer-1 (dcr-1) gene in mouse embryonic stem (ES) cells by conditional gene targeting and generated Dicer-null ES cells. These cells were viable, despite being completely defective in RNA interference (RNAi) and the generation of microRNAs (miRNAs). However, the mutant ES cells displayed severe defects in differentiation both in vitro and in vivo. Epigenetic silencing of centromeric repeat sequences and the expression of homologous small dsRNAs were markedly reduced. Re-expression of Dicer in the knockout cells rescued these phenotypes. Our data suggest that Dicer participates in multiple, fundamental biological processes in a mammalian organism, ranging from stem cell differentiation to the maintenance of centromeric heterochromatin structure and centromeric silencing.
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Affiliation(s)
- Chryssa Kanellopoulou
- The Dana-Farber Cancer Institute, Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Robert V, Bucheton A. Régulation de l’expression des séquences répétées et interférence par l’ARN. Med Sci (Paris) 2004; 20:767-72. [PMID: 15361342 DOI: 10.1051/medsci/2004208-9767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Living organisms have to fight against the invasion of many parasites. Among them are viruses and transposable elements that are able to integrate in the genome of their host. After integration, they can replicate and propagate. The defence mechanisms against these invaders are still largely unknown but are widely studied in plants as well as in fungi and animals, particularly Caenorhabditis elegans and Drosophila melanogaster. The compilation of recent data allows us to draw a general scheme for these mechanisms. In particular, it seems that the propagation of viruses, transposable elements and repeated sequences is controlled by mechanisms repressing the expression of these sequences at both transcriptional and post-transcriptional levels. Post-transcriptional regulation of repeated sequences and transposable elements is related to RNA interference (RNAi), an evolutionary conserved silencing process induced by the presence of double-stranded RNAs (dsRNAs). Many genes and molecular intermediates have now been identified, revealing the different steps of the mechanism underlying this process. Finally, different results suggest that these post-transcriptional silencing processes are involved in the development of organisms. DICER is a nuclease responsible for the processing of dsRNA into short RNA molecules (siRNAs) considered as the interfering agent. siRNAs interact with the transcript of the targeted gene and this interaction induces degradation of the transcript. DICER is also involved in the processing of small temporal RNAs (stRNA) involved in the timing of development. stRNAs have the same structure as siRNAs. They regulate their target genes by interacting with elements present in their 3'UTR and blocking translation. RNAi appears to be an universal regulatory mechanism that was still unknown a few years ago. It is now largely used in large scale inactivation of genes to determine their function, and some recent studies indicate that it might be used in human therapy.
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22
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Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R, Prasanth KV, Ried T, Shav-Tal Y, Bertrand E, Singer RH, Spector DL. From silencing to gene expression: real-time analysis in single cells. Cell 2004; 116:683-98. [PMID: 15006351 PMCID: PMC4942132 DOI: 10.1016/s0092-8674(04)00171-0] [Citation(s) in RCA: 535] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Revised: 01/21/2004] [Accepted: 01/23/2004] [Indexed: 12/29/2022]
Abstract
We have developed an inducible system to visualize gene expression at the levels of DNA, RNA and protein in living cells. The system is composed of a 200 copy transgene array integrated into a euchromatic region of chromosome 1 in human U2OS cells. The condensed array is heterochromatic as it is associated with HP1, histone H3 methylated at lysine 9, and several histone methyltransferases. Upon transcriptional induction, HP1alpha is depleted from the locus and the histone variant H3.3 is deposited suggesting that histone exchange is a mechanism through which heterochromatin is transformed into a transcriptionally active state. RNA levels at the transcription site increase immediately after the induction of transcription and the rate of synthesis slows over time. Using this system, we are able to correlate changes in chromatin structure with the progression of transcriptional activation allowing us to obtain a real-time integrative view of gene expression.
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Affiliation(s)
- Susan M Janicki
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | | | - Simone E Salghetti
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - William P Tansey
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Ravi Sachidanandam
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | | | - Thomas Ried
- Genetics Branch, Center for Cancer Research/National Cancer Institute/NIH, 50 South Drive, Bethesda, MD 20892 USA
| | - Yaron Shav-Tal
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Edouard Bertrand
- Institut de Genetique Moleculaire de Montpellier-CNRS, 1919 Route de Mende, 34293 Montpellier, France
| | - Robert H Singer
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - David L Spector
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
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23
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Pal-Bhadra M, Bhadra U, Birchler JA. Interrelationship of RNA interference and transcriptional gene silencing in Drosophila. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:433-8. [PMID: 16117678 DOI: 10.1101/sqb.2004.69.433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- M Pal-Bhadra
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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24
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Lieberman J, Song E, Lee SK, Shankar P. Interfering with disease: opportunities and roadblocks to harnessing RNA interference. Trends Mol Med 2003; 9:397-403. [PMID: 13129706 PMCID: PMC7128953 DOI: 10.1016/s1471-4914(03)00143-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA interference (RNAi) is an evolutionarily conserved mechanism for silencing gene expression by targeted degradation of mRNA. Short double-stranded RNAs, known as small interfering RNAs (siRNA), are incorporated into an RNA-induced silencing complex that directs degradation of RNA containing a homologous sequence. RNAi has been shown to work in mammalian cells, and can inhibit viral infection and control tumor cell growth in vitro. Recently, it has been shown that intravenous injection of siRNA or of plasmids expressing sequences processed to siRNA can protect mice from autoimmune and viral hepatitis. RNAi could provide an exciting new therapeutic modality for treating infection, cancer, neurodegenerative disease and other illnesses.
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Affiliation(s)
- Judy Lieberman
- Center for Blood Research and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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25
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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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26
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Abstract
Chromatin remodeling in plants has usually been discussed in relation to aspects of genome defense such as transgene silencing and the resetting of transposon activity. The role of remodeling in controlling development has been less emphasized, although well established in animal systems. This is because cell fate in plants is often held to be entirely specified on the basis of position, apparently excluding any significant role for cell ancestry and chromatin remodeling. We argue that chromatin remodeling is used to confer mitotically heritable cell fates at late stages in pattern formation. Several examples in which chromatin remodeling factors are used to confer a memory of transient events in plant development are discussed. Because the precise biochemical functions of most remodeling factors are obscure, and little is known of plant chromatin structure, the underlying mechanisms remain poorly understood.
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Affiliation(s)
- Justin Goodrich
- Institute of Cell and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, United Kingdom.
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27
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Abstract
In development, cell identity is maintained by epigenetic functions that prevent changes in cell type-specific transcription programs. Recent insights into gene silencing mechanisms by Polycomb group (PcG) and trithorax group (trxG) proteins reveal that the memory system involves a concerted process of chromatin modification, blocking of RNA polymerase II, and synthesis of noncoding RNA. Remarkably, cell memory is regulated by a balance between repressors and activators that maintains both transcription status and at the same time the possibility of switching to a different state.
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Affiliation(s)
- Valerio Orlando
- Dulbecco Telethon Institute, Institute of Genetics & Biophysics CNR, Via Pietro Castellino 111, 80131, Naples, Italy.
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28
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Jensen S, Gassama MP, Dramard X, Heidmann T. Regulation of I-transposon activity in Drosophila: evidence for cosuppression of nonhomologous transgenes and possible role of ancestral I-related pericentromeric elements. Genetics 2002; 162:1197-209. [PMID: 12454066 PMCID: PMC1462345 DOI: 10.1093/genetics/162.3.1197] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have previously shown that the activity of functional I retrotransposons (I factors) introduced into Drosophila devoid of such elements can be repressed by transgenes containing an internal fragment of the I factor itself and that this repressing effect presents the characteristic features of homology-dependent gene silencing or cosuppression. Here we show that the same transgenes can induce silencing of a nonhomologous reporter gene containing as the sole I-factor sequence its 100-bp promoter fragment. Silencing of the nonhomologous reporter gene shows strong similarities to I-factor cosuppression: It does not require any translation product from the regulating transgenes, sense and antisense constructs are equally potent, and the silencing effect is only maternally transmitted and fully reversible. A search for genomic I-like sequences containing domains with similarities to those of both the regulating and the reporter transgenes led to the identification of four such elements, which therefore could act as intermediates-or relays-in the cosuppression machinery. These results strongly suggest that ancestral transposition-defective I-related elements, which are naturally present in the Drosophila genome, may participate per se in the natural conditions of I-factor silencing.
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Affiliation(s)
- Silke Jensen
- CNRS UMR 1573, Institut Gustave Roussy, 94805 Villejuif Cedex, France
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29
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Sanders M, Maddelein W, Depicker A, Van Montagu M, Cornelissen M, Jacobs J. An active role for endogenous beta-1,3-glucanase genes in transgene-mediated co-suppression in tobacco. EMBO J 2002; 21:5824-32. [PMID: 12411500 PMCID: PMC131083 DOI: 10.1093/emboj/cdf586] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2002] [Revised: 09/06/2002] [Accepted: 09/16/2002] [Indexed: 11/14/2022] Open
Abstract
Post-transcriptional gene silencing (PTGS) is characterized by the accumulation of short interfering RNAs that are proposed to mediate sequence-specific degradation of cognate and secondary target mRNAs. In plants, it is unclear to what extent endogenous genes contribute to this process. Here, we address the role of the endogenous target genes in transgene-mediated PTGS of beta-1,3-glucanases in tobacco. We found that mRNA sequences of the endogenous glucanase glb gene with varying degrees of homology to the Nicotiana plumbaginifolia gn1 transgene are targeted by the silencing machinery, although less efficiently than corresponding transgene regions. Importantly, we show that endogene-specific nucleotides in the glb sequence provide specificity to the silencing process. Consistent with this finding, small sense and antisense 21- to 23-nucleotide RNAs homologous to the endogenous glb gene were detected. Combined, these data demonstrate that a co-suppressed endogenous glucan ase gene is involved in signal amplification and selection of homologous targets, and show that endogenous genes can actively participate in PTGS in plants. The findings are introduced as a further sophistication of the post-transciptional silencing model.
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Affiliation(s)
- Matthew Sanders
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent and Bayer Bioscience N.V., J. Plateaustraat 22, B-9000 Ghent, Belgium Present address: Devgen N.V., Technologiepark 9, B-9052 Zwijnaarde, Belgium Corresponding author e-mail:
| | - Wendy Maddelein
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent and Bayer Bioscience N.V., J. Plateaustraat 22, B-9000 Ghent, Belgium Present address: Devgen N.V., Technologiepark 9, B-9052 Zwijnaarde, Belgium Corresponding author e-mail:
| | - Anna Depicker
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent and Bayer Bioscience N.V., J. Plateaustraat 22, B-9000 Ghent, Belgium Present address: Devgen N.V., Technologiepark 9, B-9052 Zwijnaarde, Belgium Corresponding author e-mail:
| | - Marc Van Montagu
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent and Bayer Bioscience N.V., J. Plateaustraat 22, B-9000 Ghent, Belgium Present address: Devgen N.V., Technologiepark 9, B-9052 Zwijnaarde, Belgium Corresponding author e-mail:
| | - Marc Cornelissen
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent and Bayer Bioscience N.V., J. Plateaustraat 22, B-9000 Ghent, Belgium Present address: Devgen N.V., Technologiepark 9, B-9052 Zwijnaarde, Belgium Corresponding author e-mail:
| | - John Jacobs
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent and Bayer Bioscience N.V., J. Plateaustraat 22, B-9000 Ghent, Belgium Present address: Devgen N.V., Technologiepark 9, B-9052 Zwijnaarde, Belgium Corresponding author e-mail:
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30
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Novina CD, Murray MF, Dykxhoorn DM, Beresford PJ, Riess J, Lee SK, Collman RG, Lieberman J, Shankar P, Sharp PA. siRNA-directed inhibition of HIV-1 infection. Nat Med 2002; 8:681-6. [PMID: 12042777 DOI: 10.1038/nm725] [Citation(s) in RCA: 638] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
RNA interference silences gene expression through short interfering 21 23-mer double-strand RNA segments that guide mRNA degradation in a sequence-specific fashion. Here we report that siRNAs inhibit virus production by targeting the mRNAs for either the HIV-1 cellular receptor CD4, the viral structural Gag protein or green fluorescence protein substituted for the Nef regulatory protein. siRNAs effectively inhibit pre- and/or post-integration infection events in the HIV-1 life cycle. Thus, siRNAs may have potential for therapeutic intervention in HIV-1 and other viral infections.
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Affiliation(s)
- Carl D Novina
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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31
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Springer NM, Danilevskaya ON, Hermon P, Helentjaris TG, Phillips RL, Kaeppler HF, Kaeppler SM. Sequence relationships, conserved domains, and expression patterns for maize homologs of the polycomb group genes E(z), esc, and E(Pc). PLANT PHYSIOLOGY 2002; 128:1332-45. [PMID: 11950982 PMCID: PMC154261 DOI: 10.1104/pp.010742] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2001] [Revised: 11/28/2001] [Accepted: 12/21/2001] [Indexed: 05/17/2023]
Abstract
Polycomb group (PcG) proteins play an important role in developmental and epigenetic regulation of gene expression in fruit fly (Drosophila melanogaster) and mammals. Recent evidence has shown that Arabidopsis homologs of PcG proteins are also important for the regulation of plant development. The objective of this study was to characterize the PcG homologs in maize (Zea mays). The 11 cloned PcG proteins from fruit fly and the Enhancer of zeste [E(z)], extra sex combs (esc), and Enhancer of Polycomb [E(Pc)] homologs from Arabidopsis were used as queries to perform TBLASTN searches against the public maize expressed sequence tag database and the Pioneer Hi-Bred database. Maize homologs were found for E(z), esc, and E(Pc), but not for Polycomb, pleiohomeotic, Posterior sex combs, Polycomblike, Additional sex combs, Sex combs on midleg, polyhometoic, or multi sex combs. Transcripts of the three maize Enhancer of zeste-like genes, Mez1, Mez2, and Mez3, were detected in all tissues tested, and the Mez2 transcript is alternatively spliced in a tissue-dependent pattern. Zea mays fertilization independent endosperm1 (ZmFie1) expression was limited to developing embryos and endosperms, whereas ZmFie2 expression was found throughout plant development. The conservation of E(z) and esc homologs across kingdoms indicates that these genes likely play a conserved role in repressing gene expression.
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Affiliation(s)
- Nathan M Springer
- Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
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32
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Pal-Bhadra M, Bhadra U, Birchler JA. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol Cell 2002; 9:315-27. [PMID: 11864605 DOI: 10.1016/s1097-2765(02)00440-9] [Citation(s) in RCA: 316] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Two types of transgene silencing were found for the Alcohol dehydrogenase (Adh) transcription unit. Transcriptional gene silencing (TGS) is Polycomb dependent and occurs when Adh is driven by the white eye color gene promoter. Full-length Adh transgenes are silenced posttranscriptionally at high copy number or by a pulsed increase over a threshold. The posttranscriptional gene silencing (PTGS) exhibits molecular hallmarks typical of RNA interference (RNAi), including the production of 21--25 bp length sense and antisense RNAs homologous to the silenced RNA. Mutations in piwi, which belongs to a gene family with members required for RNAi, block PTGS and one aspect of TGS, indicating a connection between the two types of silencing.
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Affiliation(s)
- Manika Pal-Bhadra
- Division of Biological Sciences, 117 Tucker Hall, University of Missouri, Columbia, MO 65211, USA
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33
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Abstract
The silencing of gene expression by segments of DNA present in excess of the normal number is called cosuppression in plants and quelling in fungi. We describe a related process, meiotic silencing by unpaired DNA (MSUD). DNA unpaired in meiosis causes silencing of all DNA homologous to it, including genes that are themselves paired. A semidominant Neurospora mutant, Sad-1, fails to perform MSUD. Sad-1 suppresses the sexual phenotypes of many ascus-dominant mutants. MSUD may provide insights into the function of genes necessary for meiosis, including genes for which ablation in vegetative life would be lethal. It may also contribute to reproductive isolation of species within the genus Neurospora. The wild-type allele, sad-1(+), encodes a putative RNA-directed RNA polymerase.
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Affiliation(s)
- P K Shiu
- Department of Biological Sciences, 385 Serra Mall, Stanford University, Stanford, CA 94305, USA.
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34
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Ronsseray S, Boivin A, Anxolabéhère D. P-Element repression in Drosophila melanogaster by variegating clusters of P-lacZ-white transgenes. Genetics 2001; 159:1631-42. [PMID: 11779802 PMCID: PMC1461890 DOI: 10.1093/genetics/159.4.1631] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Drosophila, clusters of P transgenes (P-lac-w) display a variegating phenotype for the w marker. In addition, X-ray-induced rearrangements of chromosomes bearing such clusters may lead to enhancement of the variegated phenotype. Since P-lacZ transgenes in subtelomeric heterochromatin have some P-element repression abilities, we tested whether P-lac-w clusters also have the capacity to repress P-element activity in the germline. One cluster (T-1), located on a rearranged chromosome (T2;3) and derived from a line bearing a variegating tandem array of seven P-lac-w elements, partially represses the dysgenic sterility (GD sterility) induced by P elements. This cluster also strongly represses in trans the expression of P-lacZ elements in the germline. This latter suppression shows a maternal effect. Finally, the combination of variegating P-lac-w clusters and a single P-lacZ reporter inserted in subtelomeric heterochromatic sequences at the X chromosome telomere (cytological site 1A) leads to strong repression of dysgenic sterility. These results show that repression of P-induced dysgenic sterility can be elicited in the absence of P elements encoding a polypeptide repressor and that a transgene cluster can repress the expression of a single homologous transgene at a nonallelic position. Implications for models of transposable element silencing are discussed.
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Affiliation(s)
- S Ronsseray
- Laboratoire Dynamique du Génome et Evolution, Institut Jacques Monod, UMR7592, CNRS-Universités Paris 6 et 7, 75251 Paris Cedex 05, France.
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35
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Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 2001; 107:465-76. [PMID: 11719187 DOI: 10.1016/s0092-8674(01)00576-1] [Citation(s) in RCA: 887] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have investigated the role of trigger RNA amplification during RNA interference (RNAi) in Caenorhabditis elegans. Analysis of small interfering RNAs (siRNAs) produced during RNAi in C. elegans revealed a substantial fraction that cannot derive directly from input dsRNA. Instead, a population of siRNAs (termed secondary siRNAs) appeared to derive from the action of a cellular RNA-directed RNA polymerase (RdRP) on mRNAs that are being targeted by the RNAi mechanism. The distribution of secondary siRNAs exhibited a distinct polarity (5'-->3' on the antisense strand), suggesting a cyclic amplification process in which RdRP is primed by existing siRNAs. This amplification mechanism substantially augments the potency of RNAi-based surveillance, while ensuring that the RNAi machinery will focus on expressed mRNAs.
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Affiliation(s)
- T Sijen
- Hubrecht Laboratory, Center for Biomedical Genetics, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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36
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Lin SL, Ying SY. D-RNAi (messenger RNA-antisense DNA interference) as a novel defense system against cancer and viral infections. Curr Cancer Drug Targets 2001; 1:241-7. [PMID: 12188882 PMCID: PMC4384701 DOI: 10.2174/1568009013334151] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
D-RNAi (Messenger RNA-antisense DNA interference), a novel posttranscriptional phenomenon of silencing gene expression by transfection of mRNA-aDNA hybrids, was originally observed in the effects of bcl-2 on phorbol ester-induced apoptosis in human prostate cancer LNCaP cells. This phenomenon was also demonstrated in chicken embryos and a human CD4(+) T cell line, H9. The in vivo transduction of beta-catenin D-RNAi was shown to knock out more than 99% endogenous beta-catenin gene expression, while the in cell transfection of HIV-1 D-RNAi homolog rejected viral gene replication completely. D-RNAi was found to have long-term gene knockout effects resulting from a posttranscriptional gene silencing mechanism that may involve the homologous recombination between intracellular mRNA and the mRNA components of a D-RNAi construct. These findings provide a potential intracellular defense system against cancer and viral infections.
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MESH Headings
- DNA, Antisense/pharmacology
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Gene Silencing
- Humans
- Neoplasms/genetics
- Neoplasms/therapy
- RNA Processing, Post-Transcriptional/genetics
- RNA Processing, Post-Transcriptional/physiology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Transcription, Genetic
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Affiliation(s)
- Shi-Lung Lin
- Epiclone Inc., 731 South Chapel Avenue, Suite F, Alhambra, CA 91801, USA
| | - Shao-Yao Ying
- Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, BMT-401, 1333 San Pablo Street, Los Angeles, CA 90033, USA
- Address correspondence to this author at the Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, BMT-401, 1333 San Pablo Street, Los Angeles, CA 90033, USA, Pone: (323) 442-1859, Fax: (323) 442-3158,
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37
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Abstract
The assembly of DNA into regions of inaccessible chromatin, called silent chromatin, is involved in the regulation of gene expression and maintenance of chromosome stability in eukaryotes. Recent studies on Sir2-containing silencing complexes in budding yeast and HP1- and Swi6-containing silencing complexes in metazoans and fission yeast suggest a common mechanism for the assembly of these domains, which involves the physical coupling of histone modifying enzymes to histone binding proteins.
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Affiliation(s)
- D Moazed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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38
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Mattick JS, Gagen MJ. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 2001; 18:1611-30. [PMID: 11504843 DOI: 10.1093/oxfordjournals.molbev.a003951] [Citation(s) in RCA: 295] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic phenotypic diversity arises from multitasking of a core proteome of limited size. Multitasking is routine in computers, as well as in other sophisticated information systems, and requires multiple inputs and outputs to control and integrate network activity. Higher eukaryotes have a mosaic gene structure with a dual output, mRNA (protein-coding) sequences and introns, which are released from the pre-mRNA by posttranscriptional processing. Introns have been enormously successful as a class of sequences and comprise up to 95% of the primary transcripts of protein-coding genes in mammals. In addition, many other transcripts (perhaps more than half) do not encode proteins at all, but appear both to be developmentally regulated and to have genetic function. We suggest that these RNAs (eRNAs) have evolved to function as endogenous network control molecules which enable direct gene-gene communication and multitasking of eukaryotic genomes. Analysis of a range of complex genetic phenomena in which RNA is involved or implicated, including co-suppression, transgene silencing, RNA interference, imprinting, methylation, and transvection, suggests that a higher-order regulatory system based on RNA signals operates in the higher eukaryotes and involves chromatin remodeling as well as other RNA-DNA, RNA-RNA, and RNA-protein interactions. The evolution of densely connected gene networks would be expected to result in a relatively stable core proteome due to the multiple reuse of components, implying that cellular differentiation and phenotypic variation in the higher eukaryotes results primarily from variation in the control architecture. Thus, network integration and multitasking using trans-acting RNA molecules produced in parallel with protein-coding sequences may underpin both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotypic complexity into uncontested environments such as those initiated in the Cambrian radiation and those seen after major extinction events.
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Affiliation(s)
- J S Mattick
- Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
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39
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Aravin AA, Naumova NM, Tulin AV, Vagin VV, Rozovsky YM, Gvozdev VA. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr Biol 2001; 11:1017-27. [PMID: 11470406 DOI: 10.1016/s0960-9822(01)00299-8] [Citation(s) in RCA: 536] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The injection of double-stranded RNA (dsRNA) has been shown to induce a potent sequence-specific inhibition of gene function in diverse invertebrate and vertebrate species. The homology-dependent posttranscriptional gene silencing (PTGS) caused by the introduction of transgenes in plants may be mediated by dsRNA. The analysis of Caenorhabditis elegans mutants impaired with dsRNA-mediated silencing and studies in plants implicate a biological role of dsRNA-mediated silencing as a transposon-repression and antiviral mechanism. RESULTS We investigated the silencing of testis-expressed Stellate genes by paralogous Su(Ste) tandem repeats, which are known to be involved in the maintenance of male fertility in Drosophila melanogaster. We found that both strands of repressor Su(Ste) repeats are transcribed, producing sense and antisense RNA. The Stellate silencing is associated with the presence of short Su(Ste) RNAs. Cotransfection experiments revealed that Su(Ste) dsRNA can target and eliminate Stellate transcripts in Drosophila cell culture. The short fragment of Stellate gene that is homologous to Su(Ste) was shown to be sufficient to confer Su(Ste)-dependent silencing of a reporter construct in testes. We demonstrated that Su(Ste) dsRNA-mediated silencing affects not only Stellate expression but also the level of sense Su(Ste) RNA providing a negative autogenous regulation of Su(Ste) expression. Mutation in the spindle-E gene relieving Stellate silencing also leads to a derepression of the other genomic tandem repeats and retrotransposons in the germline. CONCLUSIONS Homology-dependent gene silencing was shown to be used to inhibit Stellate gene expression in the D. melanogaster germline, ensuring male fertility. dsRNA-mediated silencing may provide a basis for negative autogenous control of gene expression. The related surveillance system is implicated to control expression of retrotransposons in the germline.
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Affiliation(s)
- A A Aravin
- Department of Animal Molecular Genetics, Institute of Molecular Genetics, 123182, Moscow, Russia
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40
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Lin SL, Chuong CM, Ying SY. A Novel mRNA-cDNA interference phenomenon for silencing bcl-2 expression in human LNCaP cells. Biochem Biophys Res Commun 2001; 281:639-44. [PMID: 11237705 DOI: 10.1006/bbrc.2001.4412] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The templates required for inducing posttranscriptional gene silencing (PTGS) effects have been investigated in human prostate cancer LNCaP cells. Transfection of a mRNA-cDNA hybrid construct was found to result in a relatively long-term interference of specific gene expression. Androgen-stimulated expression of bcl-2 has been reported to increase the tumorigenic and metastatic potentials of human prostate cancer LNCaP cells, as well as their resistance to many apoptotic stimuli. The addition of bcl-2 antisense oligonucleotides, however, restored apoptosis. Our studies demonstrate gene silencing effects of the mRNA-cDNA transfection that is similar to those of PTGS/RNAi in this in vitro prostate cancer cell model. A potential RNA-directed RNA polymerase activity was also detected which is alpha-amanitin-sensitive. These findings indicate that a novel gene silencing system may exist in mammalian cells.
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Affiliation(s)
- S L Lin
- Department of Pathology, Keck School of Medicine, University of Southern California, HMR-209, 2011 Zonal Avenue, Los Angeles, California, 90033, USA
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41
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Affiliation(s)
- P A Sharp
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA.
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42
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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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43
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Sharp PA. View of life sciences in the 21st century. J Dermatol Sci 2000; 24 Suppl 1:S1-14. [PMID: 11137390 DOI: 10.1016/s0923-1811(00)00135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
As we contemplate the nature of life sciences in the 21st century, we should briefly consider the changes that have occurred in the past century. Surely, the sources of progress of this science in the next century are the advances emerging now. Furthermore, the likely pace of discovery and change in life sciences in the next century can best be estimated by a reflection on its history.
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Affiliation(s)
- P A Sharp
- Institute Professor, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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44
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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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45
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Miller WJ, Nagel A, Bachmann J, Bachmann L. Evolutionary dynamics of the SGM transposon family in the Drosophila obscura species group. Mol Biol Evol 2000; 17:1597-609. [PMID: 11070048 DOI: 10.1093/oxfordjournals.molbev.a026259] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SGM (Drosophila subobscura, Drosophila guanche, and Drosophila madeirensis) transposons are a family of transposable elements (TEs) in Drosophila with some functional and structural similarities to miniature inverted-repeat transposable elements (MITEs). These elements were recently active in D. subobscura and D. madeirensis (1-2 MYA), but in D. guanche (3-4 MYA), they gave rise to a species-specifically amplified satellite DNA making up approximately 10% of its genome. SGM elements were already active in the common ancestor of all three species, giving rise to the A-type specific promoter section of the P:-related neogene cluster. SGM sequences are similar to elements found in other obscura group species, such as the ISY elements in D. miranda and the ISamb elements in Drosophila ambigua. SGM elements are composed of different sequence modules, and some of them, i.e., LS and LS-core, are found throughout the Drosophila and Sophophora radiation with similarity to more distantly related TEs. The LS-core module is highly enriched in the noncoding sections of the Drosophila melanogaster genome, suggesting potential regulatory host gene functions. The SGM elements can be considered as a model system elucidating the evolutionary dynamics of mobile elements in their arms race with host-directed silencing mechanisms and their evolutionary impact on the structure and composition of their respective host genomes.
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Affiliation(s)
- W J Miller
- Institute of Medical Biology, General Genetics, University of Vienna, Austria.
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46
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Tchurikov NA, Chistyakova LG, Zavilgelsky GB, Manukhov IV, Chernov BK, Golova YB. Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. J Biol Chem 2000; 275:26523-9. [PMID: 10849423 DOI: 10.1074/jbc.m002833200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gene-specific silencing refers to a phenomenon in which expression of an individual gene can be specifically repressed by different mechanisms on the levels of transcription, RNA splicing, transport, degradation in nuclei or cytoplasm, or blocking of translation. In different species gene-specific silencing was observed by expression or injections of antiparallel double-stranded RNA formed by a fragment of mRNA and antisense RNA. Here we show a potent and specific gene silencing in bacteria by expression of RNA, that is complementary in a parallel orientation to Escherichia coli lon mRNA. Moreover, the expression of parallel RNA is more effective at producing interference than expression of antisense RNA corresponding to the same mRNA region. Both effects of interference mediated either by parallel RNA or antiparallel RNA gradually decrease up to the 40th generation. Together with in vitro nuclease protection studies these results indicate that a parallel RNA duplex might be formed in vivo and both types of duplexes, antiparallel or parallel, can induce gene-specific silencing by similar mechanisms.
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Affiliation(s)
- N A Tchurikov
- Department of Genome Organization and Group of Genes Chemical Synthesis, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov str. 32, Moscow 117984, Russia.
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47
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Birchler JA, Bhadra MP, Bhadra U. Making noise about silence: repression of repeated genes in animals. Curr Opin Genet Dev 2000; 10:211-6. [PMID: 10753783 DOI: 10.1016/s0959-437x(00)00065-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Repeated copies of genes, whether in tandem or dispersed, are often recognized by the cell and silenced. Tandem repeat silencing is associated with a heterochromatin-like complex. Dispersed gene silencing can be mediated by the repressive Polycomb Group complex or involve post-transcriptional silencing presumably involving double-stranded RNA. The I retrotransposable element in Drosophila appears to be susceptible to dispersed gene silencing, potentially by both post-transcriptional and transcriptional processes. Some mutations that eliminate RNA interference in Caenorhabditis elegans result in the mobilization of many transposons and two of these mutations desilence tandem repeats in the germline. One challenge for the future is to determine the nature of any relationship between post-transcriptionally and transcriptionally based mechanisms. The silencing mechanisms potentially act as a protection against high expression of transposons and viruses.
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Affiliation(s)
- J A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA.
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48
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Ketting RF, Plasterk RH. A genetic link between co-suppression and RNA interference in C. elegans. Nature 2000; 404:296-8. [PMID: 10749214 DOI: 10.1038/35005113] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Originally discovered in plants, the phenomenon of co-suppression by transgenic DNA has since been observed in many organisms from fungi to animals: introduction of transgenic copies of a gene results in reduced expression of the transgene as well as the endogenous gene. The effect depends on sequence identity between transgene and endogenous gene. Some cases of co-suppression resemble RNA interference (the experimental silencing of genes by the introduction of double-stranded RNA), as RNA seems to be both an important initiator and a target in these processes. Here we show that co-suppression in Caenorhabditis elegans is also probably mediated by RNA molecules. Both RNA interference and co-suppression have been implicated in the silencing of transposons. We now report that mutants of C. elegans that are defective in transposon silencing and RNA interference (mut-2, mut-7, mut-8 and mut-9) are in addition resistant to co-suppression. This indicates that RNA interference and co-suppression in C. elegans may be mediated at least in part by the same molecular machinery, possibly through RNA-guided degradation of messenger RNA molecules.
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Affiliation(s)
- R F Ketting
- Division of Molecular Biology, The Netherlands Cancer Institute, Centre for Biomedical Genetics, Amsterdam
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49
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Abstract
In many species, introduction of double-stranded RNA (dsRNA) induces potent and specific gene silencing, a phenomenon called RNA interference or RNAi. The apparently widespread nature of RNAi in eukaryotes, ranging from trypanosome to mouse, has sparked great interest from both applied and fundamental standpoints. Here we review the technical improvements being made to increase the experimental potential of this technique. We also discuss recent advances in uncovering the proteins that act during the RNAi process, discoveries that have revealed enticing links between transposition, transgene silencing and RNAi.
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Affiliation(s)
- J M Bosher
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP163, 67404 Illkirch Cedex, France
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50
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Sonoda S, Nishiguchi M. Graft transmission of post-transcriptional gene silencing: target specificity for RNA degradation is transmissible between silenced and non-silenced plants, but not between silenced plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000; 21:1-8. [PMID: 10652145 DOI: 10.1046/j.1365-313x.2000.00645.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Using the grafting procedure, we examined the transmission of post-transcriptional gene silencing (PTGS) in Nicotiana benthamiana which had been transformed with the coat protein gene, including the 3' non-translated region of the sweet potato feathery mottle potyvirus. Transmission of PTGS from silenced lines to non-silenced ones was bidirectional, but occurred efficiently from root stocks to scions. The level of transgene methylation in non-silenced scions grafted onto silenced root stocks was not increased. When grafted scions which had become silenced were removed from silenced root stocks and regrafted onto non-silenced or vector-transformed root stocks, PTGS was maintained. However, their progeny did not show PTGS. Previously we reported that our transgenic lines had different target specificities of PTGS for RNA degradation: one line recognized only the 3' part of the transgene mRNA while others involved the whole transgene mRNA (Sonoda et al. 1999, Phytopathology, 89, 385-391). Using these lines, we showed that target specificity of PTGS induced in non-silenced scions after grafting was determined by that in silenced root stocks. However, unexpectedly, target specificity of PTGS induced in silenced scions was not changed [corrected] by grafting onto silenced root stocks showing different target specificity, indicating that the second PTGS from silenced root stocks was not superimposed to silenced scions.
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Affiliation(s)
- S Sonoda
- National Institute of Agrobiological Resources, Kan-nondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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