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Yerlici VT, Lu MW, Hoge CR, Miller RV, Neme R, Khurana JS, Bracht JR, Landweber LF. Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. Nucleic Acids Res 2019; 47:9741-9760. [PMID: 31504770 PMCID: PMC6765146 DOI: 10.1093/nar/gkz725] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/02/2019] [Accepted: 08/20/2019] [Indexed: 11/13/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.
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Affiliation(s)
- V Talya Yerlici
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michael W Lu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Carla R Hoge
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Richard V Miller
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rafik Neme
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jaspreet S Khurana
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - John R Bracht
- Department of Biology, American University, Washington, DC 20016, USA
| | - Laura F Landweber
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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2
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Tornaletti S. Transcription arrest at DNA damage sites. Mutat Res 2005; 577:131-45. [PMID: 15904937 DOI: 10.1016/j.mrfmmm.2005.03.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2005] [Revised: 03/08/2005] [Accepted: 03/08/2005] [Indexed: 11/16/2022]
Abstract
Transcription arrest by RNA polymerase II at a DNA damage site on the transcribed strand is considered an essential step in initiation of transcription-coupled repair (TCR), a specialized repair pathway, which specifically removes lesions from transcribed strands of expressed genes. To understand how initiation of TCR occurs, it is necessary to characterize the properties of the transcription complex when it encounters a lesion in its path. The analysis of different types of arrested complexes should help us understand how an arrested RNA polymerase may signal the repair proteins to initiate a repair event. This article will review the recent literature describing how the presence of DNA damage along the DNA affects transcription elongation by RNA polymerase II and its implications for the initial steps of TCR.
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Affiliation(s)
- Silvia Tornaletti
- Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA.
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3
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Abstract
Eukaryotic mRNA synthesis is catalyzed by multisubunit RNA polymerase II and proceeds through multiple stages referred to as preinitiation, initiation, elongation, and termination. Over the past 20 years, biochemical studies of eukaryotic mRNA synthesis have largely focused on the preinitiation and initiation stages of transcription. These studies led to the discovery of the class of general initiation factors (TFIIB, TFIID, TFIIE, TFIIF, and TFIIH), which function in intimate association with RNA polymerase II and are required for selective binding of polymerase to its promoters, formation of the open complex, and synthesis of the first few phosphodiester bonds of nascent transcripts. Recently, biochemical studies of the elongation stage of eukaryotic mRNA synthesis have led to the discovery of several cellular proteins that have properties expected of general elongation factors and that have been found to play unanticipated roles in human disease. Among these candidate general elongation factors are the positive transcription elongation factor b (P-TEFb), eleven-nineteen lysine-rich in leukemia (ELL), Cockayne syndrome complementation group B (CSB), and elongin proteins, which all function in vitro to expedite elongation by RNA polymerase II by suppressing transient pausing or premature arrest by polymerase through direct interactions with the elongation complex. Despite their similar activities in elongation, the P-TEFb, ELL, CSB, and elongin proteins appear to play roles in a diverse collection of human diseases, including human immunodeficiency virus-1 infection, acute myeloid leukemia, Cockayne syndrome, and the familial cancer predisposition syndrome von Hippel-Lindau disease. here we review our current understanding of the P-TEFb, ELL, CSB, and elongin proteins, their mechanisms of action, and their roles in human disease.
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Affiliation(s)
- J W Conaway
- Howard Hughes Medical Institute, Oklahoma Medical Research Foundation, Oklahoma City 73104, USA
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4
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Sun W, Godson GN. Synthesis of polyribonucleotide chains from the 3'-hydroxyl terminus of oligodeoxynucleotides by Escherichia coli primase. J Biol Chem 1998; 273:16358-65. [PMID: 9632699 DOI: 10.1074/jbc.273.26.16358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli primase synthesizes RNA primers on DNA templates for the initiation of DNA replication. The sole known activity of primase is to catalyze synthesis of short RNA chains de novo. We now report a novel activity of primase, namely that it can synthesize RNA from the 3'-hydroxyl terminus of a pre-existing oligodeoxynucleotide. The oligonucleotide-primed synthesis of RNA by primase occurs in both of the G4oric-specific priming system and the dnaB protein associated general priming system. This priming reaction of primase is verified by a number of biochemical methods, including inhibition by modified 3'-phosphate of oligonucleotides and deoxyribonuclease I and ribonuclease H cleavages. We also show that the primed RNA is an effective primer for the synthesis of DNA chain by E. coli DNA polymerase III holoenzyme. The significance of this finding to primases generating multimeric length RNA is discussed.
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Affiliation(s)
- W Sun
- Biochemistry Department, New York University Medical Center, New York, New York 10016, USA
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5
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Reines D, Dvir A, Conaway JW, Conaway RC. Assays for investigating transcription by RNA polymerase II in vitro. Methods 1997; 12:192-202. [PMID: 9237163 DOI: 10.1006/meth.1997.0471] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
With the availability of the general initiation factors (TFIIB, TFIID, TFIIE, TFIIF, and TFIIH), it is now possible to investigate aspects of the mechanism of eukaryotic messenger RNA synthesis in purified, reconstituted RNA polymerase II transcription systems. Rapid progress in these investigations has been spurred by use of a growing number of assays that are proving valuable not only for dissecting the molecular mechanisms of transcription initiation and elongation by RNA polymerase II, but also for identifying and purifying novel transcription factors that regulate polymerase activity. Here we describe a variety of these assays and discuss their utility in the analysis of transcription by RNA polymerase II.
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Affiliation(s)
- D Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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6
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Takagi Y, Conaway JW, Conaway RC. A novel activity associated with RNA polymerase II elongation factor SIII. SIII directs promoter-independent transcription initiation by RNA polymerase II in the absence of initiation factors. J Biol Chem 1995; 270:24300-5. [PMID: 7592640 DOI: 10.1074/jbc.270.41.24300] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
General transcription factor SIII, a heterotrimer of 110-, 18-, and 15-kDa subunits, was shown previously to stimulate the overall rate of RNA chain elongation by RNA polymerase II by suppressing transient pausing by polymerase at many sites along DNA templates (Bradsher, J. N., Jackson, K. W., Conaway, R. C., and Conaway, J. W. (1993) J. Biol. Chem. 268, 25587-25593). In this report, SIII is shown to possesses the novel ability to direct robust but promiscuous transcription by RNA polymerase II on duplex DNA templates in the absence of initiation factors. Mechanistic studies reveal that SIII promotes RNA synthesis by substantially increasing the efficiency with which RNA polymerase II initiates promoter-independent transcription from the ends of duplex DNA. Remarkably, SIII appears to have a negligible effect on de novo synthesis of end-to-end transcripts. Instead, analysis of reaction products indicates that SIII is capable of promoting a dramatic increase in the ability of RNA polymerase II to extend the 3'-hydroxyl termini of duplex DNA fragments, in a template-directed reaction exhibiting no strong preference for 3'-protruding, 3'-recessed, or blunt DNA ends. Although RNA polymerase II has been shown previously to catalyze primer-dependent transcription, SIII is the first eukaryotic transcription factor found to promote this reaction. Based on these findings, we propose that SIII may suppress transient pausing by RNA polymerase II by helping to maintain the 3'-hydroxyl terminus of the nascent RNA chain in its proper position in the polymerase active site.
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Affiliation(s)
- Y Takagi
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City 73104, USA
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7
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Schweizer P, Mösinger E. Initiator-dependent transcription in vitro by a wheat germ chromatin extract. PLANT MOLECULAR BIOLOGY 1994; 25:115-130. [PMID: 8003692 DOI: 10.1007/bf00024203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The development of plant in vitro transcription systems transcribing faithfully and efficiently from a broad range of plant nuclear promoters has remained a challenge. We examined the nucleotide sequence requirements for faithful and efficient transcription in a wheat germ chromatin extract (Yamazaki et al., Plant Mol Biol Rep 8: 114-123). The wheat germ chromatin extract was tested with a series of chimeric promoter constructs containing plant promoter sequences upstream from the TATA box, TATA boxes, and cap-site sequences (from -10 to +14, relative to the major in vivo initiation site) in different combinations. The plant extract transcribed faithfully from several chimeric promoters containing the capsite sequence of the parsley chalcone synthase promoter. The transcription was sensitive to the RNA polymerase II-specific inhibitor alpha-amanitin and was only dependent on the chalcone synthase cap-site sequence which therefore fulfils the operational criteria for a plant initiator element. Mutations of the putative chalcone synthase initiator element defined a core sequence '5'TAACAAC' around the initiation site that was necessary for efficient transcription in vitro. In contrast to the extract, purified wheat germ RNA polymerase II showed no preference for transcription from the major chalcone synthase in vivo initiation site.
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Affiliation(s)
- P Schweizer
- Sandoz Agro Ltd., Agrobiological Research Station, Witterswil, Switzerland
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8
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Affiliation(s)
- P Schweizer
- Institute de Biologie Végétale, Université de Fribourg, Switzerland
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9
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de Mercoyrol L, Corda Y, Job C, Job D. Accuracy of wheat-germ RNA polymerase II. General enzymatic properties and effect of template conformational transition from right-handed B-DNA to left-handed Z-DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 206:49-58. [PMID: 1587282 DOI: 10.1111/j.1432-1033.1992.tb16900.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We investigated the accuracy of the insertion process in RNA chain elongation catalyzed by wheat germ RNA polymerase II. Error frequencies varied from 1 misinserted nucleotide per 250 polymerized correct substrates to less than 1 in 2 x 10(5), depending on template sequence and nature of the divalent metal cofactor. Higher error ratios were observed in the presence of Mn2+ compared to Mg2+, and with alternating poly[d(G-C)].poly[d(G-C)] compared to poly[d(A-T)].poly[d(A-T)]. In this latter case the eukaryotic RNA polymerase was as accurate as Escherichia coli RNA polymerase holo-enzyme. The fidelity of wheat germ RNA polymerase II was also examined in transcription of polynucleotide templates in the poly[d(G-C)] family adopting either the right-handed B or left-handed Z conformations. Error ratios for noncomplementary ATP increased markedly under experimental conditions favoring the B-to-Z conformational transition of the alternating copolymers. In accordance with the results of previous studies, the rate of productive elongation, i.e. the synthesis of poly[r(G-C)], was depressed, suggesting that the decreased accuracy of the enzyme derived from an altered competence of the enzyme to form elongation complexes on the left-handed DNA. As judged by the large difference in apparent Km values of the enzyme for complementary and noncomplementary nucleoside triphosphates, part of the discrimination between substrates seemed to take place at the initial binding step. Furthermore, the results indicate that wheat germ RNA polymerase II was able to elongate a primer with a 3'-terminal mismatch, and thus to incorporate the mismatched nucleotide stably in the nascent RAN. However, the probability of productive RNA chain elongation was much lower with noncognate than with the complementary substrates.
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Affiliation(s)
- L de Mercoyrol
- Centre de Biochimie et de Biologie Moléculaire, Centre National de la Recherche Scientifique, Marseille, France
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10
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Kuhn A, Bartsch I, Grummt I. Specific interaction of the murine transcription termination factor TTF I with class-I RNA polymerases. Nature 1990; 344:559-62. [PMID: 2181320 DOI: 10.1038/344559a0] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The 18-base-pair sequence element AGGTCGACCAGTACTCCG (the Sal box) signals termination of mouse ribosomal gene transcription. This sequence is recognized by a sequence-specific DNA-binding protein, TTF I, which mediates the termination of transcription by RNA polymerase I (pol I). Subsequently, the ends of the primary transcripts are trimmed by 10 nucleotides in a sequence-dependent 3'-terminal processing reaction. We have now investigated whether TTF I bound to its target sequence will block elongation by any RNA polymerase by steric hindrance, or whether it is specific for elongation by pol I. The results demonstrate that TTF I directs transcription termination with RNA polymerase I from species as divergent as mouse and yeast, but fails to affect elongation by heterologous polymerases (eukaryotic RNA polymerases II and III, Escherichia coli or bacteriophage T3 RNA polymerase). By contrast, purified lac repressor bound to its operator sequence stops elongation by both RNA polymerase I and II.
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Affiliation(s)
- A Kuhn
- Institut für Biochemie, Würzburg, FRG
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11
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Rodi CP, Sauerbier W. Structure of transcriptionally active chromatin: radiological evidence for requirement of torsionally constrained DNA. J Cell Physiol 1989; 141:346-52. [PMID: 2478570 DOI: 10.1002/jcp.1041410216] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Synthesis of alpha- and beta-globin RNA in DMSO-induced Friend's erythroleukemia cells and synthesis of immunoglobulin gamma- and kappa-chain RNA, total RNA, 5S RNA, and tRNA in mouse myeloma cells (MPC-11) was inhibited by gamma-irradiation. For all RNA species, synthesis decreased nearly exponentially as a function of radiation dose, whereas RNA size distributions, turnover rates, and specific activities of radioactively labeled RNA were affected only insignificantly. D37 values for the loss of synthesis of various RNA species correspond to target sizes ranging from 21,000 to 53,000 kd, or 30-80 kbp of DNA. These target sizes are several-fold larger than the structural genes in question; however, they correspond well with the size of DNA loops, or "domains" constrained by the nuclear matrix. The data suggest that the eukaryotic transcription unit is the torsionally constrained chromatin loop, transcription of which may be inactivated, or significantly reduced by a DNA single-strand break.
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MESH Headings
- Animals
- Cell Line
- Chromatin/physiology
- Chromatin/radiation effects
- Chromatin/ultrastructure
- DNA/physiology
- DNA/ultrastructure
- DNA, Single-Stranded/drug effects
- DNA, Single-Stranded/ultrastructure
- DNA-Directed RNA Polymerases/pharmacology
- Dimethyl Sulfoxide
- Gamma Rays
- Leukemia, Erythroblastic, Acute/chemically induced
- Leukemia, Erythroblastic, Acute/pathology
- Mice
- Multiple Myeloma/pathology
- RNA/biosynthesis
- RNA/radiation effects
- RNA, Nuclear/metabolism
- RNA, Nuclear/radiation effects
- Transcription, Genetic/physiology
- Tumor Cells, Cultured/pathology
- Tumor Cells, Cultured/radiation effects
- Tumor Cells, Cultured/ultrastructure
- Uridine/metabolism
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Affiliation(s)
- C P Rodi
- Institute of Human Genetics, University of Minnesota Medical School, Minneapolis 55455
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12
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Rangarajan PN, Padmanaban G. Factors regulating the transcription of eukaryotic protein coding genes and their mechanism of action — A review. J Biosci 1989. [DOI: 10.1007/bf02703171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Job D, Marmillot P, Job C, Jovin TM. Transcription of left-handed Z-DNA templates: increased rate of single-step addition reactions catalyzed by wheat germ RNA polymerase II. Biochemistry 1988; 27:6371-8. [PMID: 3219341 DOI: 10.1021/bi00417a027] [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: 01/04/2023]
Abstract
Wheat germ RNA polymerase II is able to transcribe polynucleotide templates in the poly-[d(G-C)] family, adopting either the right-handed B or left-handed Z conformations depending on the ionic environment and temperature. Thus, with poly[d(G-C)] either the B state (in MgCl2) or the associated Z* state (in MnCl2) can be established. Poly[d(G-m5C)] adopts the Z form readily in MgCl2, and poly-[d(G-br5C)] can be regarded as being "constitutively" in the Z state. In transcription studies with CpG as a primer and templates in the left-handed conformation, it is found that the rate of productive elongation, i.e., the synthesis of poly[r(G-C)], is depressed, in accordance with the results of previous studies. However, with a single triphosphate substrate, CTP, the rate of formation of the first phosphodiester bond, i.e., the synthesis of CpGpC, is about 4-fold greater with both the Z and Z* templates than with B-DNA. This transcriptional activity is also catalytic in the sense that product concentrations exceed that of the enzyme. The synthesis of CpGpC is reduced in the presence of GTP. However, the apparent Km value for GTP utilization is lower for the trinucleotide synthesis (0.1 microM) than that obtained for productive elongation (0.8 microM), a result that also holds for B-DNA templates. All transcription reactions are specifically inhibited by the fungal toxin alpha-amanitin, and, in the case of the left-handed templates, by monoclonal anti-Z-DNA antibodies. The relative probabilities of single-step addition and productive elongation imply that the major distinction between transcription of templates in the B and Z conformations involves a step following the synthesis of the first phosphodiester bond. As a result, fully competent elongation complexes do not form on the left-handed DNA.
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Affiliation(s)
- D Job
- Centre de Biochimie et de Biologie Moléculaire, Marseille, France
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14
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15
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Kalinski A, Chandra GR, Muthukrishnan S. Study of barley endonucleases and alpha-amylase genes. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67397-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Mosig H, Schäffner AR, Sieber H, Hartmann GR. Primer-independent abortive initiation by wheat-germ RNA polymerase B (II). EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 149:337-43. [PMID: 3888625 DOI: 10.1111/j.1432-1033.1985.tb08931.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Highly purified RNA polymerase B (II) from wheat germ catalyses the formation of dinucleoside tetraphosphates from ribonucleoside triphosphates in the absence of an oligonucleotide primer or additional protein factors. The reaction requires bivalent cations such as Mn2+ or Mg2+ and proceeds linearly for several hours. It is strongly inhibited by 1 microgram/ml alpha-amanitin or 2 micrograms/ml heparin. The reaction strictly depends on the addition of a specific linear or circular DNA template, such as the plasmid pSmaF or a DNA fragment containing the gene for nopaline dehydrogenase. Bacteriophage T7 D111 DNA has almost no template activity. The start sites for dinucleotide synthesis on the template are limited. With the DNA fragment containing the gene for nopaline dehydrogenase only pppApA and pppApU are synthesised substantially whereas pppUpU is formed only in trace amounts. No significant dinucleotide synthesis is observed with other ribonucleoside triphosphates either singly or in a combination of two. The various regions of the DNA fragment differ distinctly in template activity.
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17
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Thomm M, Stetter KO. Transcription in methanogens. Evidence for specific in vitro transcription of the purified DNA-dependent RNA polymerase of Methanococcus thermolithotrophicus. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 149:345-51. [PMID: 3996411 DOI: 10.1111/j.1432-1033.1985.tb08932.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The purification of the DNA-dependent RNA polymerase of Methanococcus thermolithotrophicus is described. As the first step of purification the endogenous template was removed from the enzyme by hydrophobic interaction chromatography. The purified enzyme consists of seven components with different molecular masses. Transcription studies on T7 DNA and the recombinant plasmid pMV15, containing rRNA genes of Methanococcus vannielii, revealed that only the methanogen DNA is transcribed specifically, indicating a principal structural difference between archaebacterial and eubacterial promoters. This could be shown both by analysis of ternary transcription complexes and Southern hybridization. The site of initiation was found within a restriction fragment harbouring the first 390 nucleotides of the sequence coding for mature 16S rRNA and 1100 base pairs of upstream sequences. The specific initiation on this fragment strongly suggests that the enzyme can start in vitro transcription from the promoter(s) of rRNA synthesis.
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18
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Been MD, Burgess RR, Champoux JJ. DNA strand breakage by wheat germ type 1 topoisomerase. BIOCHIMICA ET BIOPHYSICA ACTA 1984; 782:304-12. [PMID: 6329302 DOI: 10.1016/0167-4781(84)90066-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Properties of strand breakage in duplex and single-stranded DNA by the wheat germ type 1 DNA topoisomerase were investigated. Strand breakage in duplex DNA is dependent upon the use of denaturing conditions to inactivate the enzyme and terminate the reaction, whereas breakage of single-stranded DNA occurs under the normal reaction conditions and is not dependent upon denaturation. Breakage generates a free 5' hydroxyl group and enzyme bound to the 3' side of the break, presumably via the 3' phosphate group. The location of sites of breakage with both duplex and single-stranded DNA is not random. In all these respects the wheat germ enzyme closely resembles the rat liver type 1 topoisomerase. A comparison of the locations of the sites of breakage in duplex DNA generated by the topoisomerases from wheat germ and rat liver indicates a number of common sites, although the patterns of breakage are not identical.
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19
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Cooke RM, Durand R, Job C, Penon P, Teissere M, Job D. Enzymatic properties of plant RNA polymerases : An approach to the study of transcription in plants. PLANT MOLECULAR BIOLOGY 1984; 3:217-225. [PMID: 24310433 DOI: 10.1007/bf00029657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Results obtained in the past few years in the study of the reaction mechanism of plant RNA polymerases are reviewed and discussed. They suggest that valuable information can be obtained using a highly simplified transcription system composed of purified plant enzymes and cloned genes. This type of approach may provide a starting point for the development of an in vitro transcription system. The detailed study of the fundamental enzymatic properties of the plant RNA polymerases allows a comparison with the well documented corresponding bacterial enzyme.
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Affiliation(s)
- R M Cooke
- Laboratoire de Physiologie, Véǵetale Université de Perpignan, Avenue de Villeneuve, F 66025, Perpignan, Cedex, France
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20
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Risuelo G, di Mauro E. Mapping of promoter-proximal regions by in vitro transcription of two Agrobacterium tumefaciens Ti-plasmids. Mol Biol Rep 1984; 10:49-55. [PMID: 6472259 DOI: 10.1007/bf00775153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Transcription initiation sites were mapped on both the octopine pTi Ach5 and the nopaline pTI C58 plasmids of Agrobacterium tumefaciens. Transcription ternary complexes were subjected to electrophoresis on agarose gels, prior and/or subsequent to restriction endonuclease digestion of the DNA template, evidenced by autoradiography and located on the restriction maps of the two tumor-inducing plasmids. A. tumefaciens RNA polymerase promptly recognizes and starts transcription on a few sequences which include the T-DNA.
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21
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Hörcher R, Seifart KH. The duck alpha A globin but not the yeast actin gene is transcribed by a HeLa cell extract. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 139:201-8. [PMID: 6321176 DOI: 10.1111/j.1432-1033.1984.tb07995.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have investigated the transcription in a HeLa whole-cell extract of two evolutionary widely separated structural genes coding for duck alpha A globin and yeast actin. Transcription of isolated DNA fragments of the duck alpha A globin gene increases linearly up to relatively high concentrations of DNA. Size analyses and S1 mapping of the transcripts synthesized in vitro on either linear DNA fragments or supercoiled templates reveal that the alpha A globin RNA is initiated at the in vivo cap site and remains unspliced. The same assay conditions were used to transcribe the yeast actin gene. In contrast to the duck gene, size analyses and S1 mapping of the RNA products synthesized on both linear DNA fragments and the supercoiled template containing the actin gene show that the transcripts found in vitro do not stem from the in vivo cap site. The promoter of the yeast actin gene is not recognized in this system in vitro.
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22
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23
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Dynan WS, Tjian R. Isolation of transcription factors that discriminate between different promoters recognized by RNA polymerase II. Cell 1983; 32:669-80. [PMID: 6187469 DOI: 10.1016/0092-8674(83)90053-3] [Citation(s) in RCA: 637] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A new fractionation procedure separates a whole-cell HeLa extract into three components required for accurate in vitro transcription. One component (Sp1) is a promoter-specific factor required for transcription of the SV40 early and late promoters, but not for transcription of other promoters we have tested. The second component (Sp2) is a general factor required for transcription of the SV40 promoters and a series of others, including the adeno-virus 2 major late promoter, the human beta-globin promoter and the avian sarcoma virus promoter. The third component is a fraction containing the endogenous RNA polymerase II. When SV40 and adenovirus templates were present simultaneously in an in vitro transcription reaction, addition of the Sp1 factor stimulated SV40 early promoter transcription 40-fold, and inhibited adenovirus major late promoter transcription by 40%. This finding suggests that Sp1 is involved in promoter selection, and is not merely a general transcription stimulatory factor.
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Manley JL. Analysis of the expression of genes encoding animal mRNA by in vitro techniques. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1983; 30:195-244. [PMID: 6198693 DOI: 10.1016/s0079-6603(08)60687-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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25
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26
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Wilson VG, Spillman T. Changes in DNA binding by purified simian RNA polymerase II under transcribing and nontranscribing conditions. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 699:232-40. [PMID: 6297563 DOI: 10.1016/0167-4781(82)90112-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The interaction of RNA polymerase II from African Green Monkey liver tissue with SV40 DNA was examined by a DNAase protection technique. In the absence of nucleoside triphosphates, simian polymerase binds to nicked, linear SV40 DNA and protects 30 bp of binary complex DNA from DNAase I digestion. With the addition of nucleoside triphosphates to initiate transcription, polymerase protects 40 bp of the ternary complex DNA from DNAase I. Thus, a conformational change in either the polymerase, the DNA, or both occurs during the transition from binary to ternary complex, and this altered conformation allows a larger protection of template DNA. Similar results were seen with Escherichia coli RNA polymerase holoenzyme on SV40 DNA.
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27
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Job D, Durand R, Teissere M. Enzymatic properties and cooperative effects in the kinetics of wheat-germ RNA polymerases. A comparative study of the three nuclear enzyme classes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 128:35-9. [PMID: 7173212 DOI: 10.1111/j.1432-1033.1982.tb06927.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Some of the enzymatic properties of the three classes of RNA polymerase purified from wheat germ were studied. Although the four enzyme species exhibited different template specificities using synthetic polydeoxyribonucleotides, poly(dC) was the most efficiently transcribed. Furthermore, with this matrix all enzyme forms had nearly the same specific activity (approximately equal to 5500 units/mg). A comparative kinetic study of RNA synthesis catalyzed by the wheat germ RNA polymerases lead to the following results: when rate measurements were effected as a function of the concentration of purine nucleoside triphosphates, non-linear double-reciprocal plots were obtained for polymerases I and IIB, whereas linear plots were obtained for RNA polymerases IIA and III. The reaction rates were also measured as a function of UTP concentration (a nucleoside triphosphate which can only be used in the elongation step): the kinetics of the reactions catalyzed by RNA polymerases IIA and III can be accounted for by a simple ping-pong kinetic model; in contrast, negative cooperativity was obtained for enzymes I and IIB. This kinetic behaviour may signify that RNA polymerases I and IIB are allosterically regulated enzymes.
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28
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Lavialle C, Sekura R, Madden MJ, Salzman NP. Interaction between calf thymus RNA polymerase II and singly nicked Simian virus 40 DNA. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33735-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Tsuda M, Suzuki Y. Efficient and strand-selective in vitro transcription initiation by purified RNA polymerase II from a unique site of the fibroin gene. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33722-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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30
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Abstract
Bacteriophage T4 late transcription is unusual, among prokaryotes, in its complexity. Late transcription requires the host RNA polymerase, the products of T4 genes, 33, 45 and 55, and other small polypeptides, the genes of which have not been identified. In addition the DNA template must be "competent' for late transcription. First the DNA must contain the substituted base 5-hydroxymethyl cytosine in place of cytosine (this requirement is eliminated by a mutation in the T4 alc gene). Second, the DNA must be replicating, although late transcription can be uncoupled from DNA replication by mutations in the T4 genes coding for DNA ligase (gene 30) and DNA exonuclease (gene 46). We report here the location of the initiation sites of the messenger RNAs (mRNAs) synthesized in vivo from four late genes (genes 21, 22, 23 and 36) by S1 nuclease mapping and we have determined the DNA sequences at these sites. We have found strong homology to the sequence TATAAATACTATT immediately upstream from the 5' ends of the late messages and we suggest that this sequence is specifically recognized by the complex responsible for late transcription. Also, we have examine gene 23 mRNA synthetized in the absence of DNA replication using the 30- 46- mutant described above and find that it is identical to the true late transcript synthesized in normal infections.
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31
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32
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Studies of in vitro transcription by calf thymus RNA polymerase II using a novel duplex DNA template. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34669-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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33
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Lavialle C, Reuveni Y, Thoren M, Salzman N. Molecular interaction between simian virus 40 DNA and Escherichia coli RNA polymerase. Mapping of the initiation sites on supercoiled and linear DNA. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68227-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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34
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Spindler E, Stein H. R-loop mapping of calf-thymus RNA polymerase II. Transcripts in vitro on restriction fragments of adenovirus 2 DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 121:289-94. [PMID: 6277622 DOI: 10.1111/j.1432-1033.1982.tb05784.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nascent RNA, synthesized by calf thymus ENA polymerase II on the restriction endonuclease EcoRI fragment A and BamHI fragment B of adenovirus 2 DNA, was rehybridized to the template strand under conditions allowing transcription R-loop formation. Hybrids, visualized by electron microscopy, were found in looped and in branched configurations, the former being abundant, with an average loop number of roughly four per EcoRI fragment A and three per BamHI fragment B. Frequency distributions of transcription R-loops, synthesized on identical restriction fragments for different periods of time, showed similar patterns, thus pointing to a nonrandom type of transcription. A comparison of the frequency distribution of R-loops seen on the two overlapping restriction fragments reveals reasonable coincidence in the loop pattern in one out of the four possible fragment orientations, permitting correlation of the transcription R-loop pattern with the physical map of the adenovirus 2 DNA. Comparison of start sites tentatively mapped in vitro with the known promoters for RNA polymerase II in vivo suggests that a major transcription site in vitro is located in close proximity to, or identical with, two promoters in vivo at 16.1 and 16.5 map units.
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35
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Lewis MK, Burgess RR. 5 Eukaryotic RNA Polymerases. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s1874-6047(08)60277-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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36
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Nagamine Y, Bennetzen J, Sentenac A, Fromageot P. Single-stranded DNA transcription by yeast RNA polymerase B. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 656:220-7. [PMID: 6172153 DOI: 10.1016/0005-2787(81)90090-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Single-stranded DNA is not transcribed randomly by yeast RNA polymerase B. A denatured yeast DNA fragment, containing the gene for yeast alcohol dehydrogenase I, directs the transcription of defined RNA products visualized as discrete RNA . DNA hybrid bands following S1 nuclease treatment and agarose gel electrophoresis. Blocking the 3' end of the template by 3' deoxyadenosine did not change the band pattern but reduced the proportion of RNA covalently bound to the DNA from 20 to 4%. On the other hand, the band pattern was affected by the salt concentration, the nature of the divalent cation and the nucleoside triphosphate concentration. The four major RNA bands, found at low substrate concentration, hybridized to the same region of the template. This observation suggests the potential requirement for DNA destabilization in gene activation.
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37
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In vitro transcription of the yeast alcohol dehydrogenase I gene by homologous RNA polymerase B (II). Selective initiation and discontinuous elongation on a supercoiled template. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68549-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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38
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In vitro transcription by wheat germ RNA polymerase II. Initiation of RNA synthesis on relaxed, closed circular template. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69288-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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39
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Chandrasekaran E, Mendicino A, Garver F, Mendicino J. Structures of sialylated O-glycosidically and N-glycosidically linked oligosaccharides in a monoclonal immunoglobulin light chain. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69839-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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40
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Cooke R, Durand R, Teissere M, Penon P, Ricard J. Characterisation of heparin-resistant complex formation and RNA synthesis by wheat germ RNA polymerases I, II and III, in vitro on cauliflower mosaic virus DNA. Biochem Biophys Res Commun 1981; 98:36-42. [PMID: 6163430 DOI: 10.1016/0006-291x(81)91866-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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41
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Das GC, Niyogi SK. Structure, replication, and transcription of the SV40 genome. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1981; 25:187-241. [PMID: 6261296 DOI: 10.1016/s0079-6603(08)60485-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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