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Chen P, Kotov AA, Godneeva BK, Bazylev SS, Olenina LV, Aravin AA. piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. Genes Dev 2021; 35:914-935. [PMID: 33985970 PMCID: PMC8168559 DOI: 10.1101/gad.345041.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Abstract
Small noncoding piRNAs act as sequence-specific guides to repress complementary targets in Metazoa. Prior studies in Drosophila ovaries have demonstrated the function of the piRNA pathway in transposon silencing and therefore genome defense. However, the ability of the piRNA program to respond to different transposon landscapes and the role of piRNAs in regulating host gene expression remain poorly understood. Here, we comprehensively analyzed piRNA expression and defined the repertoire of their targets in Drosophila melanogaster testes. Comparison of piRNA programs between sexes revealed sexual dimorphism in piRNA programs that parallel sex-specific transposon expression. Using a novel bioinformatic pipeline, we identified new piRNA clusters and established complex satellites as dual-strand piRNA clusters. While sharing most piRNA clusters, the two sexes employ them differentially to combat the sex-specific transposon landscape. We found two piRNA clusters that produce piRNAs antisense to four host genes in testis, including CG12717/pirate, a SUMO protease gene. piRNAs encoded on the Y chromosome silence pirate, but not its paralog, to exert sex- and paralog-specific gene regulation. Interestingly, pirate is targeted by endogenous siRNAs in a sibling species, Drosophila mauritiana, suggesting distinct but related silencing strategies invented in recent evolution to regulate a conserved protein-coding gene.
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Affiliation(s)
- Peiwei Chen
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Alexei A Kotov
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Baira K Godneeva
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Sergei S Bazylev
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Ludmila V Olenina
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
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Kuan YS, Brewer-Jensen P, Bai WL, Hunter C, Wilson CB, Bass S, Abernethy J, Wing JS, Searles LL. Drosophila suppressor of sable protein [Su(s)] promotes degradation of aberrant and transposon-derived RNAs. Mol Cell Biol 2009; 29:5590-603. [PMID: 19687295 PMCID: PMC2756875 DOI: 10.1128/mcb.00039-09] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 02/16/2009] [Accepted: 08/09/2009] [Indexed: 11/20/2022] Open
Abstract
RNA-binding proteins act at various stages of gene expression to regulate and fine-tune patterns of mRNA accumulation. One protein in this class is Drosophila Su(s), a nuclear protein that has been previously shown to inhibit the accumulation of mutant transcripts by an unknown mechanism. Here, we have identified several additional RNAs that are downregulated by Su(s). These Su(s) targets include cryptic wild-type transcripts from the developmentally regulated Sgs4 and ng1 genes, noncoding RNAs derived from tandemly repeated alphabeta/alphagamma elements within an Hsp70 locus, and aberrant transcripts induced by Hsp70 promoter transgenes inserted at ectopic sites. We used the alphabeta RNAs to investigate the mechanism of Su(s) function and obtained evidence that these transcripts are degraded by the nuclear exosome and that Su(s) promotes this process. Furthermore, we showed that the RNA binding domains of Su(s) are important for this effect and mapped the sequences involved to a 267-nucleotide region of an alphabeta element. Taken together, these results suggest that Su(s) binds to certain nascent transcripts and stimulates their degradation by the nuclear exosome.
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Affiliation(s)
- Yung-Shu Kuan
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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Bergman CM, Quesneville H, Anxolabéhère D, Ashburner M. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biol 2007; 7:R112. [PMID: 17134480 PMCID: PMC1794594 DOI: 10.1186/gb-2006-7-11-r112] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 11/13/2006] [Accepted: 11/29/2006] [Indexed: 11/10/2022] Open
Abstract
An analysis of high-resolution transposable element annotations in Drosophila melanogaster suggests the existence of a global surveillance system against the majority of transposable elements families in the fly. Background The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the contribution of TEs to genomes sequences. Results Using a high-resolution annotation of TEs in Release 4 genome sequence, we revise estimates of TE abundance in Drosophila melanogaster. We show that TEs are non-randomly distributed within regions of high and low TE abundance, and that pericentromeric regions with high TE abundance are mosaics of distinct regions of extreme and normal TE density. Comparative analysis revealed that this punctate pattern evolves jointly by transposition and duplication, but not by inversion of TE-rich regions from unsequenced heterochromatin. Analysis of genome-wide patterns of TE nesting revealed a 'nesting network' that includes virtually all of the known TE families in the genome. Numerous directed cycles exist among TE families in the nesting network, implying concurrent or overlapping periods of transpositional activity. Conclusion Rapid restructuring of the genomic landscape by transposition and duplication has recently added hundreds of kilobases of TE sequence to pericentromeric regions in D. melanogaster. These events create ragged transitions between unique and repetitive sequences in the zone between euchromatic and beta-heterochromatic regions. Complex relationships of TE nesting in beta-heterochromatic regions raise the possibility of a co-suppression network that may act as a global surveillance system against the majority of TE families in D. melanogaster.
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Affiliation(s)
- Casey M Bergman
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Hadi Quesneville
- Laboratoire de Bioinformatique et Génomique, Institut Jacques Monod, place Jussieu, 75251 Paris cedex 05, France
| | - Dominique Anxolabéhère
- Laboratoire Dynamique du Génome et Évolution, Institut Jacques Monod, place Jussieu, 75251 Paris cedex 05, France
| | - Michael Ashburner
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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Rasmussen EB, Lis JT. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc Natl Acad Sci U S A 1993; 90:7923-7. [PMID: 8367444 PMCID: PMC47259 DOI: 10.1073/pnas.90.17.7923] [Citation(s) in RCA: 282] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The regulation of many eukaryotic genes occurs at the level of transcriptional elongation. On the uninduced hsp70 gene of Drosophila melanogaster, for example, an RNA polymerase II complex has initiated transcription but has paused early in elongation. In this study, we examine pausing on hsp70 and two of the small heat shock genes (hsp27 and hsp26) at high resolution, using a technique that utilizes paramagnetic particle-mediated selection of terminated run-on transcripts. This technique provides precise information on the distribution of RNA polymerase within each transcription unit. It also details the progression of 5' cap formation on the elongating transcripts. For each gene, we find polymerases paused over a relatively narrow promoter-proximal region. The regions are generally around 20 nucleotides wide, with two preferred pausing positions spaced roughly 10 nucleotides apart or about one turn of the helix. The bulk of capping occurs as transcripts pass between 20 and 30 nucleotides in length. Interestingly, in the three genes examined here, elongational pausing and 5' cap formation appear largely coincident.
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Affiliation(s)
- E B Rasmussen
- Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853
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Abstract
Major alterations in genetic activity have been observed in every organism after exposure to abnormally high temperatures. This phenomenon, called the heat shock response, was discovered in the fruit fly Drosophila. Studies with this organism led to the discovery of the heat shock proteins, whose genes were among the first eukaryotic genes to be cloned. Several of the most important aspects of the regulation of the heat shock response and of the functions of the heat shock proteins have been unraveled in Drosophila.
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Affiliation(s)
- D Pauli
- Département de Zoologie et Biologie Animale, Université de Genève, Chêne-Bougeries, Switzerland
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Lee H, Kraus KW, Wolfner MF, Lis JT. DNA sequence requirements for generating paused polymerase at the start of hsp70. Genes Dev 1992; 6:284-95. [PMID: 1737619 DOI: 10.1101/gad.6.2.284] [Citation(s) in RCA: 164] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA polymerase II is transcriptionally engaged but paused approximately 25 nucleotides from the start site of the hsp70 gene of Drosophila melanogaster in uninduced (non-heat-shocked) flies. Here, we identify regions of the hsp70 promoter that are required for formation of this paused polymerase. Various hsp70 promoter sequences are substituted for promoter sequences of a yolk protein gene, yp1, which, in males, is normally not expressed and has no paused polymerase. Run-on assays with nuclei of male transgenic flies are used to measure the level of paused polymerase on the hybrid genes. Sequences that reside upstream of the hsp70 TATA element, when fused upstream of the yp1 TATA element, specify the formation of a paused polymerase on the 5' end of this hybrid gene. Within this region are multiple copies of the GAGA element, which is known to bind a constitutively expressed factor. This element appears to play a role in generating the pause. Also, in the absence of much of this upstream region, hsp70 sequences in the vicinity of the transcriptional start and pause site participate in specifying the pause. Deletions of the pause site reduce the level of paused polymerase but do not lead to constitutive transcription. However, a connection between transcription and pausing is seen. The level of paused polymerase on the various hybrid hsp70-yp1 promoters correlates with the promoter's potential to direct heat-induced transcription.
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Affiliation(s)
- H Lee
- Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853
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Abstract
Promoter function for hsp70 gene expression in Drosophila melanogaster was studied with an in vivo competition assay. A polymer of 40 tandem copies of the pair of regulatory elements of the hsp70 gene was constructed and cloned into a plasmid vector. Various marked genes were cotransfected with the polymer plasmid into Schneider line 2 cells, and their expression was determined by enzyme activity measurements. The polymer dramatically inhibited expression of cotransfected hsp70, hsp26, and hsp83 genes, but not cotransfected copia and histone genes. Our results indicate that in vivo, a trans-acting, positive regulatory factor, which can be titrated by heat shock consensus sequences, is required for activation of heat shock genes and is specific for these genes; the coordinate induction of different heat shock genes appears to be mediated by similar, but not identical, interactions of the trans-acting induction factor and the cis-acting heat shock consensus sequences; and the uninduced or basal level expression of the transfected hsp70 gene is also due to interaction of the consensus sequence with a positively acting factor.
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9
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Abstract
Promoter function for hsp70 gene expression in Drosophila melanogaster was studied with an in vivo competition assay. A polymer of 40 tandem copies of the pair of regulatory elements of the hsp70 gene was constructed and cloned into a plasmid vector. Various marked genes were cotransfected with the polymer plasmid into Schneider line 2 cells, and their expression was determined by enzyme activity measurements. The polymer dramatically inhibited expression of cotransfected hsp70, hsp26, and hsp83 genes, but not cotransfected copia and histone genes. Our results indicate that in vivo, a trans-acting, positive regulatory factor, which can be titrated by heat shock consensus sequences, is required for activation of heat shock genes and is specific for these genes; the coordinate induction of different heat shock genes appears to be mediated by similar, but not identical, interactions of the trans-acting induction factor and the cis-acting heat shock consensus sequences; and the uninduced or basal level expression of the transfected hsp70 gene is also due to interaction of the consensus sequence with a positively acting factor.
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Lanks KW, Hitti IF, Chin NW. Substrate utilization for lactate and energy production by heat-shocked L929 cells. J Cell Physiol 1986; 127:451-6. [PMID: 3086328 DOI: 10.1002/jcp.1041270315] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The hypothesis that heat shock protein (HSP) induction depends on inhibition of respiration was tested by examining the effects of heat shock on tricarboxylic acid (TCA) cycle function. In control L929 cell cultures, glucose and exogenous pyruvate were converted primarily to lactate, and glutamine was extensively oxidized, accounting for more than one-half of the calculated ATP production. During heat shock at 42 degrees C, lactate production from all of the labeled substrates and total unlabeled lactate production increased significantly while oxygen consumption increased slightly. TCA cycle oxidation of pyruvate decreased during this period while that of glutamine increased. Uncoupling of oxidative phosphorylation caused large increases in oxygen consumption at both 37 degrees C and 42 degrees C, indicating that the capacity of the respiratory chain is not exceeded during heat shock. The net effect of these alterations in substrate utilization were decreased ATP generation and increased NADH utilization. Both 14CO2 and lactate production declined during the 24-h period after cultures were returned to 37 degrees C. On the basis of these data, we conclude that while inhibition of respiration plays no apparent role, other metabolic consequences of heat shock related to energy metabolism may be involved in HSP induction.
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Hickey E, Brandon SE, Potter R, Stein G, Stein J, Weber LA. Sequence and organization of genes encoding the human 27 kDa heat shock protein. Nucleic Acids Res 1986; 14:4127-45. [PMID: 3714473 PMCID: PMC339850 DOI: 10.1093/nar/14.10.4127] [Citation(s) in RCA: 252] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The 27 kDa human heat shock protein (hsp27) is encoded by a gene family of 4 members. Two genomic fragments hybridizing to cDNA encoding hsp27 have been isolated, characterized, and sequenced. One clone is a member of a cluster of three genes linked within a 14-18 kb region of the genome and encodes a transcript interrupted by two intervening sequences. A single open reading frame encodes a polypeptide of 22,300 deduced molecular weight. The 5' flanking region contains two transcription start sites and sequences homologous to the Drosophila consensus heat inducible control element. Induction of both potential transcripts follows heat shock in vivo. Accurate heat inducible transcription occurs at both start sites after injection into Xenopus oocytes. The second genomic clone is a processed pseudogene lacking promoter elements and is unlinked with the other members of the hsp27 gene family. The amino acid sequence of human hsp27 shows striking homology with mammalian alpha crystallin, and contains a region towards the carboxy terminus which shares homology with the small hsp of Drosophila and other organisms.
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12
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The heat shock consensus sequence is not sufficient for hsp70 gene expression in Drosophila melanogaster. Mol Cell Biol 1985. [PMID: 3920509 DOI: 10.1128/mcb.5.1.197] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A hybrid gene in which the expression of an Escherichia coli beta-galactosidase gene was placed under the control of a Drosophila melanogaster 70,000-dalton heat shock protein (hsp70) gene promoter was constructed. Mutant derivatives of this hybrid gene which contained promoter sequences of different lengths were prepared, and their heat-induced expression was examined in D. melanogaster and COS-1 (African green monkey kidney) cells. Mutants with 5' nontranscribed sequences of at least 90 and up to 1,140 base pairs were expressed strongly in both cell types. Mutants with shorter 5' extensions (of at least 63 base pairs) were transcribed and translated efficiently in COS-1 but not at all in D. melanogaster cells. Thus, in contrast to the situation in COS-1 cells, the previously defined heat shock consensus sequence which is located between nucleotides 62 and 48 of the hsp70 gene 5' nontranscribed DNA segment is not sufficient for the expression of the D. melanogaster gene in homologous cells. A second consensus-like element 69 to 85 nucleotides upstream from the cap site is postulated to be also involved in the heat-induced expression of the hsp70 gene in D. melanogaster cells.
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Amin J, Mestril R, Lawson R, Klapper H, Voellmy R. The heat shock consensus sequence is not sufficient for hsp70 gene expression in Drosophila melanogaster. Mol Cell Biol 1985; 5:197-203. [PMID: 3920509 PMCID: PMC366694 DOI: 10.1128/mcb.5.1.197-203.1985] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A hybrid gene in which the expression of an Escherichia coli beta-galactosidase gene was placed under the control of a Drosophila melanogaster 70,000-dalton heat shock protein (hsp70) gene promoter was constructed. Mutant derivatives of this hybrid gene which contained promoter sequences of different lengths were prepared, and their heat-induced expression was examined in D. melanogaster and COS-1 (African green monkey kidney) cells. Mutants with 5' nontranscribed sequences of at least 90 and up to 1,140 base pairs were expressed strongly in both cell types. Mutants with shorter 5' extensions (of at least 63 base pairs) were transcribed and translated efficiently in COS-1 but not at all in D. melanogaster cells. Thus, in contrast to the situation in COS-1 cells, the previously defined heat shock consensus sequence which is located between nucleotides 62 and 48 of the hsp70 gene 5' nontranscribed DNA segment is not sufficient for the expression of the D. melanogaster gene in homologous cells. A second consensus-like element 69 to 85 nucleotides upstream from the cap site is postulated to be also involved in the heat-induced expression of the hsp70 gene in D. melanogaster cells.
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Abstract
The response of cells to a heat shock or other stresses is the activation of a small number of genes which were previously inactive or transcribed at low levels. This response has been observed in a wide variety of bacterial, plant, and animal species. Evidence is accumulating that at least some of the proteins found in diverse species are similar, indicating a conservation of the response and the proteins in evolution. In a number of organisms a strong positive correlation has been found between the presence of heat shock proteins and ability of the organism to withstand thermal stress. This review attempts to assess the available data concerning the homology of proteins in different species, the localization of the proteins in cells, and the relationship between heat shock proteins and thermoresistance.
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Abstract
The myc gene seems to have a causal role in tumour formation in man, mouse and avian systems. The myc gene product has been localized to the nucleus, suggesting that it may be involved in the regulation of gene expression. The level of expression of the mammalian heat shock protein 70 (HSP70) gene is elevated in several tumour cell lines, implying that a cellular function expressed in these tumour lines can stimulate HSP70 production. We report here that the gene product of a rearranged mouse c-myc gene is capable of stimulating expression of chimaeric genes containing a Drosophila hsp70 promoter region and 5'-flanking sequences. This stimulation is dependent on sequences located more than 200 bases 5' of the normal start of hsp70 transcription.
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Lengyel JA, Graham ML. Transcription, export and turnover of Hsp70 and alpha beta, two Drosophila heat shock genes sharing a 400 nucleotide 5' upstream region. Nucleic Acids Res 1984; 12:5719-35. [PMID: 6431397 PMCID: PMC320026 DOI: 10.1093/nar/12.14.5719] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A highly homologous 400 nucleotide sequence flanks the 5' end and extends 64 NT into the transcribed portion of all five hsp70 and seven alpha beta heat shock genes in Drosophila melanogaster (1-4). To determine the extent to which this sequence dictates coordinate regulation, we compared the total mass, continuous labeling and pulse-labeling of hsp70 and alpha beta RNAs at different times and temperatures of heat shock. By all these measurements, expression of both hsp70 and alpha beta genes increased and decreased in parallel. Hsp70 RNA was generally synthesized at a higher rate and accumulated to a greater extent than alpha beta RNA. As the temperature of heat shock increased, however, the rate of synthesis and accumulation of hsp70 relative to alpha beta RNA decreased. Another difference was that a larger fraction of hsp 70, as compared to alpha beta RNA was exported from the nucleus. For both RNAs, export decreased as the heat shock temperature was increased. The hsp70 and alpha beta genes are thus expressed in parallel, but the homologous 5' upstream sequences do not dictate equal rates of transcription or export from the nucleus.
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Semeshin VF, Baricheva EM, Belyaeva ES, Zhimulev IF. Electron microscopical analysis of Drosophila polytene chromosomes. Chromosoma 1982. [DOI: 10.1007/bf00338490] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Voellmy R, Rungger D. Transcription of a Drosophila heat shock gene is heat-induced in Xenopus oocytes. Proc Natl Acad Sci U S A 1982; 79:1776-80. [PMID: 6804945 PMCID: PMC346063 DOI: 10.1073/pnas.79.6.1776] [Citation(s) in RCA: 81] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Xenopus cells, like many other eukaryotic cells, respond to heat treatments by increasing the rate of synthesis of a few characteristic proteins, the heat shock proteins. Because of the generality of this response, it seemed possible to examine the expression of isolated heat shock genes in a heterologous system. Phage 122 DNA, containing two identical genes coding for the Drosophila 70,000-dalton heat shock protein (hsp70 genes), was microinjected into Xenopus oocyte nuclei. The Drosophila hsp70 genes are transcribed efficiently in heat-treated oocytes (35-37 degrees C) to give RNA of the correct size and sequence content. Transcription is sensitive to low levels of alpha-amanitin and therefore is carried out by RNA polymerase II. At normal temperatures (20-28 degrees C) essentially no Drosophila-specific RNA is formed. The isolated insert fragment of phage 122 also gives RNA of correct length in heat-treated oocytes which hybridizes to the coding segment of Drosophila hsp70 genes only. At normal temperatures, however, its rate of transcription is variable and only RNA heterogeneous in size is formed.
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