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Glenn SE, Geyer PK. Investigation of the Developmental Requirements of Drosophila HP1 and Insulator Protein Partner, HIPP1. G3 (BETHESDA, MD.) 2019; 9:345-357. [PMID: 30514714 PMCID: PMC6385973 DOI: 10.1534/g3.118.200705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/30/2018] [Indexed: 12/02/2022]
Abstract
Drosophila Suppressor of Hairy-wing [Su(Hw)] is a multifunctional zinc finger DNA binding protein. Transcriptional regulation by Su(Hw) is essential in the ovary and testis, where Su(Hw) functions primarily as a repressor. Recently, the HP1a and Insulator Partner Protein 1 (HIPP1) was found to extensively co-localize with Su(Hw) and other insulator binding proteins in euchromatic regions of the genome, and with Heterochromatin Protein 1a (HP1a) in heterochromatic regions. As HIPP1 is the homolog of the human co-repressor Chromodomain Y-Like (CDYL), we tested its requirement in establishing transcriptional repression in flies. To this end, we generated multiple Hipp1 null alleles and a tagged derivative of the endogenous gene (Hipp1GFP ), using CRISPR mutagenesis. We show that HIPP1 is a widely expressed nuclear protein that is dispensable for viability, as well as female and male fertility. We find that HIPP1 and HP1a display minimum co-localization in interphase cells, and HP1a-dependent transcriptional repression of several reporter genes is HIPP1-independent, indicating that HIPP1 is not essential for HP1a-dependent heterochromatin formation. Despite Su(Hw) having a major role in promoting HIPP1 occupancy in euchromatin, we show that HIPP1 is dispensable for the transcriptional and insulator functions of Su(Hw), indicating that HIPP1 is not a critical Su(Hw) cofactor. Further studies are needed to clarify the role of HIPP1 in Drosophila development.
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Affiliation(s)
| | - Pamela K Geyer
- Molecular Medicine Program
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
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2
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Abstract
Retroelements with long-terminal repeats (LTRs) inhabit nearly all eukaryotic genomes. During the time of their rich evolutionary history they have developed highly diverse forms, ranging from ordinary retrotransposons to complex pathogenic retroviruses such as HIV-I. Errantiviruses are a group of insect endogenous LTR elements that share structural and functional features with vertebrate endogenous retroviruses. The errantiviruses illustrate one of the evolutionary strategies of retrotransposons to become infective, which together with their similarities to vertebrate retroviruses make them an attractive object of research promising to shed more light on the evolution of retroviruses.
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Affiliation(s)
- Yury Stefanov
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
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3
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Carballar-Lejarazú R, Jasinskiene N, James AA. Exogenous gypsy insulator sequences modulate transgene expression in the malaria vector mosquito, Anopheles stephensi. Proc Natl Acad Sci U S A 2013; 110:7176-81. [PMID: 23584017 PMCID: PMC3645527 DOI: 10.1073/pnas.1304722110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Malaria parasites are transmitted to humans by mosquitoes of the genus Anopheles, and these insects are the targets of innovative vector control programs. Proposed approaches include the use of genetic strategies based on transgenic mosquitoes to suppress or modify vector populations. Although substantial advances have been made in engineering resistant mosquito strains, limited efforts have been made in refining mosquito transgene expression, in particular attenuating the effects of insertions sites, which can result in variations in phenotypes and impacts on fitness due to the random integration of transposon constructs. A promising strategy to mitigate position effects is the identification of insulator or boundary DNA elements that could be used to isolate transgenes from the effects of their genomic environment. We applied quantitative approaches that show that exogenous insulator-like DNA derived from the Drosophila melanogaster gypsy retrotransposon can increase and stabilize transgene expression in transposon-mediated random insertions and recombinase-catalyzed, site-specific integrations in the malaria vector mosquito, Anopheles stephensi. These sequences can contribute to precise expression of transgenes in mosquitoes engineered for both basic and applied goals.
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Affiliation(s)
- Rebeca Carballar-Lejarazú
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900; and
| | - Nijole Jasinskiene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900; and
| | - Anthony A. James
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900; and
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697-4500
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4
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Yasuda K, Ito M, Sugita T, Tsukiyama T, Saito H, Naito K, Teraishi M, Tanisaka T, Okumoto Y. Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2013; 32:505-516. [PMID: 24078785 PMCID: PMC3782648 DOI: 10.1007/s11032-013-9885-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 05/06/2013] [Indexed: 05/02/2023]
Abstract
Transposable elements (TEs) are DNA fragments that have the ability to move from one chromosomal location to another. The insertion of TEs into gene-rich regions often affects changes in the expression of neighboring genes. Miniature Ping (mPing) is an active miniature inverted-repeat TE discovered in the rice genome. It has been found to show exceptionally active transposition in a few japonica rice varieties, including Gimbozu, where mPing insertion rendered adjacent genes stress-inducible. In the Gimbozu population, it is highly possible that several genes with modified expression profiles are segregating due to the de novo mPing insertions. In our study, we utilized a screening system for detecting de novo mPing insertions in the upstream region of target genes and evaluated the effect of mPing on the stress response of the target genes. Screening for 17 targeted genes revealed five genes with the mPing insertion in their promoters. In most cases, the alteration of gene expression was observed under stress conditions, and there was no change in the expression levels of those five genes under normal conditions. These results indicate that the mPing insertion can be used as a genetic tool to modify an expression pattern of a target gene under stress conditions without changing the expression profiles of those under natural conditions.
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Affiliation(s)
- Kanako Yasuda
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Makoto Ito
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tomohiko Sugita
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Takuji Tsukiyama
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hiroki Saito
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Ken Naito
- Genebank, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602 Japan
| | - Masayoshi Teraishi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Takatoshi Tanisaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
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5
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Galán A, Rodríguez-Navarro S. Sus1/ENY2: a multitasking protein in eukaryotic gene expression. Crit Rev Biochem Mol Biol 2012; 47:556-68. [PMID: 23057668 DOI: 10.3109/10409238.2012.730498] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The purpose of this review is to provide a complete overview on the functions of the transcription/export factor Sus1. Sus1 is a tiny conserved factor in sequence and functions through the eukaryotic kingdom. Although it was discovered recently, research done to address the role of Sus1/ENY2 has provided in deep description of different mechanisms influencing gene expression. Initially found to interact with the transcription and mRNA export machinery in yeast, it is now clear that it has a broad role in mRNA biogenesis. Sus1 is necessary for histone H2B deubiquitination, mRNA export and gene gating. Moreover, interesting observations also suggest a link with the cytoplasmatic mRNP fate. Although the role of Sus1 in human cells is largely unknown, preliminary results suggest interesting links to pathological states that range from rare diseases to diabetes. We will describe what is known about Sus1/ENY2 in yeast and other eukaryotes and discuss some exciting open questions to be solved in the future.
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Affiliation(s)
- Amparo Galán
- Centro de Investigación Príncipe Felipe, CIPF. Gene Expression coupled to RNA Transport Laboratory, Eduardo Primo Yúfera, Valencia, Spain
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6
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Soshnev AA, Li X, Wehling MD, Geyer PK. Context differences reveal insulator and activator functions of a Su(Hw) binding region. PLoS Genet 2008; 4:e1000159. [PMID: 18704163 PMCID: PMC2493044 DOI: 10.1371/journal.pgen.1000159] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Accepted: 07/10/2008] [Indexed: 11/19/2022] Open
Abstract
Insulators are DNA elements that divide chromosomes into independent transcriptional domains. The Drosophila genome contains hundreds of binding sites for the Suppressor of Hairy-wing [Su(Hw)] insulator protein, corresponding to locations of the retroviral gypsy insulator and non-gypsy binding regions (BRs). The first non-gypsy BR identified, 1A-2, resides in cytological region 1A. Using a quantitative transgene system, we show that 1A-2 is a composite insulator containing enhancer blocking and facilitator elements. We discovered that 1A-2 separates the yellow (y) gene from a previously unannotated, non-coding RNA gene, named yar for y-achaete (ac) intergenic RNA. The role of 1A-2 was elucidated using homologous recombination to excise these sequences from the natural location, representing the first deletion of any Su(Hw) BR in the genome. Loss of 1A-2 reduced yar RNA accumulation, without affecting mRNA levels from the neighboring y and ac genes. These data indicate that within the 1A region, 1A-2 acts an activator of yar transcription. Taken together, these studies reveal that the properties of 1A-2 are context-dependent, as this element has both insulator and enhancer activities. These findings imply that the function of non-gypsy Su(Hw) BRs depends on the genomic environment, predicting that Su(Hw) BRs represent a diverse collection of genomic regulatory elements.
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Affiliation(s)
- Alexey A. Soshnev
- Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Xingguo Li
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Misty D. Wehling
- Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Pamela K. Geyer
- Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
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7
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Abstract
Active and silenced chromatin domains are often in close juxtaposition to one another, and enhancer and silencer elements operate over large distances to regulate the genes in these domains. The lack of promiscuity in the function of these elements suggests that active mechanisms exist to restrict their activity. Insulators are DNA elements that restrict the effects of long-range regulatory elements. Studies on different insulators from different organisms have identified common themes in their mode of action. Numerous insulators map to promoters of genes or have binding sites for transcription factors and like active chromatin hubs and silenced loci, insulators also cluster in the nucleus. These results bring into focus potential conserved mechanisms by which these elements might function in the nucleus.
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Affiliation(s)
- Lourdes Valenzuela
- Unit on Chromatin and Transcription, NICHD/NIH, Bethesda, Maryland 20892, USA
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8
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Akbari OS, Bousum A, Bae E, Drewell RA. Unraveling cis-regulatory mechanisms at the abdominal-A and Abdominal-B genes in the Drosophila bithorax complex. Dev Biol 2006; 293:294-304. [PMID: 16545794 DOI: 10.1016/j.ydbio.2006.02.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Revised: 02/07/2006] [Accepted: 02/14/2006] [Indexed: 11/23/2022]
Abstract
Genome sequencing has revealed that in metazoans, only a small percentage of DNA actually codes for functional proteins. Research efforts have focused on elucidating the purpose of the rest of the genome, which was initially largely thought of as mere 'junk' DNA. One genomic region that is proving to be a rich source of new information is the Drosophila bithorax complex (BX-C). At this homeotic gene complex, many different classes of cis-regulatory elements, such as insulators, silencers, enhancers, and promoters, work together to tightly control gene expression during development. Recent studies have begun to unravel the intricate nature of these regulatory interactions. The BX-C was first discovered and characterized by Ed Lewis over three decades ago. In his seminal 1978 Nature paper, Lewis speculated that "substances" originating from the nongenic regions of the BX-C may regulate expression of the neighboring abdominal-A and Abdominal-B homeotic genes. A number of discoveries in the last few years suggest that he was right. The activation of some of the cis-sequences at the complex appears to be controlled by nongenic transcription, providing a further level of regulatory complexity to regions of nonprotein coding DNA. The hope is that these studies of gene regulation at the BX-C in the humble fruit fly will provide clues as to how vast intergenic regions contribute to the incredible complexity of gene regulation in other species, including humans.
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Affiliation(s)
- Omar S Akbari
- Biology Department M/S 314, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557, USA
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9
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Ruiz MT, Carareto CMA. Copy number of P elements, KP/full-sized P element ratio and their relationships with environmental factors in Brazilian Drosophila melanogaster populations. Heredity (Edinb) 2003; 91:570-6. [PMID: 13130308 DOI: 10.1038/sj.hdy.6800360] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The P transposable element copy numbers and the KP/full-sized P element ratios were determined in eight Brazilian strains of Drosophila melanogaster. Strains from tropical regions showed lower overall P element copy numbers than did strains from temperate regions. Variable numbers of full-sized and defective elements were detected, but the full-sized P and KP elements were the predominant classes of elements in all strains. The full-sized P and KP element ratios were calculated and compared with latitude. The northernmost and southernmost Brazilian strains showed fewer full-sized elements than KP elements per genome, and the strains from less extreme latitudes had many more full-sized P than KP elements. However, no clinal variation was observed. Strains from different localities, previously classified as having P cytotype, displayed a higher or a lower proportion of KP elements than of full-sized P elements, as well as an equal number of the two element types, showing that the same phenotype may be produced by different underlying genomic components of the P-M system.
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Affiliation(s)
- M T Ruiz
- Departamento de Biologia, IBILCE, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265, Jardim Nazaré, São José do Rio Preto 15054-000, SP, Brazil
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10
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Hudson AM, Cooley L. Understanding the function of actin-binding proteins through genetic analysis of Drosophila oogenesis. Annu Rev Genet 2003; 36:455-88. [PMID: 12429700 DOI: 10.1146/annurev.genet.36.052802.114101] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Much of our knowledge of the actin cytoskeleton has been derived from biochemical and cell biological approaches, through which actin-binding proteins have been identified and their in vitro interactions with actin have been characterized. The study of actin-binding proteins (ABPs) in genetic model systems has become increasingly important for validating and extending our understanding of how these proteins function. New ABPs have been identified through genetic screens, and genetic results have informed the interpretation of in vitro experiments. In this review, we describe the molecular and ultrastructural characteristics of the actin cytoskeleton in the Drosophila ovary, and discuss recent genetic analyses of actin-binding proteins that are required for oogenesis.
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Affiliation(s)
- Andrew M Hudson
- Departments of Genetics Yale University School of Medicine, P.O. Box 208005, New Haven, Connecticut 06520-8005, USA.
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11
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Chen JL, Huisinga KL, Viering MM, Ou SA, Wu CT, Geyer PK. Enhancer action in trans is permitted throughout the Drosophila genome. Proc Natl Acad Sci U S A 2002; 99:3723-8. [PMID: 11904429 PMCID: PMC122591 DOI: 10.1073/pnas.062447999] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interactions between paired homologous genes can lead to changes in gene expression. Such trans-regulatory effects exemplify transvection and are displayed by many genes in Drosophila, in which homologous chromosomes are paired somatically. Transvection involving the yellow cuticle pigmentation gene can occur by at least two mechanisms, one involving the trans-action of enhancers on a paired promoter and a second involving pairing-mediated bypass of a chromatin insulator. A system was developed to evaluate whether the action of the yellow enhancers in trans could be reconstituted outside of the natural near telomeric location of the yellow gene. To this end, transgenic flies were generated that carried a yellow gene modified by the inclusion of strategically placed recognition sites for the Cre and FLP recombinases. Independent action of the recombinases produced a pair of derivative alleles, one enhancerless and the other promoterless, at each transgene location. Transvection between the derivatives was assessed by the degree of interallelic complementation. Complementation was observed at all eight sites tested. These studies demonstrate that yellow transvection can occur at multiple genomic locations and indicate that the Drosophila genome generally is permissive to enhancer action in trans.
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Affiliation(s)
- Ji-Long Chen
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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12
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Smith JE, Cronmiller C. TheDrosophila daughterlessgene autoregulates and is controlled by both positive and negativecisregulation. Development 2001; 128:4705-14. [PMID: 11731451 DOI: 10.1242/dev.128.23.4705] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
As the only class I helix-loop-helix transcription factor in Drosophila, Daughterless (Da) has generally been regarded as a ubiquitously expressed binding partner for other developmentally regulated bHLH transcription factors. From analysis of a novel tissue-specific allele, dalyh, we show that da expression is not constitutive, but is dynamically regulated. This transcriptional regulation includes somatic ovary-specific activation, autoregulation and negative regulation. Unexpectedly, the diverse functions of da may require that expression levels be tightly controlled in a cell and/or tissue-specific manner. Our analysis of dalyh identifies it as the first springer insertion that functions as an insulating element, with its disruptive activity mediated by the product of a fourth chromosome gene, Suppressor of lyh [Su(lyh)].
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Affiliation(s)
- J E Smith
- Department of Biology, Gilmer Hall, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904-4328, USA
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13
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Abstract
Chromatin boundary elements or insulators in metazoans delimit distinct chromosomal domains of gene expression. Recently, DNA sequences with properties similar to boundary elements were also discovered in Saccharomyces cerevisiae. These sequences block the spread of transcriptionally silent chromatin, the yeast equivalent of metazoan heterochromatin, and are referred to as 'heterochromatin barriers'. These barriers share no sequence homology but all consist of multiple binding sites for various regulatory proteins. Current data suggest that barriers may function in yeast by recruiting a protein complex that precludes nucleosome assembly and thereby disrupts a contiguous array of nucleosomes required for the spread of silent chromatin.
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Affiliation(s)
- X Bi
- Department of Biochemistry, University of Nebraska, Lincoln 68588-0664, USA.
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14
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Wei W, Brennan MD. Polarity of transcriptional enhancement revealed by an insulator element. Proc Natl Acad Sci U S A 2000; 97:14518-23. [PMID: 11114171 PMCID: PMC18951 DOI: 10.1073/pnas.011529598] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcriptional enhancers for genes transcribed by RNA polymerase II may be localized upstream or downstream of the stimulated promoter in their normal chromosomal context. They stimulate transcription in an orientation-independent manner when assayed on circular plasmids. We describe a transient transformation system to evaluate the orientation preference of transcriptional enhancers in Drosophila. To accomplish this, the gypsy insulator element was used to block bidirectional action of an enhancer on circular plasmids. In this system, as in the chromosome, blocking of enhancer activity requires wild-type levels of the su(Hw) protein. We evaluated the orientation preference for the relatively large (4.4 kb) Adh larval enhancer from Drosophila melanogaster, used in conjunction with a luciferase reporter gene under the control of a minimal Adh promoter. An orientation preference was revealed by insertion of a single copy of the insulator between the enhancer and the promoter. This orientation effect was greatly amplified when the promoter was weakened by removing binding sites for critical transcription factors, consistent with a mechanism of insulator action in which the insulator intercepts signals from the enhancer by competing with the promoter. The orientation preference, as much as 100-fold, is a property of the enhancer itself because it is displayed by gene constructions introduced into the chromosome regardless of the presence of the insulator in a distal location. These findings are most easily reconciled with a facilitated tracking mechanism for enhancer function in a native chromosomal environment.
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Affiliation(s)
- W Wei
- Department of Biochemistry and Molecular Biology, University of Louisville Medical School, Louisville, KY 40202, USA
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15
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Kaffer CR, Srivastava M, Park KY, Ives E, Hsieh S, Batlle J, Grinberg A, Huang SP, Pfeifer K. A transcriptional insulator at the imprinted H19/Igf2 locus. Genes Dev 2000. [DOI: 10.1101/gad.14.15.1908] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Igf2 and H19 exhibit parent-of-origin-specific monoallelic expression. H19 is expressed from the maternal chromosome and Igf2 from the paternal. The two genes share enhancer elements and monoallelic expression of both genes is dependent on cis-acting sequences upstream of the H19 promoter. In this work we examine the mechanisms by which this region silences the maternal Igf2 allele and we demonstrate that deletion of this region can result in high levels of activation of both H19and Igf2 from a single chromosome. Moreover, by inserting thiscis element between a promoter and its enhancer at a heterologous position, we demonstrate that the sequences carry both insulator activity and the ability to be stably imprinted. We also characterize the insulator in vitro and show that it is neither enhancer nor promoter specific.
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16
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Affiliation(s)
- L Girard
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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17
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Abstract
The HM loci in Saccharomyces cerevisiae constitute region-specific but gene-nonspecific repression domains, as a number of heterologous genes transcribed by RNA polymerase II or III are silenced when placed at these loci. The promoters of the Ashbya gossypii TEF gene and the S. cerevisiae TEF1 and TEF2 genes, however, are resistant to transcriptional silencing by the HM silencers in yeast. Moreover, when interposed between the HML alpha genes and the E silencer, certain segments of these promoters block the repression effect of the silencer on the alpha genes. All of these fragments contain UASrpg (upstream activation sequence of ribosome protein genes) composed of multiple binding sites for Rap1. In fact, a 149-bp segment consisting essentially of only three tandem Rap1-binding sites from the UASrpg of yeast TEF2 exhibits silencer-blocking activity. This element also exhibits insulating activity and orientation dependence characteristic of known chromatin boundary elements. Finally, the element blocks the physical spread of heterochromatin initiated at a silencer. This segment provides the first example of chromatin domain boundary or insulator elements in yeast.
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Affiliation(s)
- X Bi
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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18
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Golovnin A, Gause M, Georgieva S, Gracheva E, Georgiev P. The su(Hw) insulator can disrupt enhancer-promoter interactions when located more than 20 kilobases away from the Drosophila achaete-scute complex. Mol Cell Biol 1999; 19:3443-56. [PMID: 10207068 PMCID: PMC84137 DOI: 10.1128/mcb.19.5.3443] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we report that the su(Hw) insulator may not necessarily separate promoters from enhancers to allow inhibition of transcription by the su(Hw) protein. For this purpose we used the strains of Drosophila melanogaster which carry inversion of the region containing the yellow gene and the achaete-scute complex (AS-C). Despite the reverse orientation of the region, the AS-C enhancers continue to activate achaete and scute gene expression. The su(Hw) insulator, located more than 20 kb away from the inversion, facilitates strong suppression of achaete and scute gene expression, although is does not separate the promoters from the AS-C enhancers.
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Affiliation(s)
- A Golovnin
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117334, Russia
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19
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Donze D, Adams CR, Rine J, Kamakaka RT. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev 1999; 13:698-708. [PMID: 10090726 PMCID: PMC316548 DOI: 10.1101/gad.13.6.698] [Citation(s) in RCA: 297] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The chromosomes of eukaryotes are organized into structurally and functionally discrete domains that provide a mechanism to compact the DNA as well as delineate independent units of gene activity. It is believed that insulator/boundary elements separate these domains. Here we report the identification and characterization of boundary elements that flank the transcriptionally repressed HMR locus in the yeast Saccharomyces cerevisiae. Deletion of these boundary elements led to the spread of silenced chromatin, whereas the ectopic insertion of these elements between a silencer and a promoter blocked the repressive effects of the silencer on that promoter at HMR and at telomeres. Sequence analysis indicated that the boundary element contained a TY1 LTR, and a tRNA gene and mutational analysis has implicated the Smc proteins, which encode structural components of chromosomes, in boundary element function.
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Affiliation(s)
- D Donze
- Unit on Chromatin and Transcription, National Institutes of Child Health and Development (NICHD) Bethesda, Maryland 20892, USA
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20
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Morris JR, Chen J, Filandrinos ST, Dunn RC, Fisk R, Geyer PK, Wu C. An analysis of transvection at the yellow locus of Drosophila melanogaster. Genetics 1999; 151:633-51. [PMID: 9927457 PMCID: PMC1460495 DOI: 10.1093/genetics/151.2.633] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Studies of a wide variety of organisms have shown that homologous sequences can exert a significant impact on each other, resulting in changes in gene sequence, gene expression, chromatin structure, and global chromosome architecture. Our work has focused on transvection, a process that can cause genes to be sensitive to the proximity of a homologue. Transvection is seen at the yellow gene of Drosophila, where it mediates numerous cases of intragenic complementation. In this article, we describe two approaches that have characterized the process of transvection at yellow. The first entailed a screen for mutations that support intragenic complementation at yellow. The second involved the analysis of 53 yellow alleles, obtained from a variety of sources, with respect to complementation, molecular structure, and transcriptional competence. Our data suggest two ways in which transvection may be regulated at yellow: (1) a transcriptional mechanism, whereby the ability of an allele to support transvection is influenced by its transcriptional competency, and (2) a structural mechanism, whereby the pairing of structurally dissimilar homologues results in conformational changes that affect gene expression.
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Affiliation(s)
- J R Morris
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Morris JR, Chen JL, Geyer PK, Wu CT. Two modes of transvection: enhancer action in trans and bypass of a chromatin insulator in cis. Proc Natl Acad Sci U S A 1998; 95:10740-5. [PMID: 9724774 PMCID: PMC27965 DOI: 10.1073/pnas.95.18.10740] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ed Lewis introduced the term "transvection" in 1954 to describe mechanisms that can cause the expression of a gene to be sensitive to the proximity of its homologue. Transvection since has been reported at an increasing number of loci in Drosophila, where homologous chromosomes are paired in somatic tissues, as well as at loci in other organisms. At the Drosophila yellow gene, transvection can explain intragenic complementation involving the yellow2 allele (y2). Here, transvection was proposed to occur by enhancers of one allele acting in trans on the promoter of a paired homologue. In this report, we describe two yellow alleles that strengthen this model and reveal an unexpected, second mechanism for transvection. Data suggest that, in addition to enhancer action in trans, transvection can occur by enhancer bypass of a chromatin insulator in cis. We propose that bypass results from the topology of paired genes. Finally, transvection at yellow can occur in genotypes not involving y2, implying that it is a feature of yellow itself and not an attribute of one particular allele.
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Affiliation(s)
- J R Morris
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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22
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Vieira C, Aubry P, Lepetit D, Biémont C. A temperature cline in copy number for 412 but not roo/B104 retrotransposons in populations of Drosophila simulans. Proc Biol Sci 1998; 265:1161-5. [PMID: 9699309 PMCID: PMC1689186 DOI: 10.1098/rspb.1998.0413] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The copy number of the retrotransposable element 412 of Drosophila simulans from populations collected worldwide shows a negative correlation with minimum temperature. No association was detected for the roo/B104 element. The possibility that selective pressures might regulate the 412 copy number in these natural populations is supported by detection of selection against the detrimental effects of 412 insertions (estimated by the proportion of insertions on the X chromosome in comparison with the autosomes) but not roo/B104. These data reveal different spatial patterns for two element families, and strongly suggest that some factors in the environment, such as temperature, may interfere with the control of retrotransposition, thus affecting important aspects of genomic evolution.
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Affiliation(s)
- C Vieira
- Laboratoire de Biométrie, Génétique, Biologie des populations, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France.
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23
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Gause M, Hovhannisyan H, Kan T, Kuhfittig S, Mogila V, Georgiev P. hobo Induced rearrangements in the yellow locus influence the insulation effect of the gypsy su(Hw)-binding region in Drosophila melanogaster. Genetics 1998; 149:1393-405. [PMID: 9649529 PMCID: PMC1460218 DOI: 10.1093/genetics/149.3.1393] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The su(Hw) protein is responsible for the insulation mediated by the su(Hw)-binding region present in the gypsy retrotransposon. In the y2 mutant, su(Hw) protein partially inhibits yellow transcription by repressing the function of transcriptional enhancers located distally from the yellow promoter with respect to gypsy. y2 mutation derivatives have been induced by the insertion of two hobo copies on the both sides of gypsy: into the yellow intron and into the 5' regulatory region upstream of the wing and body enhancers. The hobo elements have the same structure and orientation, opposite to the direction of yellow transcription. In the sequence context, where two copies of hobo are separated by the su(Hw)-binding region, hobo-dependent rearrangements are frequently associated with duplications of the region between the hobo elements. Duplication of the su(Hw)-binding region strongly inhibits the insulation of the yellow promoter separated from the body and wing enhancers by gypsy. These results provide a better insight into mechanisms by which the su(Hw)-binding region affects the enhancer function.
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Affiliation(s)
- M Gause
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 117334, Russia
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24
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Netter S, Fauvarque MO, Diez del Corral R, Dura JM, Coen D. white+ transgene insertions presenting a dorsal/ventral pattern define a single cluster of homeobox genes that is silenced by the polycomb-group proteins in Drosophila melanogaster. Genetics 1998; 149:257-75. [PMID: 9584101 PMCID: PMC1460120 DOI: 10.1093/genetics/149.1.257] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We used the white gene as an enhancer trap and reporter of chromatin structure. We collected white+ transgene insertions presenting a peculiar pigmentation pattern in the eye: white expression is restricted to the dorsal half of the eye, with a clear-cut dorsal/ventral (D/V) border. This D/V pattern is stable and heritable, indicating that phenotypic expression of the white reporter reflects positional information in the developing eye. Localization of these transgenes led us to identify a unique genomic region encompassing 140 kb in 69D1-3 subject to this D/V effect. This region contains at least three closely related homeobox-containing genes that are constituents of the iroquois complex (IRO-C). IRO-C genes are coordinately regulated and implicated in similar developmental processes. Expression of these genes in the eye is regulated by the products of the Polycomb-group (Pc-G) and trithorax-group (trx-G) genes but is not modified by classical modifiers of position-effect variegation. Our results, together with the report of a Pc-G binding site in 69D, suggest that we have identified a novel cluster of target genes for the Pc-G and trx-G products. We thus propose that ventral silencing of the whole IRO-C in the eye occurs at the level of chromatin structure in a manner similar to that of the homeotic gene complexes, perhaps by local compaction of the region into a heterochromatin-like structure involving the Pc-G products.
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Affiliation(s)
- S Netter
- Embryologie Moléculaire et Expérimentale-Centre National de la Recherche Scientifique/Unité de Recherche Associée 2227, Université Paris Sud, 91405 Orsay Cedex, France
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25
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Kidwell MG, Lisch D. Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci U S A 1997; 94:7704-11. [PMID: 9223252 PMCID: PMC33680 DOI: 10.1073/pnas.94.15.7704] [Citation(s) in RCA: 428] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A tremendous wealth of data is accumulating on the variety and distribution of transposable elements (TEs) in natural populations. There is little doubt that TEs provide new genetic variation on a scale, and with a degree of sophistication, previously unimagined. There are many examples of mutations and other types of genetic variation associated with the activity of mobile elements. Mutant phenotypes range from subtle changes in tissue specificity to dramatic alterations in the development and organization of tissues and organs. Such changes can occur because of insertions in coding regions, but the more sophisticated TE-mediated changes are more often the result of insertions into 5' flanking regions and introns. Here, TE-induced variation is viewed from three evolutionary perspectives that are not mutually exclusive. First, variation resulting from the intrinsic parasitic nature of TE activity is examined. Second, we describe possible coadaptations between elements and their hosts that appear to have evolved because of selection to reduce the deleterious effects of new insertions on host fitness. Finally, some possible cases are explored in which the capacity of TEs to generate variation has been exploited by their hosts. The number of well documented cases in which element sequences appear to confer useful traits on the host, although small, is growing rapidly.
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Affiliation(s)
- M G Kidwell
- Department of Ecology and Evolutionary Biology and The Center for Insect Science, University of Arizona, Tucson, AZ 85721, USA.
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26
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Gdula DA, Gerasimova TI, Corces VG. Genetic and molecular analysis of the gypsy chromatin insulator of Drosophila. Proc Natl Acad Sci U S A 1996; 93:9378-83. [PMID: 8790337 PMCID: PMC38435 DOI: 10.1073/pnas.93.18.9378] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Boundary or insulator elements set up independent territories of gene activity by establishing higher order domains of chromatin structure. The gypsy retrotransposon of Drosophila contains an insulator element that represses enhancer-promoter interactions and is responsible for the mutant phenotypes caused by insertion of this element. The gypsy insulator inhibits the interaction of promoter-distal enhancers with the transcription complex without affecting the functionality of promoter-proximal enhancers; in addition, these sequences can buffer a transgene from chromosomal position effects. Two proteins have been identified that bind gypsy insulator sequences and are responsible for their effects on transcription. The suppressor of Hairy-wing [su(Hw)] protein affects enhancer function both upstream and downstream of its binding site by causing a silencing effect similar to that of heterochromatin. The modifier of mdg4 [mod(mdg4)] protein interacts with su(Hw) to transform this bi-directional repression into the polar effect characteristic of insulators. These effects seem to be modulated by changes in chromatin structure.
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Affiliation(s)
- D A Gdula
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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27
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Matyunina LV, Jordan IK, McDonald JF. Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation. Proc Natl Acad Sci U S A 1996; 93:7097-102. [PMID: 8692951 PMCID: PMC38942 DOI: 10.1073/pnas.93.14.7097] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Significant differences in levels of copia [Drosophila long terminal repeat (LTR) retrotransposon] expression exist among six species representing the Drosophila melanogaster species complex (D. melanogaster, Drosophila mauritiana, Drosophila simulans, Drosophila sechellia, Drosophila yakuba, and Drosophila erecta) and a more distantly related species (Drosophila willistoni). These differences in expression are correlated with major size variation mapping to putative regulatory regions of the copia 5' LTR and adjacent untranslated leader region (ULR). Sequence analysis indicates that these size variants were derived from a series of regional duplication events. The ability of the copia LTR-ULR size variants to drive expression of a bacterial chloramphenicol acetyltransferase reporter gene was tested in each of the seven species. The results indicate that both element-encoded (cis) and host-genome-encoded (trans) genetic differences are responsible for the variability in copia expression within and between Drosophila species. This finding indicates that models purporting to explain the dynamics and distribution of retrotransposons in natural populations must consider the potential impact of both element-encoded and host-genome-encoded regulatory variation to be valid. We propose that interelement selection among retrotransposons may provide a molecular drive mechanism for the evolution of eukaryotic enhancers which can be subsequently distributed throughout the genome by retrotransposition.
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Affiliation(s)
- L V Matyunina
- Department of Genetics, University of Georgia, Athens 30602, USA
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28
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Lankenau DH, Corces VG, Engels WR. Comparison of targeted-gene replacement frequencies in Drosophila melanogaster at the forked and white loci. Mol Cell Biol 1996; 16:3535-44. [PMID: 8668169 PMCID: PMC231348 DOI: 10.1128/mcb.16.7.3535] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
P element-induced gene conversion has been previously used to modify the white gene of Drosophila melanogaster in a directed fashion. The applicability of this approach of gene targeting in Drosophila melanogaster, however, has not been analyzed quantitatively for other genes. We took advantage of the P element-induced forked allele, f(hd), which was used as a target, and we constructed a vector containing a modified forked fragment for converting f(hd). Conversion frequencies were analyzed for this locus as well as for an alternative white allele, w(eh812). Combination of both P element-induced mutant genes allowed the simultaneous analysis of conversion frequencies under identical genetic, developmental, and environmental conditions. This paper demonstrates that gene conversion through P element-induced gap repair can be applied with similar success rates at the forked locus and in the white gene. The average conversion frequency at forked was 0.29%, and that at white was 0.17%. These frequencies indicate that in vivo gene targeting in Drosophila melanogaster should be applicable for other genes in this species at manageable rates. We also confirmed the homolog dependence of reversions at the forked locus, indicating that P elements transpose via a cut-and-paste mechanism. In a different experiment, we attempted conversion with a modified forked allele containing the su(Hw) binding site. Despite an increased sample size, there were no conversion events with this template. One interpretation (under investigation) is that the binding of the su(Hw) product prevents double-strand break repair.
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Affiliation(s)
- D H Lankenau
- Department of Developmental Genetics, German Cancer Research Center, Heidelberg, Germany
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Awasaki T, Juni N, Yoshida KM. An eye imaginal disc-specific transcriptional enhancer in the long terminal repeat of the tom retrotransposon is responsible for eye morphology mutations of Drosophila ananassae. MOLECULAR & GENERAL GENETICS : MGG 1996; 251:161-6. [PMID: 8668126 DOI: 10.1007/bf02172914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Optic morphology (Om) mutations of Drosophila ananassae are semidominant, neomorphic and nonpleiotropic, map to at least 22 loci scattered throughout the genome, and are associated with the insertion of the tom retrotransposon. Molecular and genetic analyses have revealed that eye morphology defects of Om mutants are caused by the ectopic or excessive expression of Om genes in the eye imaginal discs of third instar larvae. It is therefore assumed that the tom element carries tissue-specific gene regulatory sequences which enhance expression of the Om genes. In the present study, we examined whether or not the long terminal repeats (LTR) of the tom element contain such an eye imaginal disc-specific enhancer, using D. melanogaster transformants containing a lacZ gene ligated to the tom LTR. Analyses of lacZ gene expression in the eye imaginal discs of third instar larvae of 18 independently established transformant lines showed that the tom LTR was capable of enhancing lacZ expression in all the transformant lines, but the degree of enhancement varied between lines. In addition, the effect of the tom LTR lacZ gene evidently changed when the tom LTR construct was relocated to different chromosomal positions. On the basis of these findings, it is hypothesized that ectopic and excessive expression of the Om genes in the eye imaginal discs is induced by an eye imaginal disc-specific enhancer present in the tom LTR, the effect of which may be subject to chromosomal position effects.
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Affiliation(s)
- T Awasaki
- Department of Zoology, Faculty of Science, Hokkaido University, Sapporo, Japan
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30
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Abstract
Recent progress in understanding boundary and insulator elements has concentrated on the identification of their protein components. BEAF-32 is a protein present in the scs' element of Drosophila that is also localized to most interband regions and puffs of polytene chromosomes, suggesting a role in the organization of structural chromosomal domains. The suppressor of Hairy-wing and modifier of mdg4 proteins have been characterized as components of the gypsy insulator. The latter seems to play a crucial role in conferring on the insulator its ability to unidirectionally affect enhancer function.
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Affiliation(s)
- T I Gerasimova
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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31
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Gao GP, Herrera RJ. Enrichment of middle repetitive element Bm-1 transcripts in translationally active RNA fractions of the silkmoth, Bombyx mori. Genetica 1996; 97:173-82. [PMID: 8901137 DOI: 10.1007/bf00054624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The Bm-1 repetitive element family represents a group of transcribed repetitive sequences in the genome of the silkmoth Bombyx mori. In the Bm-5 and BmN permanent cell lines studied here, alpha-amanitin inhibition and nuclear 'run-on' experiments demonstrated that approximately 80% of the Bm-1 transcripts are produced by RNA polymerase II. Bm-1 transcripts are dramatically enriched in poly A+ and polysomal RNA fractions compared to total RNA in these two cell lines. In the Bm-5 cell line, from total to poly A+ and polysomal RNA fractions, Bm-1 transcripts are enriched approximately 4 and 2 times, respectively, while in the BmN cell line these same fractions are enriched about 2 and 19 times compared to total RNA. This suggests that the Bm-1 transcripts may be involved in post-transcriptional processes or control of translation. Our data also revealed less size heterogeneity of Bm-1 transcripts in polysomal as compared to nuclear fractions. In the Bm-5 and BmN cell lines, the size of most transcripts containing Bm-1 sequences increases from approximately 1700 nt in the nucleus to 3000 nt in the polysomal fraction, both fractions with RNA much larger than the Bm-1 consensus sequence (250 bp). This raises the possibility that some Bm-1 elements are transcribed as part of larger transcripts containing mRNA by way of 'read-through', and may be involved in post-transcriptional regulation of gene expression as cis and/or trans acting elements.
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Affiliation(s)
- G P Gao
- Department of Biological Sciences, Florida International University, Miami 33199, USA
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32
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Graham JE, Spanier JG, Jarvik JW. Isolation and characterization of Pioneer1, a novel Chlamydomonas transposable element. Curr Genet 1995; 28:429-36. [PMID: 8575015 DOI: 10.1007/bf00310811] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
During the course of this study a novel family of Chlamydomonas mobile elements has been identified in natural isolate strain 224. The first member of this class to be characterized, a 2.8-kb element named Pioneer1, was trapped in an intron of the nitrate reductase structural gene, NIT1. This element has been cloned and completely sequenced and found to be unusual in structure. Pioneer elements are present in a very low-copy number of three per genome in strain 224. The copy number increased by one upon transposition of Pioneer1. Hybridization of Pioneer1 to a variety of Chlamydomonas strains confirmed that this element differed from previously described Chlamydomonas transposons. It also indicated that related elements are present in low-copy number in natural isolate strains 356 and S1D2, but not in the most commonly used laboratory strains 137c and 21 gr. For these reasons, members of the Pioneer family might prove useful as insertional mutagens.
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Affiliation(s)
- J E Graham
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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33
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Gerasimova TI, Gdula DA, Gerasimov DV, Simonova O, Corces VG. A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation. Cell 1995; 82:587-97. [PMID: 7664338 DOI: 10.1016/0092-8674(95)90031-4] [Citation(s) in RCA: 239] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The suppressor of Hairy wing (su(Hw)) protein inhibits the function of transcriptional enhancers located distally from the promoter with respect to the location of su(Hw)-binding sites. This polarity is due to the ability of the su(Hw)-binding region to form a chromatin insulator. Mutations in modifier of mdg4 (mod(mdg4)) enhance the effect of su(Hw) by inhibiting the function of enhancers located on both sides of the su(Hw)-binding region. This inhibition results in a variegated expression pattern, and mutations in mod(mdg4) act as classical enhancers of position-effect variegation. The mod(mdg4) and su(Hw) proteins interact with each other. The mod(mdg4) protein controls the nature of the repressive effect of su(Hw): in the absence of mod(mdg4) protein, su(Hw) exerts a bidirectional silencing effect, whereas in the presence of mod(mdg4), the silencing effect is transformed into unidirectional repression.
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Affiliation(s)
- T I Gerasimova
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Abstract
Reverse transcription has been an important mediator of genomic change. This influence dates back more than three billion years, when the RNA genome was converted into the DNA genome. While the current cellular role(s) of reverse transcriptase are not yet completely understood, it has become clear over the last few years that this enzyme is still responsible for generating significant genomic change and that its activities are one of the driving forces of evolution. Reverse transcriptase generates, for example, extra gene copies (retrogenes), using as a template mature messenger RNAs. Such retrogenes do not always end up as nonfunctional pseudogenes but form, after reinsertion into the genome, new unions with resident promoter elements that may alter the gene's temporal and/or spatial expression levels. More frequently, reverse transcriptase produces copies of nonmessenger RNAs, such as small nuclear or cytoplasmic RNAs. Extremely high copy numbers can be generated by this process. The resulting reinserted DNA copies are therefore referred to as short interspersed repetitive elements (SINEs). SINEs have long been considered selfish DNA, littering the genome via exponential propagation but not contributing to the host's fitness. Many SINEs, however, can give rise to novel genes encoding small RNAs, and are the migrant carriers of numerous control elements and sequence motifs that can equip resident genes with novel regulatory elements [Brosius J. and Gould S.J., Proc Natl Acad Sci USA 89, 10706-10710, 1992]. Retrosequences, such as SINEs and portions of retroelements (e.g., long terminal repeats, LTRs), are capable of donating sequence motifs for nucleosome positioning, DNA methylation, transcriptional enhancers and silencers, poly(A) addition sequences, determinants of RNA stability or transport, splice sites, and even amino acid codons for incorporation into open reading frames as novel protein domains. Retroposition can therefore be considered as a major pacemaker for evolution (including speciation). Retroposons, with their unique properties and actions, form the molecular basis of important evolutionary concepts, such as exaptation [Gould S.J. and Vrba E., Paleobiology 8, 4-15, 1982] and punctuated equilibrium [Elredge N. and Gould S.J. in Schopf T.J.M. (ed). Models in Paleobiology. Freeman, Cooper, San Francisco, 1972, pp. 82-115].
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Affiliation(s)
- J Brosius
- Institute for Experimental Pathology, ZMBE University of Münster, Germany.
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35
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Tomkiel J, Fanti L, Berloco M, Spinelli L, Tamkun JW, Wakimoto BT, Pimpinelli S. Developmental genetical analysis and molecular cloning of the abnormal oocyte gene of Drosophila melanogaster. Genetics 1995; 140:615-27. [PMID: 7498741 PMCID: PMC1206639 DOI: 10.1093/genetics/140.2.615] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Studies of the abnormal oocyte (abo) gene of Drosophila melanogaster have previously been limited to the analysis of a single mutant allele, abnormal oocyte1 (abo1). The abo1 mutation causes a maternal-effect lethality that can be partially rescued zygotically by the abo+ allele and by increasing the dosage of specific regions of heterochromatin denoted ABO. This report describes the properties of abo2, a new P-element-induced allele that allowed us to reexamine the nature of maternal-effect defect. Comparisons of the phenotype of progeny of abo1/abo1 and abo1/abo2 females show that the preblastoderm lethality previously described as a component of the abo mutant maternal effect results from a recessive fertilization defect associated with the abo1 chromosome. We demonstrate here that the abo-induced maternal effect lethality occurs predominately late in embryogenesis after cuticle deposition but before hatching. The phenocritical period for zygotic rescue by heterochromatin coincides with this period of late embryogenesis. We have used the abo2 mutation to map and molecularly clone the gene. We show that the abo gene is located in the 32C cytogenetic interval and identify the putative abo transcript from mRNA isolated from adult females. Using germline transformation, we show that a 9-kb genomic fragment to which the transcript maps, partially fulfills requirement for maternal and zygotic abo+ function.
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Affiliation(s)
- J Tomkiel
- Department of Genetics, University of Washington, Seattle 98195, USA
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36
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Georgiev PG, Corces VG. The su(Hw) protein bound to gypsy sequences in one chromosome can repress enhancer-promoter interactions in the paired gene located in the other homolog. Proc Natl Acad Sci U S A 1995; 92:5184-8. [PMID: 7761470 PMCID: PMC41873 DOI: 10.1073/pnas.92.11.5184] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The suppressor of Hairy-wing [su(Hw)] protein exerts a polar effect on gene expression by repressing the function of transcriptional enhancers located distally from the promoter with respect to the location of su(Hw) binding sequences. The directionality of this effect suggests that the su(Hw) protein specifically interferes with the basic mechanism of enhancer action. Moreover, mutations in modifier of mdg4 [mod(mdg4)] result in the repression of expression of a gene when the su(Hw) protein is bound to sequences in the copy of this gene located in the homologous chromosome. This effect is dependent on the presence of the su(Hw) binding region from the gypsy retrotransposon in at least one of the chromosomes and is enhanced by the presence of additional gypsy sequences in the other homology. This phenomenon is inhibited by chromosomal rearrangements that disrupt pairing, suggesting that close apposition between the two copies of the affected gene is important for trans repression of transcription. These results indicate that, in the absence of mod-(mdg4) product, the su(Hw) protein present in one chromosome can act in trans and inactivate enhancers located in the other homolog.
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Affiliation(s)
- P G Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow
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37
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Pflugfelder GO, Heisenberg M. Optomotor-blind of Drosophila melanogaster: a neurogenetic approach to optic lobe development and optomotor behaviour. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART A, PHYSIOLOGY 1995; 110:185-202. [PMID: 7712063 DOI: 10.1016/0300-9629(94)00159-q] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The gene optomotor-blind (omb) plays a crucial role in Drosophila optic lobe development. Various mutations in omb lead to different structural defects in the adult optic lobes with correlated behavioural phenotypes. Molecular analysis of omb allows one to trace back behavioural defects to the spatio-temporal misexpression of the gene in mutant development.
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Slusarski DC, Motzny CK, Holmgren R. Mutations that alter the timing and pattern of cubitus interruptus gene expression in Drosophila melanogaster. Genetics 1995; 139:229-40. [PMID: 7705626 PMCID: PMC1206321 DOI: 10.1093/genetics/139.1.229] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The cubitus interruptus (ci) gene is a member of the Drosophila segment polarity gene family and encodes a protein with a zinc finger domain homologous to the vertebrate Gli genes and the nematode tra-1 gene. Three classes of existing mutations in the ci locus alter the regulation of ci expression and can be used to examine ci function during development. The first class of ci mutations causes interruptions in wing veins four and five due to inappropriate expression of the ci product in the posterior compartment of imaginal discs. The second class of mutations eliminates ci protein early in embryogenesis and causes the deletion of structures that are derived from the region including and adjacent to the engrailed expressing cells. The third class of mutations eliminates ci protein later in embryogenesis and blocks the formation of the ventral naked cuticle. The loss of ci expression at these two different stages in embryonic development correlates with the subsequent elimination of wingless expression. Adults heterozygous for the unique ciCe mutation have deletions between wing veins three and four. A similar wing defect is present in animals mutant for the segment polarity gene fused that encodes a putative serine/threonine kinase. In ciCe/+ and fused mutants, the deletions between wing veins three and four correlate with increased ci protein levels in the anterior compartment. Thus, proper regulation of both the ci mRNA and protein appears to be critical for normal Drosophila development.
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Affiliation(s)
- D C Slusarski
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208-3500
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Kuzin AB, Lyubomirskaya NV, Khudaibergenova BM, Ilyin YV, Kim AI. Precise excision of the retrotransposon gypsy from the forked and cut loci in a genetically unstable D. melanogaster strain. Nucleic Acids Res 1994; 22:4641-5. [PMID: 7984412 PMCID: PMC308512 DOI: 10.1093/nar/22.22.4641] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The genetically unstable Mutator Strain of D. melanogaster is characterised by a high frequency of spontaneous mutations and their reversions. Three forked mutants were obtained independently and several reversions arose spontaneously with frequency of 10(-3)-10(-4). The sites of integration and excision of the gypsy retrotransposon were analysed by Southern blot analysis and sequencing of PCR fragments. In all cases gypsy had inserted at the end of the third exon of the major transcript of the forked gene, causing the duplication of TCCA target sequence. All the reversions resulted from precise excision of the gypsy. A double mutant containing ct6 and f1, caused by gypsy insertions into untranslated regions of the corresponding genes, was constructed. Two spontaneous ct6f+ revertants as well as one ct+f1 revertant were obtained from this line. Sequence analysis of gypsy integration and excision sites revealed that in all cases gypsy excision was also precise. These experiments constitute the first demonstration of precise excision of LTR-containing elements from their host genomes.
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Affiliation(s)
- A B Kuzin
- V.A. Engelhardt Institute of Molecular Biology, Academy of Sciences of Russia, Moscow
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Hochstenbach R, Harhangi H, Schouren K, Hennig W. Degenerating gypsy retrotransposons in a male fertility gene on the Y chromosome of Drosophila hydei. J Mol Evol 1994; 39:452-65. [PMID: 7807535 DOI: 10.1007/bf00173414] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
During the evolution of the Y chromosome of Drosophila hydei, retrotransposons became incorporated into the lampbrush loop pairs formed by several of the male fertility genes on this chromosome. Although insertions of retrotransposons are involved in many spontaneous mutations, they do not affect the functions of these genes. We have sequenced gypsy elements that are expressed as constituents of male fertility gene Q in the lampbrush loop pair Nooses. We find that these gypsy elements are all truncated and specifically lost those sequences that may interfere with the continuity of lampbrush loop transcription. Only defective coding regions are found within the loop. Gypsy is not transcribed in loops of many other Drosophila species harboring the family. These results suggest that any contribution of gypsy to the function of male fertility gene Q does not depend on a conserved DNA sequence.
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Affiliation(s)
- R Hochstenbach
- Department of Molecular and Developmental Genetics, Faculty of Sciences, Catholic University of Nijmegen, The Netherlands
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41
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Abstract
"Insulator elements" have been identified that define the limits of transcriptionally active chromatin domains, protecting them against the repressive influence of neighboring heterochromatin.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, NICHHD, NIH, Bethesda, Maryland 20892
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42
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Grandbastien MA, Audeon C, Casacuberta JM, Grappin P, Lucas H, Moreau C, Pouteau S. Functional analysis of the tobacco Tnt1 retrotransposon. Genetica 1994; 93:181-9. [PMID: 7813914 DOI: 10.1007/bf01435250] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Retroelements represent by far the largest and most widespread class of mobile genetic elements. Representative of several classes of retrotransposons have been characterized in a broad range of plant species, but only a few of them have been shown to be active. Among these, the tobacco Tnt1 retrotransposon has been isolated after insertion mutagenesis and is one of the very few to be transcriptionally active. Tnt1 expression is strongly regulated in a tissue-specific and developmental manner. Moreover, Tnt1 expression is induced by a range of biotic or abiotic elicitors, which all have in common the ability to induce the plant defense response. Regulatory sequences involved in this elicitor-mediated induction have been located in the LTR U3 region. The link between Tnt1 activation and the plant defense response might represent an example of the involvement of transposable elements in genome restructurations needed in response to environmental fluctuations such as pathogen attacks.
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Affiliation(s)
- M A Grandbastien
- Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique--INRA, Cedex, France
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43
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Ito H, Hamabata T, Hori SH. Transcriptional activation of the Drosophila melanogaster glucose-6-phosphate dehydrogenase gene by insertion of defective P elements. MOLECULAR & GENERAL GENETICS : MGG 1993; 241:637-46. [PMID: 8264538 DOI: 10.1007/bf00279906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Tandem insertions of defective P elements (1.15 kb KP and 0.6 kb core P) accelerate the transcription rate of the glucose-6-phosphate dehydrogenase (G6PD) gene in Drosophila melanogaster. In this report, we have analyzed the activation mechanism of the G6PD promoter by in vitro transcription and gel retardation assays. Results showed that one cis-acting region in the core P and two such regions in the KP are associated with activation of the G6PD promoter, and that putative transcriptional regulatory protein(s) which specifically bind to each of the cis-acting regions are present in nuclear extracts of Canton S embryos. On the other hand, the P elements do not activate the normal actin 5C promoter, but activate the promoter when the 20 bp sequence around the G6PD transcription start site is placed in front of the promoter. It appears that the GC-rich region in this 20 bp sequence is required for the activation.
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Affiliation(s)
- H Ito
- Department of Zoology, Faculty of Science, Hokkaido University, Sapporo, Japan
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44
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Harrison DA, Gdula DA, Coyne RS, Corces VG. A leucine zipper domain of the suppressor of Hairy-wing protein mediates its repressive effect on enhancer function. Genes Dev 1993; 7:1966-78. [PMID: 7916729 DOI: 10.1101/gad.7.10.1966] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The suppressor of Hairy-wing [su(Hw)] protein mediates the mutagenic effect of the gypsy retrotransposon by repressing the function of transcriptional enhancers controlling the expression of the mutant gene. A structural and functional analysis of su(Hw) was carried out to identify domains of the protein responsible for its negative effect on enhancer action. Sequence comparison among the su(Hw) proteins from three different species allows the identification of evolutionarily conserved domains with possible functional significance. An acidic domain located in the carboxy-terminal end of the Drosophila melanogaster protein is not present in su(Hw) from other species, suggesting a nonessential role for this part of the protein. A second acidic domain located in the amino-terminal region of su(Hw) is present in all species analyzed. This domain is dispensable in the D. melanogaster protein when the carboxy-terminal acidic domain is present, but the protein is nonfunctional when both regions are simultaneously deleted. Mutations in the zinc fingers result in su(Hw) protein unable to interact with DNA in vivo, indicating a functional role for this region of the protein in DNA binding. Finally, a region of su(Hw) homologous to the leucine zipper motif is necessary for the negative effect of this protein on enhancer function, suggesting that su(Hw) might exert this effect by interacting, directly or indirectly, with transcription factors bound to these enhancers.
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Affiliation(s)
- D A Harrison
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218
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Roseman RR, Pirrotta V, Geyer PK. The su(Hw) protein insulates expression of the Drosophila melanogaster white gene from chromosomal position-effects. EMBO J 1993; 12:435-42. [PMID: 8382607 PMCID: PMC413226 DOI: 10.1002/j.1460-2075.1993.tb05675.x] [Citation(s) in RCA: 195] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations in the suppressor of Hairy-wing [su(Hw)] locus reverse the phenotype of a number of tissue-specific mutations caused by insertion of a gypsy retrotransposon. The su(Hw) gene encodes a zinc finger protein which binds to a 430 bp region of gypsy shown to be both necessary and sufficient for its mutagenic effects. su(Hw) protein causes mutations by inactivation of enhancer elements only when a su(Hw) binding region is located between these regulatory sequences and a promoter. To understand the molecular basis of enhancer inactivation, we tested the effects of su(Hw) protein on expression of the mini-white gene. We find that su(Hw) protein stabilizes mini-white gene expression from chromosomal position-effects in euchromatic locations by inactivating negative and positive regulatory elements present in flanking DNA. Furthermore, the su(Hw) protein partially protects transposon insertions from the negative effects of heterochromatin. To explain our current results, we propose that su(Hw) protein alters the organization of chromatin by creating a new boundary in a pre-existing domain of higher order chromatin structure. This separates enhancers and silencers distal to the su(Hw) binding region into an independent unit of gene activity, thereby causing their inactivation.
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Affiliation(s)
- R R Roseman
- Department of Biochemistry, University of Iowa, College of Medicine, Iowa City 52242
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Geyer PK, Corces VG. DNA position-specific repression of transcription by a Drosophila zinc finger protein. Genes Dev 1992; 6:1865-73. [PMID: 1327958 DOI: 10.1101/gad.6.10.1865] [Citation(s) in RCA: 318] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Expression of the yellow (y) gene of Drosophila melanogaster is controlled by a series of tissue-specific transcriptional enhancers located in the 5' region and intron of the gene. Insertion of the gypsy retrotransposon in the y2 allele at -700 bp from the start of transcription results in a spatially restricted phenotype: Mutant tissues are those in which yellow expression is controlled by enhancers located upstream from the insertion site, but all other structures whose enhancers are downstream of the insertion site are normally pigmented. This observation can be reproduced by inserting just a 430-bp fragment containing the suppressor of Hairy-wing [su(Hw)]-binding region of gypsy into the same position where this element is inserted in y2, suggesting that the su(Hw)-binding region is sufficient to confer the mutant phenotype. Insertion of this sequence into various positions in the y gene gives rise to phenotypes that can be rationalized assuming that the presence of the su(Hw) protein inhibits the action of those tissue-specific enhancers that are located more distally from the su(Hw)-binding region with respect to the promoter. These results are discussed in light of current models that explain long-range effects of enhancers on gene expression.
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Affiliation(s)
- P K Geyer
- Department of Biochemistry, University of Iowa, College of Medicine, Iowa City 52242
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47
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Abstract
Studies of transcriptional control sequences responsible for regulated and basal-level RNA synthesis from promoters of Drosophila melanogaster retrotransposons reveal novel aspects of gene regulation and lead to identification of trans-acting factors that can be involved in RNA polymerase II transcription not only of retrotransposons, but of many other cellular genes. Comparisons between promoters of retrotransposons and some other Drosophila genes demonstrate that there is a greater variety in basal promoter structure than previously thought and that many promoters may contain essential sequences downstream from the RNA start site.
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Affiliation(s)
- I R Arkhipova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
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48
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Woodruff RC. Transposable DNA elements and life history traits. I. Transposition of P DNA elements in somatic cells reduces the lifespan of Drosophila melanogaster. Genetica 1992; 86:143-54. [PMID: 1334906 DOI: 10.1007/bf00133717] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As an initial study of the influence of transposable DNA elements on life history traits, and as a model system for estimating the impact of somatic genetic damage on longevity, the effect of P DNA element movement in somatic cells on adult lifespan was measured in Drosophila melanogaster males. Lifespan was significantly reduced in males that contained the somatically active P[ry+ delta 2-3](99B) element and 17, 4, 3, but not just a single P element. Furthermore, there appears to be a direct correlation between the number of transposing P elements and the amount of lifespan reduction. This reduction in lifespan observed in males with somatically active P elements is probably due to genetic damage in embryos, larvae and pupae from P-element excisions and insertions, leading to changes in gene structure and regulation, chromosome breakage, and subsequent cell death in adults. This hypothesis is supported in this study by a significant increase in recessive sex-linked lethal mutations in the same males that had reduced lifespans and by the previous observation of chromosome breakage in somatic cells of similar males. The evolutionary implications of these results are discussed, including the possible influence of somatic DNA transpositions on fitness and other life history traits.
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Affiliation(s)
- R C Woodruff
- Department of Biological Sciences, Bowling Green State University, OH 43403
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49
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von Sternberg RM, Novick GE, Gao GP, Herrera RJ. Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA. Genetica 1992; 86:215-46. [PMID: 1334910 DOI: 10.1007/bf00133722] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Transposable and interspersed repetitive elements (TIREs) are ubiquitous features of both prokaryotic and eukaryotic genomes. However, controversy has arisen as to whether these sequences represent useless 'selfish' DNA elements, with no cellular function, as opposed to useful genetic units. In this review, we selected two insect species, the Dipteran Drosophila and the Lepidopteran Bombyx mori (the silkmoth), in an attempt to resolve this debate. These two species were selected on the basis of the special interest that our laboratory has had over the years in Bombyx with its well known molecular and developmental biology, and the wealth of genetic data that exist for Drosophila. In addition, these two species represent contrasting repetitive element types and patterns of distribution. On one hand, Bombyx exhibits the short interspersion pattern in which Alu-like TIREs predominate while Drosophila possesses the long interspersion pattern in which retroviral-like TIREs are prevalent. In Bombyx, the main TIRE family is Bm-1 while the Drosophila group contains predominantly copia-like elements, non-LTR retroposons, bacterial-type retroposons and fold-back transposable elements sequences. Our analysis of the information revealed highly non-random patterns of both TIRE biology and evolution, more indicative of these sequences acting as genomic symbionts under cellular regulation rather than useless or selfish junk DNA. In addition, we extended our analysis of potential TIRE functionality to what is known from other eukaryotic systems. From this study, it became apparent that these DNA elements may have originated as innocuous or selfish sequences and then adopted functions. The mechanism for this conversion from non-functionality to specific roles is a process of coevolution between the repetitive element and other cellular DNA often times in close physical proximity. The resulting interdependence between repetitive elements and other cellular sequences restrict the number of evolutionarily successful mutational changes for a given function or cistron. This mutual limitation is what we call genome canalization. Well documented examples are discussed to support this hypothesis and a mechanistic model is presented for how such genomic canalization can occur. Also proposed are empirical studies which would support or invalidate aspects of this hypothesis.
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Affiliation(s)
- R M von Sternberg
- Department of Biological Sciences, Florida International University, Miami 33199
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50
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Abstract
Transposable elements, and retroviral-like elements in particular, are a rich potential source of genetic variation within a host's genome. Many mutations of endogenous genes in phylogenetically diverse organisms are due to insertion of elements that affect gene expression by altering the normal pattern of regulation. While few such associations are known to have been maintained over time, two recently elucidated examples suggest transposable elements may have a significant impact in evolution of gene expression. The first example, concerning the mouse sex-limited protein (Slp), clearly establishes that ancient retroviral enhancer sequences now confer hormonal dependence on the adjacent gene. The second example shows that within the human amylase gene family, salivary specific expression has arisen due to inserted sequences, deriving perhaps from a conjunction of two retrotransposable elements.
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Affiliation(s)
- D M Robins
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor 48109
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