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Mangiarotti G, Giorda R, Ceccarelli A, Perlo C. mRNA stabilization controls the expression of a class of developmentally regulated genes in Dictyostelium discoideum. Proc Natl Acad Sci U S A 2010; 82:5786-90. [PMID: 16593597 PMCID: PMC390637 DOI: 10.1073/pnas.82.17.5786] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During the development of Dictyostelium discoideum, several thousand new mRNA species appear in the cytoplasm after the cells have formed stable aggregates. Here we show that six of these late mRNAs, corresponding to six clones randomly chosen from a genomic library, are synthesized from the very beginning of development at a rate comparable to that observed late in development but that transcripts do not accumulate until after aggregation. The early- and late-synthesized mRNAs are identical in size and compete with each other for hybridization to the genomic clones. The early-synthesized mRNAs do not accumulate in the cytoplasm in the preaggregation stage because they are very unstable. Their stability, estimated from the kinetics of incorporation during continuous labeling with (32)P, increases by perhaps an order of magnitude in the postaggregation stage. We conclude that mRNA stabilization is the major controlling factor of the expression of these genes.
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Affiliation(s)
- G Mangiarotti
- Cattedra di Biologia Generale, Universitá di Torino, Ospedale San Luigi di Orbassano, Turin, Italy
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2
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Blumberg DD, Margolskee JP, Barklis E, Chung SN, Cohen NS, Lodish HF. Specific cell-cell contacts are essential for induction of gene expression during differentiation of Dictyostelium discoideum. Proc Natl Acad Sci U S A 2010; 79:127-31. [PMID: 16593139 PMCID: PMC345675 DOI: 10.1073/pnas.79.1.127] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Postaggregation Dictyostelium discoideum cells contain 2000-3000 mRNA species that are absent from pre-aggregation cells. These aggregation-dependent sequences compose 30% of the mass of the late mRNA and represent the transcription products of an additional 11% of the single-copy genome. By analysis of mutants that are blocked at different stages of differentiation, we show that induction of expression of these genes is correlated with the formation of tight cell-cell contacts that resist EDTA. In particular, mutants that exhibit chemotaxis and aggregate to form loose mounds but do not form cell-cell contacts that resist EDTA fail to induce these late mRNA and protein species. By contrast, mutants that form normal contacts but progress no further through development do express the late mRNA species. Thus, interactions at the cell surface are involved in developmental induction of a large group of coregulated mRNAs. We have employed two independent assays for these developmentally regulated mRNAs: hybridization of gel-separated RNAs to cloned nuclear DNAs and hybridization of mRNA to a cDNA probe specific for the population of 2000-3000 regulated sequences.
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Affiliation(s)
- D D Blumberg
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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3
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Affiliation(s)
- Igor B Dawid
- Laboratory of Molecular Genetics, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892.
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4
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Benoit GR, Tong JH, Balajthy Z, Lanotte M. Exploring (novel) gene expression during retinoid-induced maturation and cell death of acute promyelocytic leukemia. Semin Hematol 2001; 38:71-85. [PMID: 11172541 DOI: 10.1016/s0037-1963(01)90007-1] [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: 01/13/2023]
Abstract
During recent years, reports have shown that biological responses of acute promyelocytic leukemia (APL) cells to retinoids are more complex than initially envisioned. PML-RARalpha chimeric protein disturbs various biological processes such as cell proliferation, differentiation, and apoptosis. The distinct biological programs that regulate these processes stem from specific transcriptional activation of distinct (but overlapping) sets of genes. These programs are sometimes mutually exclusive and depend on whether the signals are delivered by RAR or RXR agonists. Furthermore, evidence that retinoid nuclear signaling by retinoid, on its own, is not enough to trigger these cellular responses is rapidly accumulating. Indeed, work with NB4 cells show that the fate of APL cells treated by retinoid depends on complex signaling cross-talk. Elucidation of the sequence of events and cascades of transcriptional regulation necessary for APL cell maturation will be an additional tool with which to further improve therapy by retinoids. In this task, the classical techniques used to analyze gene expression have proved time consuming, and their yield has been limited. Global analyses of the APL cell transcriptome are needed. We review the technical approaches currently available (differential display, complementary DNA microarrays), to identify novel genes involved in the determination of cell fate.
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Affiliation(s)
- G R Benoit
- INSERM U-496, Institut Universitaire d'Hématologie, H pital Saint-Louis, Paris, France
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5
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Clark MD, Panopoulou GD, Cahill DJ, Büssow K, Lehrach H. Construction and analysis of arrayed cDNA libraries. Methods Enzymol 1999; 303:205-33. [PMID: 10349647 DOI: 10.1016/s0076-6879(99)03015-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
For any attempt to understand the biology of an organism the incorporation of a cDNA-based approach is unavoidable, because it is a major approach to studying gene function. The complete sequence of the genome alone is not sufficient to understand any organism; its gene regulation, expression, splice variation, posttranslational modifications, and protein-protein interactions all need to be addressed. Because the majority of vertebrate genes have probably been identified as ESTs the next stage of the Human Genome Project is attributing functional information to these sequences. In most cases hybridization-based approaches on arrayed pieces of DNA represent the most efficient way to study the expression level and splicing of a gene in a given tissue. Similar technology, now being applied at the protein level using protein expression libraries, high-density protein membranes, and antibody screening, should allow studies of protein localization and modifications. Coupled to these approaches is the use of technologies, which although lacking the highly parallel nature of hybridization, can potentially characterize large numbers of samples individually and with high accuracy. Automated gel-based DNA sequencing is an example of such a technique; protein sequencing and mass fingerprinting are further examples. In the case of mass spectroscopic analysis, the speed and sensitivity are vastly superior to that of gel-based approaches; however, the preparation of samples is more tedious. Our laboratory is developing a system to characterize DNA samples by mass spectrometry, allowing more rapid genotyping than is currently possible using gel-based technologies ([symbol: see text]. Gut, [symbol: see text]. Berlin and H. Lehrach, personal communication, 1998). Such technology would make information on gene polymorphisms widely accessible. Data generated using all of these techniques at the DNA and protein level will be connected by both protein expression libraries and database comparisons; finally, two hybrid library screens will identify many of the protein-protein interactions, linking genes together. In this way we will start to understand the interplay between genes on a global scale, both at the level of molecular interaction and the biological processes they regulate.
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Affiliation(s)
- M D Clark
- Max Planck Institut für Molekulare Genetik, Berlin, Dahlem, Germany
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6
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Sakata M, Kurachi H, Morishige K, Ogura K, Yamaguchi M, Nishio Y, Ikegami H, Miyake A, Murata Y. Messenger RNA differential display reverse-transcriptase-polymerase-chain-reaction analysis of a progestogen-suppressive gene in a human endometrial-cancer cell line. Int J Cancer 1998; 78:125-9. [PMID: 9724104 DOI: 10.1002/(sici)1097-0215(19980925)78:1<125::aid-ijc20>3.0.co;2-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Progestogen suppresses the progression of endometrial cancer and has an important effect on the secretory change of human endometrium. We characterized the progestogen-induced alterations of gene expression in a human endometrial-cancer cell line using a mRNA differential-display reverse-transcriptase-polymerase-chain-reaction (DDRT-PCR) method. After 5-day incubation of Ishikawa endometrial-cancer cells, with or without 100 nM medroxyprogesterone acetate (M PA), total RNA was isolated from confluent cells. We identified 8 candidate genes by mRNA differential display by screening up to approximately 3,000 mRNA species. Among these, 2 genes named T21A and T21B showed a decrease in mRNA by MPA treatment when analyzed by Northern blot. Nucleotide sequence showed that clone T21A was part of human mitochondrial short-chain enoyl-CoA hydratase cDNA. The other clone, T21B, showed no homology with any known nucleotide sequences. Northern-blot analysis using T21A and T21B clones as probes showed a decrease in mRNA in human endometrium from the luteal stage, with high serum estradiol and progesterone levels, as compared with that from the early follicular stage, with low serum estradiol and progesterone levels, and that from the pre-ovulatory stage with high serum estradiol and low progesterone levels. These findings suggest that mRNA DDRT-PCR could be used to identify the candidate genes regulated by progestogen in human endometrial cancer and in normal human endometrium.
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Affiliation(s)
- M Sakata
- Department of Obstetrics and Gynecology, Osaka University Medical School, Suita, Japan
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7
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Calvet JP. Molecular approaches for analyzing differential gene expression: differential cDNA library construction and screening. Pediatr Nephrol 1991; 5:751-7. [PMID: 1768589 DOI: 10.1007/bf00857891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Complementary deoxyribonucleic acid (cDNA) libraries can be used as a means to isolate and identify cell-specific messenger ribonucleic acid (mRNA) sequences. The basic elements of cDNA library construction and screening are reviewed in the context of analyzing differentially expressed mRNAs. A brief overview of the recombinant DNA systems applied to cDNA library construction and the principles of screening cDNA libraries by plaque hybridization are provided. Methods for comparing mRNA populations by differential screening and by competition hybridization are discussed, and methods for constructing subtracted cDNA libraries, enriched in differentially expressed sequences, are presented. Also reviewed are the analysis of differentially expressed cDNAs by Southern and Northern hybridization, RNase protection, polymerase chain reaction, and sequencing.
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Affiliation(s)
- J P Calvet
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City 66103
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8
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Kalland KH, Kalvenes MB, Oyan AM, Haukenes G. Study of transcription in measles virus-infected Vero cells using cDNA probes prepared from poly(A)RNA from uninfected and infected cells. APMIS 1991; 99:33-41. [PMID: 1671552 DOI: 10.1111/j.1699-0463.1991.tb05115.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
From af primary plasmid cDNA library prepared from measles virus-infected Vero cell poly(A)RNA, 435 clones selected at random were used to examine the sensitivity and specificity of cDNA probes derived from total poly(A)RNA from uninfected and infected Vero cells. The correlation between the abundance level of a particular species in the cDNA probe and the hybridization signal strength generated by the corresponding cDNA clone on a filter was reliably determined only when at least three independently prepared filters were examined. Variation in the amount of target plasmid was the most important cause of spurious signals. Variation in cDNA insert length did not disturb the signal strength within certain limits. cDNA species with abundance levels down to 0.08-0.01% were able to produce a hybridization signal above background. Unspecific cross-hybridization was shown to define the sensitivity limit of mixed cDNA probes. Despite the many false signals present at different stages, cDNA probes provided valuable information: the cDNA probes were used to monitor relative RNA expression levels and to clone five different measles virus transcripts and 2 host cell transcripts more abundantly expressed in infected cells. The abundance levels of the measles virus nucleocapsid, phosphoprotein, matrix, fusion protein and haemagglutinin genes were 1.5%, 1.5%, 1%, 0.75% and 0.5%, respectively, of the total cDNA library.
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Affiliation(s)
- K H Kalland
- Department of Microbiology and Immunology, Gade Institute, University of Bergen, Norway
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9
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cDNA cloning and characterization of interleukin 2-induced genes in a cloned T helper lymphocyte. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38396-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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10
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Blumberg DD, Comer JF, Walton EM. Ca++ antagonists distinguish different requirements for cAMP-mediated gene expression in the cellular slime mold, Dictyostelium discoideum. Differentiation 1989; 41:14-21. [PMID: 2553517 DOI: 10.1111/j.1432-0436.1989.tb00727.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cyclic AMP is essential for the accumulation of many prespore mRNAs and can advance the time of appearance of mRNAs specifically enriched in prestalk cells. Additionally, when late-developing cells are washed free of cAMP, a number of growth phase mRNAs reaccumulate. This reaccumulation can be suppressed by cAMP. These effects of cAMP are all mediated through the cell surface cAMP receptor and can occur under conditions where the receptor-associated adenylate cyclase is inactive, indicating that the initial intracellular transduction event necessary for expression of these mRNAs does not depend upon cAMP synthesis. The dihydropyridine derivatives, nifedipine and nitrendipine, are highly specific Ca++ channel blockers. They are shown here to prevent the influx of Ca++ from the external medium that occurs in response to cAMP binding to the cell surface receptor during development. These two compounds as well as another Ca++ antagonist, 8-N,N-diethylamino)octyl-3,4,5-trimethoxy-benzoate (TMB-8) and a calmodulin inhibitor, N-(6-amino-hexyl)-5-chloro-1-naphthalene sulfonamide (W7), all specifically decrease cAMP-mediated prespore mRNA accumulation in a dose-dependent manner. They also prevent cAMP from suppressing the expression of the growth phase genes. The growth phase mRNAs reaccumulate in cAMP-treated cells in the presence of increasing concentrations of these drugs. By contrast, cAMP induction of the pre-stalk-enriched mRNA is not as significantly affected by these agents. These results raise the possibility that the cell surface cAMP receptor can couple to different signal transduction systems and thereby induce or suppress the expression of different sets of cAMP-regulated genes during development.
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Affiliation(s)
- D D Blumberg
- Department of Biological Sciences, University of Maryland Baltimore County, Catonsville 21228
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11
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Pavlovic J, Banz E, Parish RW. The effects of transcription on the nucleosome structure of four Dictyostelium genes. Nucleic Acids Res 1989; 17:2315-32. [PMID: 2704621 PMCID: PMC317598 DOI: 10.1093/nar/17.6.2315] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Micrococcal nuclease digestion of Dictyostelium discoideum nuclei from various developmental stages was used to investigate transcription-related changes in the chromatin structure of the coding region of four genes. Gene activity was determined by Northern blotting and nuclear run on experiments. During strong transcription of the developmentally regulated cysteine proteinase I gene, a smear superimposed on a nucleosomal ladder was observed, indicating perturbation of nucleosomal structure was occurring. However, two other developmentally regulated genes, discoidin I and pSC253, showed only slight nucleosome disruption during high levels of transcription. The chromatin structure of a fourth gene (pCZ22) was disrupted throughout development, even at those stages where transcription was greatly reduced. We suggest that although nucleosome structure can be transiently perturbed by the passage of the transcription complex in vivo, the degree of perturbation and the speed with which nucleosomes reassemble is also influenced by the DNA sequence.
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Affiliation(s)
- J Pavlovic
- Institut für Immunologie und Virologie, Universität Zürich, Switzerland
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12
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Kidane GZ, Samaras N, Spithill TW. Cloning of Developmentally Regulated Genes from Leishmania major and Expression following Heat Induction. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)84989-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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13
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Lu X, Werner D. Construction and quality of cDNA libraries prepared from cytoplasmic RNA not enriched in poly(A)+RNA. Gene X 1988; 71:157-64. [PMID: 2463957 DOI: 10.1016/0378-1119(88)90087-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Poly(A)+RNA and cytoplasmic RNA of Ehrlich ascites tumor cells grown in vivo were used to study the quality and efficiency of cDNA synthesis. It was found that the rates of oligo(dT)-primed and unprimed reverse transcription were very similar in both cases. The size distributions of the cDNA strands prepared from unfractionated RNA reflected the size of cytoplasmic mRNA populations including a significant fraction of long molecules up to 6 kb. The fraction of cDNAs primed on rRNAs by oligo(dT) was found to be as low as 2-3%. Following second-strand synthesis by means of RNase H-induced nick translation by DNA polymerase I the overall yields in double-stranded cDNA were slightly higher when unfractionated cytoplasmic RNA was used as starting template. In repeated experiments we obtained an average yield of 2.2 micrograms of double-stranded cDNA when 70 micrograms of unfractionated cytoplasmic RNA was used as starting material. This amount of cDNA synthesized in one assay was sufficient to construct representative cDNA libraries in different vectors. Southern hybridizations of DNA isolated from cDNA libraries with various radiolabelled probes show that the libraries constructed from cDNA synthesized from cytoplasmic RNA not enriched in poly(A)+RNA contain a high ratio of full-length cDNA clones. The results suggest that representative cDNA libraries of high quality can be constructed without pre-isolation of poly(A)+RNA fractions.
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Affiliation(s)
- X Lu
- Institut für Zell- und Tumorbiologie, Deutsches Krebsforschungszentrum, Heidelberg, F.R.G
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14
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Golden JW, Carrasco CD, Mulligan ME, Schneider GJ, Haselkorn R. Deletion of a 55-kilobase-pair DNA element from the chromosome during heterocyst differentiation of Anabaena sp. strain PCC 7120. J Bacteriol 1988; 170:5034-41. [PMID: 3141375 PMCID: PMC211568 DOI: 10.1128/jb.170.11.5034-5041.1988] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The filamentous cyanobacterium Anabaena sp. strain PCC 7120 produces terminally differentiated heterocysts in response to a lack of combined nitrogen. Heterocysts are found approximately every 10th cell along the filament and are morphologically and biochemically specialized for nitrogen fixation. At least two DNA rearrangements occur during heterocyst differentiation in Anabaena sp. strain PCC 7120, both the result of developmentally regulated site-specific recombination. The first is an 11-kilobase-pair (kb) deletion from within the 3' end of the nifD gene. The second rearrangement occurs near the nifS gene but has not been completely characterized. The DNA sequences found at the recombination sites for each of the two rearrangements show no similarity to each other. To determine the topology of the rearrangement near the nifS gene, cosmid libraries of vegetative-cell genomic DNA were constructed and used to clone the region of the chromosome involved in the rearrangement. Cosmid clones which spanned the DNA separating the two recombination sites that define the ends of the element were obtained. The restriction map of this region of the chromosome showed that the rearrangement was the deletion of a 55-kb DNA element from the heterocyst chromosome. The excised DNA was neither degraded nor amplified, and its function, if any, is unknown. The 55-kb element was not detectably transcribed in either vegetative cells or heterocysts. The deletion resulted in placement of the rbcLS operon about 10 kb from the nifS gene on the chromosome. Although the nifD 11-kb and nifS 55-kb rearrangements both occurred under normal aerobic heterocyst-inducing conditions, only the 55-kb excision occurred in argon-bubbled cultures, indicating that the two DNA rearrangements can be regulated differently.
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Affiliation(s)
- J W Golden
- Department of Biology, Texas A&M University, College Station 77843
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15
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Epstein-Barr virus shuttle vector for stable episomal replication of cDNA expression libraries in human cells. Mol Cell Biol 1988. [PMID: 2841588 DOI: 10.1128/mcb.8.7.2837] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efficient transfection and expression of cDNA libraries in human cells has been achieved with an Epstein-Barr virus-based subcloning vector (EBO-pcD). The plasmid vector contains a resistance marker for hygromycin B to permit selection for transformed cells. The Epstein-Barr virus origin for plasmid replication (oriP) and the Epstein-Barr virus nuclear antigen gene have also been incorporated into the vector to ensure that the plasmids are maintained stably and extrachromosomally. Human lymphoblastoid cells can be stably transformed at high efficiency (10 to 15%) by such plasmids, thereby permitting the ready isolation of 10(6) to 10(7) independent transformants. Consequently, entire high-complexity EBO-pcD expression libraries can be introduced into these cells. Furthermore, since EBO-pcD plasmids are maintained as episomes at two to eight copies per cell, intact cDNA clones can be readily isolated from transformants and recovered by propagation in Escherichia coli. By using such vectors, human cells have been stably transformed with EBO-pcD-hprt to express hypoxanthine-guanine phosphoribosyltransferase and with EBO-pcD-Leu-2 to express the human T-cell surface marker Leu-2 (CD8). Reconstruction experiments with mixtures of EBO-pcD plasmids demonstrated that one clone of EBO-pcD-hprt per 10(6) total clones or one clone of EBO-pcD-Leu-2 per 2 x 10(4) total clones can be recovered intact from the transformed cells. The ability to directly select for expression of very rare EBO-pcD clones and to then recover these episomes should make it possible to clone certain genes where hybridization and immunological screening methods are not applicable but where a phenotype can be scored or selected in human cell lines.
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16
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Pears CJ, Williams JG. Multiple copies of a G-rich element upstream of a cAMP-inducible Dictyostelium gene are necessary but not sufficient for efficient gene expression. Nucleic Acids Res 1988; 16:8467-86. [PMID: 2843819 PMCID: PMC338570 DOI: 10.1093/nar/16.17.8467] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cysteine proteinase 1 (CP1) and cysteine proteinase 2 (CP2) genes of Dictyostelium discoideum encode co-ordinately expressed mRNA sequences which are inducible by extracellular cAMP. There are short, G-rich sequence elements upstream of both genes and we have previously shown that deletion of these elements from the CP2 gene abolishes cAMP-inducibility. We show here that the G-rich element from the CP1 gene is functionally homologous to that in the CP2 gene by reconstituting cAMP-inducibility in a deletion mutant of the CP2 gene using CP1-derived sequences. Both the CP1 and CP2 genes contain multiple G-rich elements. We show that efficient induction requires at least two copies of the CP1 element and that their relative orientation is unimportant. Two copies of an inverted relative orientation are, however, inactive when moved upstream of their normal position and are incapable of conferring cAMP-inducibility on a heterologous gene. These observations suggest that these sequences are either essential promoter elements, not themselves interacting with the inducer, or that their interaction with a separate class of control sequences is necessary for inducible expression.
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Affiliation(s)
- C J Pears
- Imperial Cancer Research Fund, Clare Hall Laboratories, Herts, UK
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17
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Singleton CK, Gregoli PA, Manning SS, Northington SJ. Characterization of genes which are transiently expressed during the preaggregative phase of development of Dictyostelium discoideum. Dev Biol 1988; 129:140-6. [PMID: 2842207 DOI: 10.1016/0012-1606(88)90168-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have identified and characterized three genes, the I genes (I for induced), which are induced during the preaggregative phase of the developmental program of Dictyostelium discoideum. None of these genes are expressed in cells growing vegetatively on bacteria or in axenic broth, and their induction during early development is due to transcriptional activation. Developmental expression of I6, I8, and I11 occurs even in the absence of protein synthesis. Their induction is very rapid and occurs essentially at the onset of development. The expression is transient, peaking between 2 and 4 hr followed by a rapid loss of expression. These characteristics suggest that the induction of I6, I8, and I11 is a primary result of the initiation of development, and thus they represent the first such genes isolated. Although their expression behavior shares these characteristics, examination of their expression under various conditions of development and in a variety of aggregation-deficient mutant strains reveals that the details of the regulation and developmental control of these three genes are distinct.
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Affiliation(s)
- C K Singleton
- Department of Molecular Biology, Vanderbilt University, Nashville, Tennessee 37235
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18
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Margolskee RF, Kavathas P, Berg P. Epstein-Barr virus shuttle vector for stable episomal replication of cDNA expression libraries in human cells. Mol Cell Biol 1988; 8:2837-47. [PMID: 2841588 PMCID: PMC363503 DOI: 10.1128/mcb.8.7.2837-2847.1988] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Efficient transfection and expression of cDNA libraries in human cells has been achieved with an Epstein-Barr virus-based subcloning vector (EBO-pcD). The plasmid vector contains a resistance marker for hygromycin B to permit selection for transformed cells. The Epstein-Barr virus origin for plasmid replication (oriP) and the Epstein-Barr virus nuclear antigen gene have also been incorporated into the vector to ensure that the plasmids are maintained stably and extrachromosomally. Human lymphoblastoid cells can be stably transformed at high efficiency (10 to 15%) by such plasmids, thereby permitting the ready isolation of 10(6) to 10(7) independent transformants. Consequently, entire high-complexity EBO-pcD expression libraries can be introduced into these cells. Furthermore, since EBO-pcD plasmids are maintained as episomes at two to eight copies per cell, intact cDNA clones can be readily isolated from transformants and recovered by propagation in Escherichia coli. By using such vectors, human cells have been stably transformed with EBO-pcD-hprt to express hypoxanthine-guanine phosphoribosyltransferase and with EBO-pcD-Leu-2 to express the human T-cell surface marker Leu-2 (CD8). Reconstruction experiments with mixtures of EBO-pcD plasmids demonstrated that one clone of EBO-pcD-hprt per 10(6) total clones or one clone of EBO-pcD-Leu-2 per 2 x 10(4) total clones can be recovered intact from the transformed cells. The ability to directly select for expression of very rare EBO-pcD clones and to then recover these episomes should make it possible to clone certain genes where hybridization and immunological screening methods are not applicable but where a phenotype can be scored or selected in human cell lines.
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Affiliation(s)
- R F Margolskee
- Department of Biochemistry, Stanford University School of Medicine, California 94305
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19
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Brunet JF, Denizot F, Golstein P. A differential molecular biology search for genes preferentially expressed in functional T lymphocytes: the CTLA genes. Immunol Rev 1988; 103:21-36. [PMID: 3134293 DOI: 10.1111/j.1600-065x.1988.tb00747.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
One approach to the isolation of molecules involved in T cell-mediated cytolysis stems from the postulate of a possible correlation between molecular phenotype and molecular functional involvement. Accordingly, CTL-specific molecules have been looked for, using a strategy based on the differential screening of a subtracted cDNA library. This led to the isolation and characterization of the following structures, expressed mostly (but no exclusively) in CTLs and inducible upon lymphocyte activation: CTLA-1 and CTLA-3 (serine-proteases), CTLA-4 (a member of the Ig superfamily) and CTLA-2 alpha and beta (homologues to the proregion of cysteine-proteases). The theoretical and practical limitations and the prospects of this type of approach are discussed.
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Affiliation(s)
- J F Brunet
- Centre d'Immunologie INSERM-CNRS de Marseille-Luminy, France
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Wiles MV, Alexander CM, Goodfellow PN. Isolation of an abundantly expressed sequence from the human X chromosome by differential screening. SOMATIC CELL AND MOLECULAR GENETICS 1988; 14:31-9. [PMID: 2829364 DOI: 10.1007/bf01535047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A cDNA library was constructed from poly(A)+ RNA derived from MP2H4, a mouse-human somatic cell hybrid, containing as its only human contribution an X-6 translocation chromosome. This library was screened with [32P] c-DNA derived from MP2H4 and counterscreened with a phenotypically similar mouse cell line. From a screen of 4000 recombinants, seven clones were isolated which hybridized more strongly with cDNA derived from the mouse-human hybrid than with the mouse only cell line. Southern blot analysis showed that four of the seven clones originate from the human genome, three of these contain repeat sequences, and one, SCR10, is devoid of repeats. SCR10 identifies a 1-kb mRNA transcribed from the human X chromosome mapping to the region Xq13-q13.3 or Xq21.3-q22 and is an abundantly and ubiquitously expressed gene. A near, or full-length clone of SCR10, SCAR, was isolated and sequenced; the conceptional translation of this sequence encodes a basic protein of 27.5 kd. Sequences homologous to SCAR were detected in primates, rodents, avians, and Xenopus.
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Affiliation(s)
- M V Wiles
- Laboratory of Human Molecular Genetics, Imperial Cancer Research Fund, London, U.K
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21
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Identification and characterization of mRNAs regulated by nerve growth factor in PC12 cells. Mol Cell Biol 1987. [PMID: 3670309 DOI: 10.1128/mcb.7.9.3156] [Citation(s) in RCA: 195] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Differential screening of cDNA libraries was used to detect and prepare probes for mRNAs that are regulated in PC12 rat pheochromocytoma cells by long-term (2-week) treatment with nerve growth factor (NGF). In response to NGF, PC12 cells change from a chromaffin cell-like to a sympathetic-neuron-like phenotype. Thus, one aim of this study was to identify NGF-regulated mRNAs that may be associated with the attainment of neuronal properties. Eight NGF-regulated mRNAs are described. Five of these increase 3- to 10-fold and three decrease 2- to 10-fold after long-term NGF exposure. Each mRNA was characterized with respect to the time course of the NGF response, regulation by agents other than NGF, and rat tissue distribution. Partial sequences of the cDNAs were used to search for homologies to known sequences. Homology analysis revealed that one mRNA (increased 10-fold) encodes the peptide thymosin beta 4 and a second mRNA (decreased 2-fold) encodes tyrosine hydroxylase. Another of the increased mRNAs was very abundant in sympathetic ganglia, barely detectable in brain and adrenals, and undetectable in all other tissues surveyed. One of the decreased mRNAs, by contrast, was very abundant in the adrenals and nearly absent in the sympathetic ganglia. With the exception of fibroblast growth factor, which is the only other agent known to mimic the differentiating effects of NGF on PC12 cells, none of the treatments tested (epidermal growth factor, insulin, dibutyryl cyclic AMP, dexamethasone, phorbol ester, and depolarization) reproduced the regulation observed with NGF. These and additional findings suggest that the NGF-regulated mRNAs may play roles in the establishment of the neuronal phenotype and that the probes described here will be useful to study the mechanism of action of NGF and the development and differentiation of neurons.
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22
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Leonard DG, Ziff EB, Greene LA. Identification and characterization of mRNAs regulated by nerve growth factor in PC12 cells. Mol Cell Biol 1987; 7:3156-67. [PMID: 3670309 PMCID: PMC367950 DOI: 10.1128/mcb.7.9.3156-3167.1987] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Differential screening of cDNA libraries was used to detect and prepare probes for mRNAs that are regulated in PC12 rat pheochromocytoma cells by long-term (2-week) treatment with nerve growth factor (NGF). In response to NGF, PC12 cells change from a chromaffin cell-like to a sympathetic-neuron-like phenotype. Thus, one aim of this study was to identify NGF-regulated mRNAs that may be associated with the attainment of neuronal properties. Eight NGF-regulated mRNAs are described. Five of these increase 3- to 10-fold and three decrease 2- to 10-fold after long-term NGF exposure. Each mRNA was characterized with respect to the time course of the NGF response, regulation by agents other than NGF, and rat tissue distribution. Partial sequences of the cDNAs were used to search for homologies to known sequences. Homology analysis revealed that one mRNA (increased 10-fold) encodes the peptide thymosin beta 4 and a second mRNA (decreased 2-fold) encodes tyrosine hydroxylase. Another of the increased mRNAs was very abundant in sympathetic ganglia, barely detectable in brain and adrenals, and undetectable in all other tissues surveyed. One of the decreased mRNAs, by contrast, was very abundant in the adrenals and nearly absent in the sympathetic ganglia. With the exception of fibroblast growth factor, which is the only other agent known to mimic the differentiating effects of NGF on PC12 cells, none of the treatments tested (epidermal growth factor, insulin, dibutyryl cyclic AMP, dexamethasone, phorbol ester, and depolarization) reproduced the regulation observed with NGF. These and additional findings suggest that the NGF-regulated mRNAs may play roles in the establishment of the neuronal phenotype and that the probes described here will be useful to study the mechanism of action of NGF and the development and differentiation of neurons.
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Affiliation(s)
- D G Leonard
- Department of Biochemistry, New York University School of Medicine, New York 10016
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23
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Abstract
Regulation of variant surface glycoprotein (VSG) mRNA turnover in Trypanosoma brucei was studied in bloodstream forms, in procyclic cells, and during in vitro transformation of bloodstream forms to procyclic cells by approach-to-equilibrium labeling and pulse-chase experiments. Upon initiation of transformation at 27 degrees C in the presence of citrate-cis-aconitate, the half-life of VSG mRNA was reduced from 4.5 h in bloodstream forms to 1.2 h in transforming cells. Concomitantly, an approximately 25-fold decrease in the rate of transcription was observed, resulting in a 100-fold reduction in the steady-state level of de novo-synthesized VSG mRNA. This low level of expression was maintained for at least 7 h, finally decreasing to an undetectable level after 24 h. Transcription of the VSG gene in established procyclic cells was undetectable. For comparison, the turnover of polyadenylated and nonpolyadenylated RNA, beta-tubulin mRNA, and mini-exon-derived RNA (medRNA) was studied. For medRNA, no significant changes in the rate of transcription or stability were observed during differentiation. In contrast, while the rate of transcription of beta-tubulin mRNA in in vitro-cultured bloodstream forms, transforming cells, and established procyclic cells was similar, the half life was four to five times longer in procyclic cells (t1/2, 7 h) than in cultured bloodstream forms (t1/2, 1.4 h) or transforming cells (t1/2, 1.7 h). Inhibition of protein synthesis in bloodstream forms at 37 degrees Celsius caused a dramatic 20-fold decrease in the rate of VSG mRNA synthesis and a 6-fold decrease in half-life to 45 min, while beta-tubulin mRNA was stabilized 2- to 3-fold and mRNA stability remained unaffected. It is postulated that triggering transformation or inhibiting protein synthesis induces changes in the abundance of the same regulatory molecules which effect the shutoff of VSG gene transcription in addition to shortening the half-life of VSG mRNA.
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Abstract
Regulation of variant surface glycoprotein (VSG) mRNA turnover in Trypanosoma brucei was studied in bloodstream forms, in procyclic cells, and during in vitro transformation of bloodstream forms to procyclic cells by approach-to-equilibrium labeling and pulse-chase experiments. Upon initiation of transformation at 27 degrees C in the presence of citrate-cis-aconitate, the half-life of VSG mRNA was reduced from 4.5 h in bloodstream forms to 1.2 h in transforming cells. Concomitantly, an approximately 25-fold decrease in the rate of transcription was observed, resulting in a 100-fold reduction in the steady-state level of de novo-synthesized VSG mRNA. This low level of expression was maintained for at least 7 h, finally decreasing to an undetectable level after 24 h. Transcription of the VSG gene in established procyclic cells was undetectable. For comparison, the turnover of polyadenylated and nonpolyadenylated RNA, beta-tubulin mRNA, and mini-exon-derived RNA (medRNA) was studied. For medRNA, no significant changes in the rate of transcription or stability were observed during differentiation. In contrast, while the rate of transcription of beta-tubulin mRNA in in vitro-cultured bloodstream forms, transforming cells, and established procyclic cells was similar, the half life was four to five times longer in procyclic cells (t1/2, 7 h) than in cultured bloodstream forms (t1/2, 1.4 h) or transforming cells (t1/2, 1.7 h). Inhibition of protein synthesis in bloodstream forms at 37 degrees Celsius caused a dramatic 20-fold decrease in the rate of VSG mRNA synthesis and a 6-fold decrease in half-life to 45 min, while beta-tubulin mRNA was stabilized 2- to 3-fold and mRNA stability remained unaffected. It is postulated that triggering transformation or inhibiting protein synthesis induces changes in the abundance of the same regulatory molecules which effect the shutoff of VSG gene transcription in addition to shortening the half-life of VSG mRNA.
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Sweeney GE, Watts DI, Turnock G. Differential gene expression during the amoebal-plasmodial transition in Physarum. Nucleic Acids Res 1987; 15:933-45. [PMID: 3029710 PMCID: PMC340499 DOI: 10.1093/nar/15.3.933] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have prepared cDNA libraries for amoebae and plasmodia of the acellular slime mould, Physarum polycephalum. Differential screening was used to isolate cell-type-specific cDNA clones (in bacteriophage M13) and both libraries yielded approximately 5% of such sequences. The amoebal- and plasmodial-specific clones were used to assay changes in transcription during the amoebal-plasmodial transition. The results obtained substantiate the view that the switch from amoebal to plasmodial characteristics occurs over several nuclear division cycles. With one exception, the specific cDNAs came from single-gene families. Southern blotting experiments also showed that they hybridised to identical restriction fragments from amoebal and plasmodial DNAs indicating that genomic rearrangements are unlikely to be involved in the regulation of these genes.
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26
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Singleton CK, Delude RL, McPherson CE. Characterization of genes which are deactivated upon the onset of development in Dictyostelium discoideum. Dev Biol 1987; 119:433-41. [PMID: 3803712 DOI: 10.1016/0012-1606(87)90047-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have identified and begun characterizations of the differential expression of 15 genes whose corresponding mRNA levels decrease during the preaggregative period of the developmental program of Dictyostelium discoideum. Upon the onset of development, the mRNAs decrease from 5- to 1000-fold over the first 8 hr. The rates of loss of each mRNA were similar to one another but distinct, and the decreases were dependent on progress through the developmental program. One exception to this dependency was observed, and the decrease in this mRNA was dependent on the absolute time after initiation of development instead of progress through development. With two exceptions, the decreases in mRNA levels were dependent on developmental conditions and were not seen when cells were shaken in starvation buffer. When the polysomal distributions of each species were examined, three classes were found: most showed no significant shifts off of polysomes upon initiation of development, two were characterized by a 20% shift to nonpolysomal RNA fractions upon development, and two gave a 40-50% shift. Collectively, these characterizations reveal differences in behavior which suggest that deactivation of genes upon initiation of development in Dictyostelium involves more than one regulatory pathway.
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Cochran BH, Zumstein P, Zullo J, Rollins B, Mercola M, Stiles CD. Differential colony hybridization: molecular cloning from a zero data base. Methods Enzymol 1987; 147:64-85. [PMID: 2444861 DOI: 10.1016/0076-6879(87)47099-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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29
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Bernier F, Pallotta D, Lemieux G. Molecular cloning of mRNAs expressed specifically during spherulation of Physarum polycephalum. BIOCHIMICA ET BIOPHYSICA ACTA 1986; 867:234-43. [PMID: 3755618 DOI: 10.1016/0167-4781(86)90039-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A cDNA library was constructed using the poly(A)+ RNA extracted from spherulating Physarum polycephalum microplasmodia. This library (740 clones) was screened by differential hybridization with 32P-labeled poly(A)+ RNA from growing plasmodia and developing spherules. The results showed that at least 30% of the clones corresponded to mRNAs expressed specifically in spherulating plasmodia. The 35 spherulation-specific cDNA clones giving the strongest hybridization signals were analysed. From this group, four different sequences complementary to very abundant mRNAs were identified. They each accounted for 1.5% of 4.5% of all the clones in the library and probably represented the most abundant spherulation-specific mRNAs. In addition, four less abundant mRNAs were identified from stage-specific clones giving weaker hybridization signals. These sequences represented individually between 0.3% and 0.7% of the clones in the library. Northern blots showed that these eight different sequences were absent from plasmodia and were most abundant 24-36 h after the induction of spherulation. Similar results were also obtained when spherulation was induced by the addition of a sublethal concentration of ferrous iron ions to the growth medium. Hybridization of the spherule-specific clones to Southern blots of genomic DNA suggested the presence of one copy for each gene.
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30
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Structural analysis of a developmentally regulated sequence encoding for a cysteine proteinase in Dictyostelium discoideum. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf00333975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Analysis of the expression of two genes of Dictyostelium discoideum which code for developmentally regulated cysteine proteinases. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf00333976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Galau GA, Hughes DW, Dure L. Abscisic acid induction of cloned cotton late embryogenesis-abundant (Lea) mRNAs. PLANT MOLECULAR BIOLOGY 1986; 7:155-70. [PMID: 24302301 DOI: 10.1007/bf00021327] [Citation(s) in RCA: 182] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/1986] [Accepted: 06/03/1986] [Indexed: 05/02/2023]
Abstract
Earlier studies found that cotton (Gossypium hirsutum L.) cotyledons contain several mRNAs which are more abundant during late embryogenesis than in mid-embryogenesis or early germination. They are here termed 'Late embryogenesis-abundant' mRNAs, encoded by Lea loci. Complementary DNA clones for 18 such mRNA sequences, defined at a hybridization criterion of Tm-15°C, were identified in a mature embryo cDNA library by differential cDNA hybridization. At a lower hybridization criterion, some sequence homology was found within several of these cloned Lea mRNA sequences. Each Lea mRNA sequence comprises 0.04-1.3% of mature embryo poly(A)(+) mRNA, a level ten-fold to several hundred-fold higher than in young embryo or 24 h seedling poly(A)(+) mRNA. Of 18 Lea mRNA sequences examined in cultured young embryos, the level of at least 13 are specifically increased by exogenous abscisic acid (ABA), several to a level near that in normal mature embryos. However, the abundance of several of the sequences does not appear to be significantly modulated by ABA. The LEA polypeptides encoded by 10 Lea mRNA sequences were identified by hybrid-arrested translation. They include most of the late embryogenesis-abundant, ABA-inducible, polypeptides previously identified. Preliminary results suggest that many of the individual Lea mRNA sequences are transcribed from 1-3 genes in each of cotton's two subgenomes.
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Affiliation(s)
- G A Galau
- Department of Botany, University of Georgia, 30602, Athens, GA, U.S.A
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33
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Natzle JE, Hammonds AS, Fristrom JW. Isolation of genes active during hormone-induced morphogenesis in Drosophila imaginal discs. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)57253-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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34
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Dickson JG, Prentice HM, Kenimer JG, Walsh FS. Identification and characterization of neuron-specific and developmentally regulated gene transcripts in the chick embryo spinal cord. J Neurochem 1986; 46:787-93. [PMID: 2419498 DOI: 10.1111/j.1471-4159.1986.tb13041.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Clones corresponding to neuron-specific and developmentally regulated messenger RNA species in the chick have been isolated from a complementary DNA library prepared using polyadenylated RNA from 7-day embryonic spinal cord. The library was initially screened by differential complementary DNA hybridization procedures for clones identifying polyadenylated RNAs present in embryonic spinal cord but absent from or at low abundance in liver tissue. A high proportion of selected recombinant plasmids were found to identify different RNA species which, although present in 14-day embryonic spinal cord, could not be detected in a corresponding region of the developing chick CNS that is devoid of neuronal cell bodies, the optic nerve. The neuron-specific assignment of these mRNAs within the developing neuroectoderm was confirmed using bulk-isolated neuronal and glial-enriched cell fractions from 7-day embryonic spinal cord. In addition, several distinctive patterns of developmentally regulated expression of neuron-specific messenger RNA species have been observed in the chick spinal cord. The studies lay a foundation for detailed examination of the regional and temporal distribution and control of neuronal gene expression in the chick spinal cord during embryogenesis.
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35
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Pears CJ, Mahbubani HM, Williams JG. Characterization of two highly diverged but developmentally co-regulated cysteine proteinase genes in Dictyostelium discoideum. Nucleic Acids Res 1985; 13:8853-66. [PMID: 3909109 PMCID: PMC318956 DOI: 10.1093/nar/13.24.8853] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The cysteine proteinase 1 and 2 mRNA sequences of Dictyostelium discoideum encode proteins with a high degree of homology to plant and animal sulphydryl proteinases. The two mRNA sequences are co-ordinate in their regulation, both being first expressed late during cellular aggregation, prematurely induced in response to exogenous cAMP and several-fold enriched in prestalk over prespore cells. The two proteins are considerably diverged, with only 43% overall homology but all residues known to be important in catalysis are conserved and both contain a hydrophobic leader peptide which forms part of an N-terminal domain of just over 100 amino acids not found in the mature form of known cysteine proteinases. We have determined the sequence organization of both genes and find differences both in the number and position of introns. The close co-regulation of these two genes suggests that they may play a common role in Dictyostelium development, presumably in the autodigestion of cellular protein which occurs during differentiation. However, the low degree of sequence homology and major differences in gene organization indicate that they have undergone a considerable period of separate evolution and that they may differ in their precise function.
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36
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Kurkinen M, Barlow DP, Hogan BL. Tissue-specific gene expression in mouse F9 embryonal carcinoma cells: type IV collagen. Ann N Y Acad Sci 1985; 460:267-73. [PMID: 3868951 DOI: 10.1111/j.1749-6632.1985.tb51174.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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37
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Kopachik W, Bergen LG, Barclay SL. Genes selectively expressed in proliferating Dictyostelium amoebae. Proc Natl Acad Sci U S A 1985; 82:8540-4. [PMID: 3866239 PMCID: PMC390952 DOI: 10.1073/pnas.82.24.8540] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Few eukaryotic genes are expressed only during cell growth and division. We found that the slime mold Dictyostelium discoideum is unusual in that it expresses many genes only during proliferation. Thirty-two percent (304/950) of the sequences in a cDNA library made from vegetative mRNA were homologous to RNAs that are present at high levels during growth but at low or undetectable levels during differentiation when no cell growth occurs. In vitro translation assays confirmed that one-third of the vegetative cell mRNAs decreased in steady-state levels during differentiation. These vegetative cell-specific transcripts identified a diverse coordinately regulated class of genes: (i) 9 of the 10 cDNAs tested hybridized to unique small transcripts ranging from 400 to 620 bases long; (ii) the sequences showed various degrees of homology to related species; (iii) transcript levels synchronously fell by a factor of greater than 20 during development and synchronously increased during germination. This class of genes may play important roles in normal cell proliferation.
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38
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Cardelli JA, Knecht DA, Wunderlich R, Dimond RL. Major changes in gene expression occur during at least four stages of development of Dictyostelium discoideum. Dev Biol 1985; 110:147-56. [PMID: 2408940 DOI: 10.1016/0012-1606(85)90072-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spectrum of proteins synthesized at different stages of development of the cellular slime mold Dictyostelium discoideum was analyzed by two-dimensional (2D) gel electrophoresis. Of the approximately 400 proteins detected by this method 189 show changes in their relative rate of synthesis. Most of these changes occur during four distinct stages of development: commencement of development immediately following removal of nutrients (early interphase), early aggregation, late aggregation, and culmination. During commencement the synthesis of 19 proteins begins, the relative rate of synthesis of 21 other proteins increases, and 16 proteins show a rapid decrease in their synthetic rate. During early aggregation the largest change occurs in the spectrum of proteins being synthesized. Specifically, the synthesis of 29 new proteins begins and an increase occurs in the relative synthetic rate of 43 others. During late aggregation, when tight cell-cell contacts form, a reduction takes place in the synthetic rate of most of these induced proteins in addition to the synthesis of 12 new proteins. At least two of these induced proteins are synthesized exclusively in prespore and eventually spore cells. Finally, during culmination, 23 new proteins begin to be synthesized and the synthetic rate of 12 other proteins increases. Five of the 23 newly synthesized proteins appear to be stalk-cell specific. In general, synthesis of spore-cell specific proteins begins just following the formation of tight aggregates while stalk-cell specific proteins are induced during culmination. The relative amounts of mRNAs coding for most of the early developmentally regulated proteins have been estimated by their translation in rabbit reticulocyte lysates and subsequent analysis of protein products by 2D gel electrophoresis. For most of those proteins whose rate of synthesis increases in vivo following starvation there is a parallel increase in the cellular level of the functional mRNAs encoding them. This suggests that the genes coding for these mRNAs may be under transcriptional control. In contrast, the mRNAs coding for most of the proteins whose synthetic rate decreases early in development are under translational control and persist in the cell in an inactive state.
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39
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Engel DA, Samanta H, Brawner ME, Lengyel P. Interferon action: transcriptional control of a gene specifying a 56,000-Da protein in Ehrlich ascites tumor cells. Virology 1985; 142:389-97. [PMID: 4060577 DOI: 10.1016/0042-6822(85)90346-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The exposure of cells to interferons enhances the accumulation of particular mRNAs and of the corresponding proteins. A cDNA clone (clone 202) complementary to an mRNA (202 mRNA) whose level is enhanced over 12-fold in mouse Ehrlich ascites tumor cells upon exposure to beta-interferon for 10 hr has previously been isolated. The level of this mRNA was also increased in other beta-interferon-responsive mouse cell lines (i.e., L929, L1210S) but not in a line (L1210R) which is not responsive to beta-interferon. The extent of induction in Ehrlich ascites tumor cells depended on the beta-interferon concentration and reached its maximal level between 300 and 1000 units of interferon/ml. Nuclei isolated from Ehrlich ascites tumor cells which had been exposed to beta-interferon produced in vitro more 202 specific RNA than nuclei from control Ehrlich ascites tumor cells: an increase in this production was detectable 2 hr after beginning the exposure of the cells to 1000 units/ml of beta-interferon and the increase reached its maximal level, around 18-fold, after 18 hr exposure. Much, if not all of this increase, appeared to be due to an increase in the rate of synthesis of the RNA and not to a decrease in its rate of turnover. The 202 mRNA was translated in a reticulocyte lysate into a 56,000-Da protein.
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40
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Dowds BC, Loomis WF. Cloning and expression of a cDNA that comprises part of the gene coding for a spore coat protein of Dictyostelium discoideum. Mol Cell Biol 1985; 4:2273-8. [PMID: 6549045 PMCID: PMC369055 DOI: 10.1128/mcb.4.11.2273-2278.1984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The three major spore coat proteins of Dictyostelium discoideum are developmentally regulated, cell-type-specific proteins. They are packaged in prespore vesicles and then secreted to form the outer layer of spore coats. We have isolated a cDNA clone from the gene coding for one of these proteins, SP96, a glycoprotein of 96,000 daltons. We screened the cDNA bank by the method of hybrid select translation followed by immunoprecipitation of the translation products with SP96-specific polyclonal antiserum. We found that the gene was first transcribed into stable mRNA a few hours before the time of detection of SP96 synthesis and that the mRNA, like the protein, accumulated specifically in prespore cells and spores. SP96 constituted the same proportion of newly synthesized protein as the proportion of its message in polyadenylated RNA. SP96 appeared to be encoded by a single gene as judged by Southern blot analysis of digested genomic DNA hybridized to the cDNA clone.
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41
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Cloning and expression of a cDNA that comprises part of the gene coding for a spore coat protein of Dictyostelium discoideum. Mol Cell Biol 1985. [PMID: 6549045 DOI: 10.1128/mcb.4.11.2273] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The three major spore coat proteins of Dictyostelium discoideum are developmentally regulated, cell-type-specific proteins. They are packaged in prespore vesicles and then secreted to form the outer layer of spore coats. We have isolated a cDNA clone from the gene coding for one of these proteins, SP96, a glycoprotein of 96,000 daltons. We screened the cDNA bank by the method of hybrid select translation followed by immunoprecipitation of the translation products with SP96-specific polyclonal antiserum. We found that the gene was first transcribed into stable mRNA a few hours before the time of detection of SP96 synthesis and that the mRNA, like the protein, accumulated specifically in prespore cells and spores. SP96 constituted the same proportion of newly synthesized protein as the proportion of its message in polyadenylated RNA. SP96 appeared to be encoded by a single gene as judged by Southern blot analysis of digested genomic DNA hybridized to the cDNA clone.
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42
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Jackson DA, Cook PR, Patel SB. Attachment of repeated sequences to the nuclear cage. Nucleic Acids Res 1984; 12:6709-26. [PMID: 6091035 PMCID: PMC320111 DOI: 10.1093/nar/12.17.6709] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Nuclear DNA is probably organized into loops by attachment to a sub-structure in vivo. When HeLa cells are lysed in Triton and 2M NaCl the resulting nucleoids contain naked DNA which is supercoiled so the loops must remain intact. We have attempted to identify sequences responsible for attaching these loops to the nuclear sub-structure by progressively detaching DNA with various nucleases. Fragments at the 5' end of the ribosomal RNA locus, and a variety of transcribed and repeated sequences, are shown to lie relatively close to attachment points. This implies that sequences cannot be arranged randomly. However no "attachment sequence" could be identified.
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43
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Abstract
Flagellar amputation in Chlamydomonas reinhardtii induces the accumulation of a specific set of RNAs, many of which encode flagellar proteins. We prepared a cDNA clone bank from RNA isolated from cells undergoing flagellar regeneration. From this bank, we selected clones that contain RNA sequences that display several different patterns of abundance regulation. Based on quantitation of the relative amounts of labeled, cloned cDNAs hybridizing to dots of RNA on nitrocellulose filters, the cloned sequences were divided into five regulatory classes: class I RNAs remain at constant abundance during flagellar regeneration; classes II, III, and IV begin to increase in abundance within a few minutes after deflagellation, reach maximal abundance at successively later times during regeneration, and return to control cell levels within 2 to 3 h; and class V RNA abundance decreases during flagellar regeneration. Alpha- and beta-tubulin mRNAs are included in regulatory class IV. The abundance kinetics of alpha-tubulin mRNAs differ slightly from those of beta-tubulin mRNAs. The availability of these clones makes possible studies on the mechanisms controlling the abundance of a wide variety of different RNA species during flagellar regeneration in Chlamydomonas.
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Schloss JA, Silflow CD, Rosenbaum JL. mRNA abundance changes during flagellar regeneration in Chlamydomonas reinhardtii. Mol Cell Biol 1984; 4:424-34. [PMID: 6546968 PMCID: PMC368719 DOI: 10.1128/mcb.4.3.424-434.1984] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flagellar amputation in Chlamydomonas reinhardtii induces the accumulation of a specific set of RNAs, many of which encode flagellar proteins. We prepared a cDNA clone bank from RNA isolated from cells undergoing flagellar regeneration. From this bank, we selected clones that contain RNA sequences that display several different patterns of abundance regulation. Based on quantitation of the relative amounts of labeled, cloned cDNAs hybridizing to dots of RNA on nitrocellulose filters, the cloned sequences were divided into five regulatory classes: class I RNAs remain at constant abundance during flagellar regeneration; classes II, III, and IV begin to increase in abundance within a few minutes after deflagellation, reach maximal abundance at successively later times during regeneration, and return to control cell levels within 2 to 3 h; and class V RNA abundance decreases during flagellar regeneration. Alpha- and beta-tubulin mRNAs are included in regulatory class IV. The abundance kinetics of alpha-tubulin mRNAs differ slightly from those of beta-tubulin mRNAs. The availability of these clones makes possible studies on the mechanisms controlling the abundance of a wide variety of different RNA species during flagellar regeneration in Chlamydomonas.
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Watts DJ. Protein synthesis during development and differentiation in the cellular slime mould Dictyostelium discoideum. Biochem J 1984; 220:1-14. [PMID: 6331403 PMCID: PMC1153588 DOI: 10.1042/bj2200001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Back E, Müller F, Tobler H. Structural organization of the two main rDNA size classes of Ascaris lumbricoides. Nucleic Acids Res 1984; 12:1313-32. [PMID: 6322104 PMCID: PMC318579 DOI: 10.1093/nar/12.3.1313] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The two main rDNA size classes in the genome of Ascaris lumbricoides consist of 8.8 kb and 8.4 kb long repeating units present in a quantitative ratio of roughly 10:1. They both contain the genes coding for 18 , 5.8S and 26S ribosomal RNAs. The length heterogeneity is due to a 450 bp long spacer region localized in the longer repeating unit which begins 870 bp upstream of the 5'-end 18S gene. A few additional microheterogeneities in base sequence occur at the 5'-end of the 26S gene. The 18S, 5.8S and 26S coding regions have been mapped on both the 8.8 kb and 8.4 kb repeating units and the localization of the 5'- and 3'-ends of the 18S and 26S genes has been performed by S1 protection. No intervening sequences are present in either coding region of the two main rDNA size classes.
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Abstract
We have transformed Dictyostelium discoideum amoebae by using derivatives of a plasmid, pAG60, which was designed for transformation of mammalian cells. The plasmid carries the promoter region of the herpes simplex virus type 1 thymidine kinase gene linked to the bacterial gene kan, which codes for the enzyme aminoglycoside 3'-phosphotransferase. kan is derived from the Tn5 transposon. Expression of the phosphotransferase permits direct selection of transformed cells by their resistance to the antibiotic G-418. pAG60 is incapable of transforming D. discoideum but is made transformation proficient by cloning D. discoideum sequences into the tetracycline resistance gene. The majority of transformed cells grow and develop normally and differentiate to give G-418-resistant spores. These transformants are unstable and rapidly lose their G-418-resistance during growth in the absence of antibiotic selection. Southern blots show that these unstable G-418-resistant transformants carry the pBR322 and kan sequences of pAG60. The pAG60-D. discoideum recombinant plasmids used for transformation were constructed in a way that might make them mutagenic. We have isolated several developmental mutants after transformation of D. discoideum with libraries of pAG60-D. discoideum recombinant plasmids. These mutants are G-418 resistant and carry pAG60 in their nuclear DNA. We recovered a pAG60-D. discoideum recombinant plasmid from several developmental mutants. This plasmid transforms D. discoideum at an elevated frequency and integrates into the nuclear genome. We speculate that integration can result in insertional inactivation of genes that are essential for differentiation but not for growth. Mutagenic transformation occurred only if the transforming plasmid had homology with D. discoideum nuclear DNA. A mammalian cell transformation vector, pSV2-neo, carried no D. discoideum sequences and was able to transform. However, pSV2-neo transformation was not mutagenic. These results suggest that direct inactivation and recovery of genes that are essential for differentiation of D. discoideum will be possible.
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Abstract
We have transformed Dictyostelium discoideum amoebae by using derivatives of a plasmid, pAG60, which was designed for transformation of mammalian cells. The plasmid carries the promoter region of the herpes simplex virus type 1 thymidine kinase gene linked to the bacterial gene kan, which codes for the enzyme aminoglycoside 3'-phosphotransferase. kan is derived from the Tn5 transposon. Expression of the phosphotransferase permits direct selection of transformed cells by their resistance to the antibiotic G-418. pAG60 is incapable of transforming D. discoideum but is made transformation proficient by cloning D. discoideum sequences into the tetracycline resistance gene. The majority of transformed cells grow and develop normally and differentiate to give G-418-resistant spores. These transformants are unstable and rapidly lose their G-418-resistance during growth in the absence of antibiotic selection. Southern blots show that these unstable G-418-resistant transformants carry the pBR322 and kan sequences of pAG60. The pAG60-D. discoideum recombinant plasmids used for transformation were constructed in a way that might make them mutagenic. We have isolated several developmental mutants after transformation of D. discoideum with libraries of pAG60-D. discoideum recombinant plasmids. These mutants are G-418 resistant and carry pAG60 in their nuclear DNA. We recovered a pAG60-D. discoideum recombinant plasmid from several developmental mutants. This plasmid transforms D. discoideum at an elevated frequency and integrates into the nuclear genome. We speculate that integration can result in insertional inactivation of genes that are essential for differentiation but not for growth. Mutagenic transformation occurred only if the transforming plasmid had homology with D. discoideum nuclear DNA. A mammalian cell transformation vector, pSV2-neo, carried no D. discoideum sequences and was able to transform. However, pSV2-neo transformation was not mutagenic. These results suggest that direct inactivation and recovery of genes that are essential for differentiation of D. discoideum will be possible.
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Kurkinen M, Barlow DP, Helfman DM, Williams JG, Hogan BL. Isolation of cDNA clones for basal lamina components: type IV procollagen. Nucleic Acids Res 1983; 11:6199-209. [PMID: 6312413 PMCID: PMC326367 DOI: 10.1093/nar/11.18.6199] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have isolated cDNA clones for mouse type IV procollagen from a library constructed from total poly A+RNA of 13.5 day mouse embryo parietal endoderm (PE) cells. In Northern analysis these clones hybridise to a 6.8 kb RNA which is abundant in embryonic PE cells and in differentiated F9 teratocarcinoma cells. Hybrid selection and in vitro translation of the cDNA specific mRNA produced a single polypeptide of Mr = 165 000. This polypeptide was specifically immunoprecipitated with mouse type IV procollagen antisera and comigrated on SDS-gel electrophoresis with one of the two in vitro synthesised chains of type IV procollagen. Undifferentiated F9 teratocarcinoma cells can be induced by retinoic acid and dibutyryl cAMP to differentiate in vitro into endoderm-like cells which resemble mouse PE cells in synthesising large amounts of basement membrane proteins, including type IV procollagen. Here we show, using one of the cDNA clones as a probe for type IV procollagen, that an increase in cellular concentration of type IV procollagen mRNA occurs within 24 to 48 hours of induction, reaching a constant high level by 72 hours.
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Williams L, McDonald C, Jackson S, McIntosh E, Higgins S. Isolation and characterisation of genomic and cDNA clones for an androgen-regulated secretory protein of rat seminal vesicles. Nucleic Acids Res 1983; 11:5021-36. [PMID: 6308568 PMCID: PMC326234 DOI: 10.1093/nar/11.15.5021] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Testosterone controls the synthesis of seminal vesicle protein F in male rats by regulating the cellular concentration of its mRNA (mRNAF). Phage lambda recombinants have been isolated containing the complete F gene. In addition plasmids have been constructed containing cDNAF sequences some of which are probably full-length (approximately 700 bp). Detailed restriction mapping shows that the F gene is 1.7 kbp long and contains approximately 1.0 kbp of intervening sequence arranged in at least two introns (420 bp and 600 bp). Part of cDNAF has been sequenced showing that the terminal 125 bp of the 3' untranslated region of mRNAF has substantial (greater than 70%) sequence homology with the 3' end of the mRNA coding for another androgen-dependent seminal vesicle protein (protein S). The cloned F gene has been detected in liver and seminal vesicle DNA along with an homologous but structurally different gene. The hormonal control of mRNAF was examined with cDNAF. A pronounced (approximately 3000-fold) differential response to testosterone was observed.
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