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Lund G, Lauria M, Guldberg P, Zaina S. Duplication-Dependent CG Suppression of the Seed Storage Protein Genes of Maize. Genetics 2003; 165:835-48. [PMID: 14573492 PMCID: PMC1462805 DOI: 10.1093/genetics/165.2.835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
This study investigates the prevalence of CG and CNG suppression in single- vs. multicopy DNA regions of the maize genome. The analysis includes the single- and multicopy seed storage proteins (zeins), the miniature inverted-repeat transposable elements (MITEs), and long terminal repeat (LTR) retrotransposons. Zein genes are clustered on specific chromosomal regions, whereas MITEs and LTRs are dispersed in the genome. The multicopy zein genes are CG suppressed and exhibit large variations in CG suppression. The variation observed correlates with the extent of duplication each zein gene has undergone, indicating that gene duplication results in an increased turnover of cytosine residues. Alignment of individual zein genes confirms this observation and demonstrates that CG depletion results primarily from polarized C:T and G:A transition mutations from a less to a more extensively duplicated gene. In addition, transition mutations occur primarily in a CG or CNG context suggesting that CG suppression may result from deamination of methylated cytosine residues. Duplication-dependent CG depletion is likely to occur at other loci as duplicated MITEs and LTR elements, or elements inserted into duplicated gene regions, also exhibit CG depletion.
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Affiliation(s)
- Gertrud Lund
- Plant Biochemistry Laboratory, Department of Plant Biology, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark.
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Abstract
Gene silencing has evolved in a broad range of organisms probably as defense mechanisms against invasive nucleic acids. Two major strategies are utilized. Transcriptional gene silencing (TGS) acts to prevent RNA synthesis and posttranscriptional gene silencing (PTGS) acts to degrade existing RNA. Although the final effects are similar, the mechanisms of TGS and PTGS are species specific. In most eukaryotes, gene silencing is associated with de novo DNA methylation. However, Caenorhabditis elegans shows an efficient PTGS-like mechanism but lacks a DNA methylation system. Additionally, key enzymes involved in plant and nematode PTGS, the cellular RNA-directed RNA polymerases, appear to be missing in Drosophila melanogaster. In this review, we discuss common features of TGS and PTGS that have been identified across species but for TGS we will concentrate only on methylation-mediated gene inactivation. This effort is complicated by the vague borders between gene silencing and normal gene regulation. Mechanisms that are involved in gene silencing are also used to regulate controlled expression of endogenous genes. To outline the general aspects, gene silencing will be defined as narrowly as possible. The intention behind this review is to stimulate discussion and we seek to facilitate this by introducing speculative concepts that could lead to some reappraisal of the literature.
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Affiliation(s)
- Michael Wassenegger
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Martinsried, Germany
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Mourrain P, Béclin C, Vaucheret H. Are gene silencing mutants good tools for reliable transgene expression or reliable silencing of endogenous genes in plants? GENETIC ENGINEERING 2001; 22:155-70. [PMID: 11501375 DOI: 10.1007/978-1-4615-4199-8_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- P Mourrain
- Laboratoire de Biologie Cellulaire INRA 78026 Versailles, France
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Abstract
Epigenetic silencing of transgenes and endogenous genes can occur at the transcriptional level (TGS) or at the posttranscriptional level (PTGS). Because they can be induced by transgenes and viruses, TGS and PTGS probably reflect alternative (although not exclusive) responses to two important stress factors that the plant's genome has to face: the stable integration of additional DNA into chromosomes and the extrachromosomal replication of a viral genome. TGS, which results from the impairment of transcription initiation through methylation and/or chromatin condensation, could derive from the mechanisms by which transposed copies of mobile elements and T-DNA insertions are tamed. PTGS, which results from the degradation of mRNA when aberrant sense, antisense, or double-stranded forms of RNA are produced, could derive from the process of recovery by which cells eliminate pathogens (RNA viruses) or their undesirable products (RNA encoded by DNA viruses). Mechanisms involving DNA-DNA, DNA-RNA, or RNA-RNA interactions are discussed to explain the various pathways for triggering (trans)gene silencing in plants.
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Affiliation(s)
- M. Fagard
- Laboratoire de Biologie Cellulaire, INRA, 78026 Versailles Cedex, France; e-mail:
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Cogoni C, Macino G. Homology-dependent gene silencing in plants and fungi: a number of variations on the same theme. Curr Opin Microbiol 1999; 2:657-62. [PMID: 10607623 DOI: 10.1016/s1369-5274(99)00041-7] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Homology-dependent gene silencing is a phenomenon that occurs in a broad range of organisms and has implications for both basic and applied science. Gene silencing is a mechanism that controls invading transposons and provides protection against virus infections. It also has evolutionary implications in genome maintenance. Recent studies have begun to unravel the molecular mechanisms of this puzzling phenomenon.
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Affiliation(s)
- C Cogoni
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Universita' di Roma La Sapienza, Roma, 00161, Italy.
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Vaucheret H, Béclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Mourrain P, Palauqui JC, Vernhettes S. Transgene-induced gene silencing in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 16:651-659. [PMID: 10069073 DOI: 10.1046/j.1365-313x.1998.00337.x] [Citation(s) in RCA: 220] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- H Vaucheret
- Laboratoire de Biologie Cellulaire, INRA, Versailles, France.
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Mittelsten Scheid O, Afsar K, Paszkowski J. Release of epigenetic gene silencing by trans-acting mutations in Arabidopsis. Proc Natl Acad Sci U S A 1998; 95:632-7. [PMID: 10939915 PMCID: PMC18472 DOI: 10.1073/pnas.95.2.632] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene silencing in plants inactivates trans-genes introduced into plants and/or endogenous homologous genes. This stable but potentially reversible loss of gene activity resembles epigenetic changes that occur in normal development. The stability of silencing implies the involvement of trans-acting components, although none of them have been identified so far. Here we report the finding of second-site mutations interfering with maintenance of the silent state. We mutagenized Arabidopsis thaliana plants carrying a silent transgene encoding hygromycin phosphotransferase (hpt) and therefore show a heritable hygromycin-sensitive phenotype. The M2 generation was screened for hygromycin resistance. Eight putative mutants (som1 to 8) were found that expressed the transgene and transmitted the expressed state to their progeny. All mutations were shown to reactivate a silent transgenic test locus in trans. The level of DNA methylation at the hpt locus and at centromeric repeats was found to be reduced in the som mutants. Complementation crosses indicated complex epigenetic interactions among the som mutant alleles and with the previously described ddm1 allele, which elicits DNA hypomethylation [Vongs, A., Kakutani, T, Martiensen, R.A. & Richards, E.J. (1993) Science 260, 1926-1928]. Som mutants can be classified into three groups: (i) allelic or interacting with ddm1 and with each other (som 1,4, and 5), (ii) nonallelic with ddm1 and som mutants of group A (som2), and (iii) mutants with slow resilencing after out-crosses, which hinders their classification (som 3, 6, 7 and 8).
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Caplan A, Berger PH, Naderi M. Phenotypic Variation Between Transgenic Plants: What is Making Gene Expression Unpredictable? ACTA ACUST UNITED AC 1998. [DOI: 10.1007/978-94-015-9125-6_27] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Mittelsten Scheid O, Jakovleva L, Afsar K, Maluszynska J, Paszkowski J. A change of ploidy can modify epigenetic silencing. Proc Natl Acad Sci U S A 1996; 93:7114-9. [PMID: 8692954 PMCID: PMC38945 DOI: 10.1073/pnas.93.14.7114] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A silent transgene in Arabidopsis thaliana was reactivated in an outcross but not upon selfing of hemizygous plants. This result could only be explained by assuming a genetic difference between the transgene-free gametes of the wild-type and hemizygous transgenic plants, respectively, and led to the discovery of ploidy differences between the parental plants. To investigate whether a change of ploidy by itself can indeed influence gene expression, we performed crosses of diploid or tetraploid plants with a strain containing a single copy of a transgenic resistance gene in an active state. We observed reduced gene expression of the transgene in triploid compared with diploid hybrids. This led to loss of the resistant phenotype at various stages of seedling development in part of the population. The gene inactivation was reversible. Thus, an increased number of chromosomes can result in a new type of epigenetic gene inactivation, creating differences in gene expression patterns. We discuss the possible impact of this finding for genetic diploidization in the light of widespread, naturally occurring polyploidy and polysomaty in plants.
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Abstract
Homology-dependent gene silencing phenomena in plants have received considerable attention, especially when it was discovered that the presence of homologous sequences not only affected the stability of transgene expression, but that the activity of endogenous genes could be altered after insertion of homologous transgenes into the genome. Homology-mediated inactivation most likely comprises at least two different molecular mechanisms that induce gene silencing at the transcriptional or posttranscriptional level, respectively. In this review we discuss different mechanistic models for plant-specific inactivation mechanisms and their relationship with repeat-specific silencing phenomena in other species.
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Affiliation(s)
- P. Meyer
- Max-Delbruck-Laboratorium in der MPG, Carl-von-Linne Weg 10, Koln, D-50829 Germany, Centre for Plant Biochemistry & Biotechnology and Department of Genetics, University of Leeds, Leeds LS2 9JT, United Kingdom, Max-Planck-Institut fur Zuchtungsforschung, Carl-von-Line Weg 10, Koln, D-50829 Germany
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Henskens YM, Veerman EC, Nieuw Amerongen AV. Cystatins in health and disease. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1996; 377:71-86. [PMID: 8868064 DOI: 10.1515/bchm3.1996.377.2.71] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proteolytic enzymes have many physiological functions in plants, bacteria, viruses, protozoa and mammals. They play a role in processes such as food digestion, complement activation or blood coagulation. The action of proteolytic enzymes is biologically controlled by proteinase inhibitors and increasing attention is being paid to the physiological significance of these natural inhibitors in pathological processes. The reason for this growing interest is that uncontrolled proteolysis can lead to irreversible damage e.g. in chronic inflammation or tumor metastasis. This review focusses on the possible role of the cystatins, natural and specific inhibitors of the cysteine proteinases, in pathological processes.
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Affiliation(s)
- Y M Henskens
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam (ACTA), Netherlands
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Puchta H, Swoboda P, Gal S, Blot M, Hohn B. Somatic intrachromosomal homologous recombination events in populations of plant siblings. PLANT MOLECULAR BIOLOGY 1995; 28:281-92. [PMID: 7599313 DOI: 10.1007/bf00020247] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Intrachromosomal homologous recombination in whole tobacco plants was analyzed using beta-glucuronidase as non-selectable marker. We found that recombination frequencies were additive for transgenes in allelic positions and could be enhanced by treatment of plants with DNA-damaging agents. We compared the patterns of distribution of recombination events of different transgenic lines of tobacco and Arabidopsis with the respective Poisson distributions. Some lines showed Poisson-like distributions, indicating that recombination at the transgene locus was occurring in a random fashion in the plant population. In other cases, however, the distributions deviated significantly from Poisson distributions indicating that for specific transgene loci and/or configurations recombination events are not randomly distributed in the population. This was due to overrepresentation of plants with especially many as well as especially few recombination events. Analysis of one tobacco line indicated furthermore that the distribution of recombination events could be influenced by treating the seedlings with external factors. Our results suggest that different plant individuals, or parts of them, might exhibit different transient 'states' of recombination competence. A possible model relating 'recombination silencing' and transcription silencing to heterochromatization of the transgene locus is discussed.
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Affiliation(s)
- H Puchta
- Friedrich Miescher-Institut, Basel, Switzerland
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