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Khashimova ZS, Abidova MK, Mavlonov GT. Influence of gibberellin-binding proteins of the cotton plant on the functioning of the genome. Chem Nat Compd 2013. [DOI: 10.1007/bf02319292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Banfalvi G, Sarkar N. Effect of mercury substitution of DNA on its susceptibility to cleavage by restriction endonucleases. DNA Cell Biol 1995; 14:445-50. [PMID: 7748494 DOI: 10.1089/dna.1995.14.445] [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: 01/26/2023] Open
Abstract
Mercurated DNA was synthesized in vitro by substituting Hg-dCTP or Hg-dUMP for dCTP in one strand of M13mp8DNA in a DNA polymerase I reaction. Restriction enzymes, including Sma I, Pst I, Bam HI, Hind III, and Hinc II, were completely inactive when their recognition sites were fully substituted with Hg-dCMP, while Hg-dUMP containing DNA was hydroxlyzed to some extent. Under conditions favoring star activities, or when DNA was substituted with a low level of mercury-nucleotide, DNA was cleaved by restriction enzymes. Susceptibility to degrading and synthesizing enzymes and insensitivity to restriction endonucleases of fully mercurated DNA makes mercuration an attractive molecular "tag" for in vitro manipulation and selective isolation of Hg-DNA.
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Affiliation(s)
- G Banfalvi
- Department I, Semmelweis University Medical School, Budapest, Hungary
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Jost JP, Geiser M, Seldran M. Specific modulation of the transcription of cloned avian vitellogenin II gene by estradiol-receptor complex in vitro. Proc Natl Acad Sci U S A 1985; 82:988-91. [PMID: 3856262 PMCID: PMC397178 DOI: 10.1073/pnas.82.4.988] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Avian vitellogenin-cauliflower mosaic virus hybrid gene is effectively transcribed in vitro in the homologous embryonic liver nuclei system. The transcription of the hybrid gene is modulated by the addition of an estradiol-receptor preparation that has been shown to bind selectively to an upstream region of cloned vitellogenin gene. Stimulation of the transcription of cloned vitellogenin hybrid gene by estradiol receptor is alpha-amanitin sensitive, hormone dependent, and promoter specific. Simian virus 40 and Escherichia coli promoters are not stimulated by the estradiol-receptor complex. The endogenous silent vitellogenin II gene (wild type) present in the nuclei is not turned on by the addition of estradiol-receptor complex. Deletion or inversion of the DNA sequence where the estradiol-receptor complex binds results in the complete suppression of the in vitro stimulation of transcription by estradiol receptor. Correct initiation of the transcription was demonstrated by primer extension studies of the newly synthesized RNA.
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Wujcik KM, Morgan RA, Huang RC. Transcription of intracisternal A-particle genes in mouse myeloma and Ltk- cells. J Virol 1984; 52:29-36. [PMID: 6481855 PMCID: PMC254485 DOI: 10.1128/jvi.52.1.29-36.1984] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In vivo- and in vitro-synthesized RNA from the murine plasmacytoma MOPC-315 was found to hybridize to all regions of a 7.2-kilobase-pair intracisternal A-particle (IAP) gene. IAP-specific transcripts were also detected in mouse Ltk- cells, but not in cells derived from normal tissues (kidney, liver, spleen) of 6-week-old BALB/c mice. Three RNA species of 7.2, 5.3, and 3.8 kilobases were identified by Northern blot analysis of MOPC-315 polyadenylated RNA. The 7.2- and 5.3-kilobase transcripts were found in greater levels in nuclear as compared with whole cell RNA, suggesting the involvement of one or more of the following mechanisms: RNA processing, preferential nuclear transport, or differential RNA stability. We show that the primary IAP transcript is initiated within the long terminal repeat by hybridization analysis with restriction digests of cloned IAP DNA and [gamma-S]pppApNp ... RNA synthesized in nuclei with [gamma-S]ATP as the RNA initiating probe. Low concentrations of alpha-amanitin (2 micrograms/ml) inhibited IAP RNA synthesis by greater than 90%, suggesting that RNA polymerase II is responsible for IAP transcription.
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Gilmour RS, Allan M, Paul J. Accurate initiation of human epsilon-globin RNA synthesis by Escherichia coli RNA polymerase in isolated nuclei of K562 erythroleukemia cells. Proc Natl Acad Sci U S A 1984; 81:4051-4. [PMID: 6330734 PMCID: PMC345366 DOI: 10.1073/pnas.81.13.4051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The human epsilon-globin gene was transcribed in vitro in isolated K562 cell nuclei by using exogenous Escherichia coli RNA polymerase (EC 2.7.7.6). Newly formed RNA transcripts were distinguished from nuclear RNA molecules by (i) incorporating mercurated UTP into RNA under conditions in which the endogenous polymerase II is inactive and (ii) subsequently isolating the mercurated RNA by affinity chromatography on thiolated Sepharose. A specific 5'-end-labeled probe spanning the epsilon-globin gene cap site was used in nuclease S1 mapping studies to examine the in vitro initiation site of the isolated transcripts. It was found that transcription occurred from the coding strand only and originated almost entirely from a point that was identical to that of the major cap site for epsilon-globin mRNA in vivo.
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Immunoglobulin gene expression in a coupled transcription/translation system from mouse plasmacytoma cell-free extracts. Biochem Genet 1981; 19:1183-209. [PMID: 6802131 DOI: 10.1007/bf00484573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mouse plasmacytoma cytoplasmic extracts and sonicated nuclei have been incubated under conditions which resulted in translation and transcription, respectively. When the cell-free systems were combined, incorporation of radioactive precursors into RNA and protein was enhanced and extended. Coupling of transcription and translation was indicted by the inhibition of protein synthesis, and specifically immunoglobulin synthesis, by actinomycin D and alpha-amanitin. When immunoglobulin synthesis was investigated in MOPC-104E cells Which contain both lambda and K mRNAs but secrete only lambda light chains, the extracts synthesized both K and Lambda light chains. These results indicated that the unexpressed MOPC-104E K mRNA could be translated on homologous ribosomes under the appropriate conditions and suggested that postranscriptional controls may play a role in k-chain gene expression in MOPC-104E cells.
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Bhattacharya S, Sarkar N. Study of deoxyribonucleic acid replication in permeable cells of Bacillus subtilis using mercurated nucleotide substrates. Biochemistry 1981; 20:3029-34. [PMID: 6788077 DOI: 10.1021/bi00514a007] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Chikaraishi DM, Danna KJ. Simian virus 40 transcriptional complexes incorporate mercurated nucleotides into RNA in vitro. J Virol 1981; 37:511-7. [PMID: 6260999 PMCID: PMC171031 DOI: 10.1128/jvi.37.1.511-517.1981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Simian virus 40 Sarkosyl transcriptional complexes incorporated mercurated nucleotide precursors into preinitiated RNA chains. Synthesis with mercurated precursors was three- to fivefold slower than with nonmercurated nucleotides (12 to 20 pmol per 10(6) cells per h at 25 degrees C), and 50 to 70% of the RNA product bound specifically to sulfhydryl-agarose. The amount of mercurated CMP incorporated into RNA was measured by specific binding of [35S]cysteine to the mercury residues. More than 90% of the mercurated RNA hybridized to simian virus 40 DNA.
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Teyssot B, Houdebine LM. Role of prolactin in the transcription of beta-casein and 28-S ribosomal genes in the rabbit mammary gland. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 110:263-72. [PMID: 7192213 DOI: 10.1111/j.1432-1033.1980.tb04864.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Isolated mammary nuclei were incubated in the presence of HgCTP and the neosynthesized RNA was isolated with a SH-Sepharose column. The concentration of beta-casein mRNA and 28-S ribosomal RNA in the neosynthesized RNA fractions was evaluated using [3H]DNA probes complementary to beta-casein mRNA and 28-S rRNA respectively. In the unstimulated pseudopregnant rabbit, the transcription of both genes was easily detectable. Injections of prolactin progressively enhanced the transcription rate of both genes and preferentially the beta-casein gene. A comparison between the transcription rates and the accumulation of the corresponding gene products in the cell revealed that there is a good correlation between these two parameters for the 28-S rRNA gene. By contrast, the acceleration of beta-casein gene transcription by prolactin is unable to account for the simultaneous accumulation of beta-casein mRNA, indicating that prolactin is a potent stabilizer of casein mRNA. Injections of CB154 into lactating rabbits (a drug which suppresses the secretion of prolactin by hypophysis), induced a rapid drop of beta-casein mRNA concentration and a slow decline of beta-casein gene transcription. Simultaneously the drug was responsible for a marked and rapid decrease of 28-S rRNA gene transcription, while the concentration of the rRNA remained elevated. During weaning the transcription of the beta-casein gene and, to a lower degree, the transcripton of the 28-S rRNA gene proceeded more slowly and this phenomenon was accompanied by a progressive decline of the RNA concentrations.
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Di Mauro E, Ballario P, Pedone F. Escherichia coli ribonucleic acid polymerase binding to the deoxyribonucleic acid of the echinoid Paracentrotus lividus: properties of the complexes and distribution of stable binding sites. Biochemistry 1980; 19:1392-6. [PMID: 6992863 DOI: 10.1021/bi00548a020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe the properties of the complexes that form between Escherichia coli RNA polymerase and Paracentrotus lividus DNA: dissociation kinetics, temperature dependence of the complex formation, resistance to heparin, and range of RNA polymerase-DNA weight/weight ratios that give rise to the stable binding events. The amount and distribution of the sites that form stable binding [class A sites as defined by Hinkle & Chamberlin [Hinkle, D., & Chamberlin, M. J. (1972) J. Mol. Biol. 70, 157]] with E. coli RNA polymerase were determined by the analysis of the dissociation of complexes formed by the enzyme on DNA fragments of various length. The P. lividus appears to form 3.1 X 10(5) stable (t1/2 greater than or equal to 15 min) complexes per haploid genome; the great majority of these complexes shows a short-range distribution (1000-2000 base pairs). The observed attributes of the stable binding sites of P. lividus DNA for E. coli RNA polymerase (amount, distribution, and quantitative ability to start in vitro RNA chains) point to the conclusion that E. coli and sea urchin DNA are nearly indistinguishable by the criteria adopted. The behavior of the sea urchin stable binding sites for the E. coli enzyme is not consistent with the expected behavior of the in vivo promoters.
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Brown TD, Pragnell IB, Paul J. Transcription of Friend virus proviral sequences in isolated nuclei. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 104:459-67. [PMID: 6988216 DOI: 10.1111/j.1432-1033.1980.tb04448.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Transcription studies using isolated Friend nuclei and Escherichia coli polymerase are presented. Combination of the techniques of thiol-Sepharose chromatography and cDNA-Sepharose hybridisation has resulted in a system in which the transcription of the Friend virus proviral sequences with endogenous and E. coli polymerase can be examined. The results show that the percentage of Friend viral-specific sequences in RNA transcribed by E. coli RNA polymerase and by endogenous RNA polymerase in isolated nuclei are similar. The percentage of viral-specific sequences synthesized in isolated nuclei is similar to that found in Friend cell nuclear RNA.
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Bitter GA, Roeder RG. Transcription of viral genes in chromatin from adenovirus 2 transformed cells by exogenous eukaryotic RNA polymerases. Nucleic Acids Res 1979; 7:433-52. [PMID: 493152 PMCID: PMC328027 DOI: 10.1093/nar/7.2.433] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The transcription of chromatin from adenovrius 2 transformed rat cells by murine plasmacytoma RNA polymerases I, II and III has been studied. Both the total RNA synthesis and transcription of the integrated adenovirus 2 genes by RNA polymerase II represent de novo DNA transcription as assessed by their sensitivity to actinomycin D. It is shown that each RNA polymerase class has characteristic ionic strength activation profiles and metal ion requirements. RNA polymerase II transcribes the integrated adenovirus 2 genes in chromatin at a frequency 25- to 50-fold higher than their sequences are represented in the genome. In contrast, no detectable viral RNA is synthesized when deproteinized DNA is transcribed. In the presence of Mn2+, all three RNA polymerases (I, II and III) transcribe the integrated viral genes at approximately the same relative frequencey. However, the Mg2+ as divalent cation, the proportion of the total RNA which represents viral gene transcripts is increased 3- to 4-fold with RNA polymerase II, while it remains unchanged for RNA polymerases I or III.
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Weck PK, Wagner RR. Vesicular stomatitis virus infection reduces the number of active DNA-dependent RNA polymerases in myeloma cells. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50614-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Reff ME, Davidson RL. In vitro DNA dependent synthesis of globin RNA sequences from erythroleukemic cell chromatin. Nucleic Acids Res 1979; 6:275-87. [PMID: 284320 PMCID: PMC327688 DOI: 10.1093/nar/6.1.275] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Murine erythroleukemic cells in culture accumulate cytoplasmic globin mRNA during differentiation induced by dimethyl sulfoxide (DMSO)1. Chromatin was prepared from DMSO induced erythroleukemic cells that were transcribing globin RNA in order to determine whether in vitro synthesis of globin RNA sequences was possible from chromatin. RNA was synthesized in vitro using 5-mercuriuridine triphosphate and exogenous Escheria coli RNA polymerase. Newly synthesized mercurated RNA was purified from endogenous chromatin associated RNA by affinity chromatography on a sepharose sulfhydryl column, and the globin RNA sequence content of the mercurated RNA was assayed by hybridization to cDNA globin. The synthesis of globin RNA sequences was shown to occur and to be sensitive to actinomycin and rifampicin and insensitive to alpha-amanitin. In contrast, synthesis of globin RNA sequence synthesis was not detected in significant amounts from chromatin prepared from uninduced erythroleukemic cells, nor from uninduced cell chromatin to which globin RNA was added prior to transcription. Isolated RNA:cDNA globin hybrids were shown to contain mercurated RNA by affinity chromatography. These results indicated that synthesis of globin RNA sequences from chromatin can be performed by E. coli RNA polymerase.
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Varmus HE, Ringold G, Yamamoto KR. Regulation of mouse mammary tumor virus gene expression by glucocorticoid hormones. MONOGRAPHS ON ENDOCRINOLOGY 1979; 12:253-78. [PMID: 226870 DOI: 10.1007/978-3-642-81265-1_14] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Several laboratories have documented that glucocorticoid hormones markedly stimulate the expression of mouse mammary tumor virus genes in a variety of mouse mammary tumor cells and in infected heterologous cells. The effect of the hormone appears to be a rapid and specific augmentation of the synthesis of viral RNA, mediated by interaction with glucocorticoid receptor proteins. The availability of virus-specific reagents and recent developments in the molecular biology of RNA tumor viruses now permit a highly refined analysis of hormonal regulation in this experimental system.
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Ganguly R, Banerjee MR. RNA synthesis in isolated nuclei of lactating mammary cells in presence of unmodified and mercury-labeled CTP. Nucleic Acids Res 1978; 5:4463-77. [PMID: 724523 PMCID: PMC342762 DOI: 10.1093/nar/5.11.4463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Isolated nuclei of lactating mouse mammary gland were capable of supporting DNA-dependent RNA synthesis in vitro in presence of unmodified and mercurated CTP (Hg-CTP) at high ionic condition at 25 degrees C. In presence of unmodified CTP, [3H]UMP incorporation into RNA increased linearly upto 180 min. The kinetic pattern of the reaction and the rate of RNA synthesis were essentially similar when CTP was replaced by Hg-CTP. Both in unmodified and Hg-CTP containing reactions, 70-80% of RNA synthesis was inhibited by alpha-amanitin. Presence of poly(A) in a small portion of the in vitro synthesized messenger-like RNA was detectable by oligo(dT) cellulose chromatography. Both poly(A)+ and poly(A)- RNAs sedimented with a clear peak around 15S region in a formamide-sucrose denaturing gradient. The Hg-RNA after separation from endogenous nuclear RNA by SH-agarose affinity column chromatography also sedimented around 15S region in a formamide-sucrose gradient. The Hg-RNA synthesized in the isolated mammary cell nuclei in vitro should now permit monitoring hormonal regulation of specific gene (casein) transcription in the mammary cells by molecular hybridization of the Hg-RNA with cDNA to casein mRNA.
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Mory Y, Gefter M. RNA synthesis in isolated nuclei: the use of mercurated nucleotides. Nucleic Acids Res 1978; 5:3899-912. [PMID: 724503 PMCID: PMC342718 DOI: 10.1093/nar/5.10.3899] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We have used uridine 5' triphosphate-5-mercury (Hg-UTP) in place of UTP to study RNA synthesis in a previously described isolated nuclei system (1). Employing isopycnic density gradient centrifugation to separate RNAs based upon their relative content of Hg-U, several conclusions can be drawn. In vitro RNA synthesis consists of end addition onto pre-initiated HnRNA molecules as well as apparent initiation of new HnRNA molecules de novo. Synthesis in our system continues linearly for greater than two hours. The chain elongation rate has been measured to be about 500 nucleotides per minute. The methods used to make these measurements are generally applicable to other in vitro systems.
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Abstract
As the pluripotent cells of early embryos differentiate, each progressively loses the potency to develop into several phenotypes. Ultimately, each cell becomes irreversibly restricted to the expression of a single phenotype. Although in many instances details regarding those restriction events are well known, there is little information concerning the nature of the gene transcription changes involved. A model that accounts for the diminution of developmental potential as resulting from progressive, irreversible repression of previously active genes is presented. A scheme of progressive gene repression, rather than selective gene activation, is most consistent with observations from experimental embryology as well as from more recent biochemical experimentation.
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Dierks-Ventling C, Stalder J, Gautschi J. Characterization of chick liver chromatin and analysis of its in vitro transcription products. Nucleic Acids Res 1978; 5:2643-56. [PMID: 566911 PMCID: PMC342192 DOI: 10.1093/nar/5.7.2643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Carefully controlled preparation of chromatin from purified chick liver nuclei yielded over 50% native chromatin as shown by the analysis of the nucleosome pattern after micrococcal nuclease digestion. The size of DNA in this chromatin as analyzed on alkaline sucrose gradients varied from 10S to 19S, the majority being 14S. All endogenous RNA polymerases were represented in the chromatin preparation although to different extents: RNA polymerase I was the most and RNA polymerase II the least abundant. Initiation studies showed that endogenous RNA polymerase II was capable of initiating RNA chains during 5 min. Saturation of chromatin with purified homologous RNA polymerase II increased initiation to 10 min. The addition of heparin caused the RNA transcribed to be larger in size and of increased yield. Chromatin transcription with added purified RNA polymerase II in the presence of heparin produced RNA as large as 32S. A chromatin preparation of this kind would therefore be suitable to transcribe any eukaryotic gene invitro provided additional homologous RNA polymerase II is used.Images
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Van Broeckhoven C, De Wachter R. The reactions of mercurated pyrimidine nucleotides with thiols and with hydrogen sulfide. Nucleic Acids Res 1978; 5:2133-51. [PMID: 673847 PMCID: PMC342149 DOI: 10.1093/nar/5.6.2133] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In the presence of thiols, 5-mercuripyrimidine nucleotides are quantitatively converted to 5-thiomercuri derivatives, but these compounds are unstable and decompose at a rate dependent on the nature of the thiol. The decomposition involves three different reactions and proceeds via a symmetrical mercury derivative of the nucleotide. The end product is the unmodified nucleotide. Similar reactions occur in the presence of hydrogen sulfide. Since mercurated nucleoside triphosphates are substrates for RNA- and DNA polymerase only in the form of thiomercuri derivatives, this implies that when DNA is replicated or transcribed in vitro with a mercurated substrate, the latter is rapidly demercurated to the unmodified substrate which is incorporated as well. Hence the product of the in vitro synthesis can only be partially mercurated in any one pyrimidine. Also, formation of cross-links in the resulting polymer is possible.
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Abstract
Hg-UMP-containing transcripts made from chick erythroid chromatins with E. coli RNA polymerase hybridize to chick globin cDNA. Contamination with endogenous globin RNA has been largely removed by purification on SH-agarose columns at 55 degrees C. Some endogenous globin mRNA sequences remain, probably as hybrids with "anti-sense" Hg-transcripts produced by RNA-dependent RNA synthesis. Heating to 115 degrees C before SH-agarose chromatography eliminates these contaminants. Hg-transcripts from adult and embryonic erythroid chromatins purified by this method are hybridized to globin cDNA; they contain a 4- to 6-fold higher proportion of globin-specific sequences (10-13 PPM) than do transcripts from brain chromatin. Dissociation of erythroid chromatins in salt and urea, followed by reconstitution using standard methods, destroys even this low degree of specificity.
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Nguyen-Huu MC, Sippel AA, Hynes NE, Groner B, Schütz G. Preferential transcription of the ovalbumin gene in isolated hen oviduct nuclei by RNA polymerase B. Proc Natl Acad Sci U S A 1978; 75:686-90. [PMID: 273231 PMCID: PMC411321 DOI: 10.1073/pnas.75.2.686] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The synthesis of ovalbumin mRNA sequences was studied in isolated nuclei from hen oviduct. Two different methods of analysis were used to distinguish in vitro synthesized from preexisting mRNA sequences: (i) Mercurated ribonucleotides were used for in vitro RNA synthesis, and the newly synthesized RNA was purified by chromatography on sulfhydryl-agarose and hybridized to radioactive ovalbumin cDNA. (ii) [3H]UTP was used to label the in vitro synthesized RNA. Hybridization to unlabeled mercurated cDNA, RNase A digestion, and subsequent purification of the hybrids on SH-agarose allowed the quantitation of newly synthesized ovalbumin mRNA sequences. Approximately 0.1% of the newly synthesized RNA was identified as ovalbumin RNA by both methods. The synthesis of ovalbumin RNA progressed during the incubation of nuclei and was sensitive to actinomycin D and low concentrations of alpha-amanitin. The preferential in vitro transcription of the ovalbumin gene (1000-fold over random transcription of the chicken genome) by RNA polymerase B (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) suggests that the specificity of in vitro RNA synthesis is retained in isolated nuclei.
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Astrin SM. Transcription of chromatin from cells transformed by SV40 virus. Methods Cell Biol 1978; 19:359-71. [PMID: 211397 DOI: 10.1016/s0091-679x(08)60035-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Gould HJ, Maryanka D, Fey SJ, Cowling GJ, Allan J. The assay of globin gene transcription in reconstituted chromatin. Methods Cell Biol 1978; 19:387-422. [PMID: 692420 DOI: 10.1016/s0091-679x(08)60038-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Schäfer KP. Mercurated nucleotides: assessment of a new tool to study RNA synthesis and processing in isolated nuclei. Nucleic Acids Res 1977; 4:4465-79. [PMID: 600804 PMCID: PMC343252 DOI: 10.1093/nar/4.12.4465] [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: 12/23/2022] Open
Abstract
Mercurated pyrimidine nucleotides have been used to study RNA synthesis and processing in isolated nuclei from mouse L cells. 5-mercuridine triphosphate (5-Hg-UTP) or 5-Hg-CTP are accepted as substrates by the purified RNA polymerases (I+III) and (II) from mouse cells, respectively, as well as by the enzymes still bound to the nuclear chromatin. In nuclei, RNA synthesis in the presence of Hg-UTP is reduced to 60-70% of a control. 30-60% of RNA labeled in vitro with (3H)UTP in isolated nuclei is not retained on sulfhydryl sepharose columns. Sucrose gradient analysis reveals a size distribution of the non-bound RNA similar to non-mercurated control RNA. Hg-RNA is found in a single peak from 4-10S. Chase experiments indicate that this RNA is the original transcript. It is argued that Hg-nucleotides may cause premature chain termination. Methylation of RNA in vitro by S-adenosyl methionine ((3H)SAM) is reduced to 75% of controls in the presence of Hg-UTP. Only 6% of the methyl groups appear in Hg-RNA. Polyadenylation is reduced as well. 15% of poly(A) (+)RNA are found in control assays whereas only 1% of Hg-RNA carries a poly(A) end added in vitro. These results limit the use of mercurated nucleotides for studies of nuclear RNA synthesis and processing.
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Giesecke K, Sippel AE, Nguyen-Huu MC, Groner B, Hynes NE, Wurtz T, Schütz G. A RNA-dependent RNA polymerase activity: implications for chromatin transcription experiments. Nucleic Acids Res 1977; 4:3943-58. [PMID: 339205 PMCID: PMC343212 DOI: 10.1093/nar/4.11.3943] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mercurated nucleoside triphosphates have been used for transcription of chicken oviduct chromatin with E. coli RNA polymerase. The newly synthesized RNA was purified from preexisting RNA by SH-agarose chromatography and analyzed for the content of specific mRNA sequences. The apparent preferential production of ovalbumin mRNA sequences was not inhibited by actinomycin D, although total RNA synthesis was reduced by more than 90%. Furthermore, when globin mRNA alone, or added to oviduct chromatin, was incubated in the transcription assay, a significant fraction of this mRNA was retained on SH-agarose. The copurification of chromatin associated RNA with in vitro synthesized mercurated RNA was mainly due to a RNA-dependent synthesis of complementary sequences by the bacterial enzyme. Although denaturation of the transcripts prior to SH-agarose chromatography leads to a reduced contamination with endogenous ovalbumin specific RNA, we are unable to show that the messenger-specific RNA sequences purified with the newly mercurated RNA results from a DNA-dependent reaction.
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Gjerset RA, McCarthy BJ. Limited accessibility of chromatin satellite DNA to RNA polymerase from Escherichia coli. Proc Natl Acad Sci U S A 1977; 74:4337-40. [PMID: 337295 PMCID: PMC431936 DOI: 10.1073/pnas.74.10.4337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
An attempt was made to elucidate some of the factors influencing the fidelity with which isolated chromatin from mouse L-cells is transcribed by RNA polymerase from Escherichia coli by analyzing the in vitro transcript for the presence of satellite sequences. These sequences are absent from cellular RNA and therefore reflect aberrant transcription. The results indicate that satellite sequences are underrepresented in chromatin transcripts relative to those of DNA. This selectivity is insensitive to many variables in procedures for the isolation and transcription of chromatin. However, lowering the ratio of enzyme to template further reduced the proportion of satellite sequences in the transcript. We conclude that a primary factor influencing the extent of aberrant transcription is the level of enzyme used. Under limiting enzyme conditions, an efficient selection against satellite sequences is observed. However, under conditions of enzyme excess, the enzyme initiates chains at weaker secondary promoters localized in regions of the chromatin containing satellite DNA.
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Schäfer KP. Mercurated nucleotides: assessment of a new tool to study RNA synthesis and processing in isolated nuclei. Nucleic Acids Res 1977; 4:3109-22. [PMID: 909801 PMCID: PMC342638 DOI: 10.1093/nar/4.9.3109] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mercurated pyrimidine nucleotides have been used to study RNA synthesis and processing in isolated nuclei from mouse L cells. 5-mercuridine triphosphate (5-Hg-UTP) or 5-Hg-CTP are accepted as substrates by the purified RNA polymerases (I + III) and (II) from mouse cells, respectively, as well as by the enzymes still bound to the nuclear chromatin. In nuclei, RNA synthesis in the presence of Hg-UTP is reduced to 60-70% of a control. 30-60% of RNA labeled in vitro with (3H)UTP in isolated nuclei is not retained on sulfhydryl sepharose columns. Sucrose gradient analysis reveals a size distribution of the non-bound RNA similar to non-mercurated control RNA. Hg-RNA is found in a single peak from 4-10S. Chase experiments indicate that this RNA is the original transcript. It is argued that Hg-nucleotides may cause premature chain termination. Methylation of RNA in vitro by S-adenosyl methionine ((3H)SAM) is reduced to 75% of controls in the presence of Hg-UTP. Only 6% of the methyl groups appear in Hg-RNA. Polyadenylation is reduced as well. 15% of poly(A) (+)RNA are found in control assays whereas only 1% of Hg-RNA carries a poly(A) end added in vitro. These results limit the use of mercurated nucleotides for studies of nuclear RNA synthesis and processing.
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Konkel DA, Ingram VM. RNA aggregation during sulfhydryl-agarose chromatography of mercurated RNA. Nucleic Acids Res 1977; 4:1979-88. [PMID: 896479 PMCID: PMC342535 DOI: 10.1093/nar/4.6.1979] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Isolation of newly synthesized mercurated RNA transcripts by chromatography on sulfhydryl-agarose has recently been used to reduce contamination by endogenous RNA derived from the chromatin template. We show that substantial RNA aggregation occurs during standard isolation procedures, causing significant retention of endogenous (unmercurated) RNA on sulfhydryl-agarose. We describe methods to reduce substantially this problem and discuss the implications of our findings for interpretation of previous hybridization and transcription experiments.
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Orkin SH, Swerdlow PS. Globin RNA synthesis in vitro by isolated erythroleukemic cell nuclei: direct evidence for increased transcription during erythroid differentiation. Proc Natl Acad Sci U S A 1977; 74:2475-9. [PMID: 267941 PMCID: PMC432195 DOI: 10.1073/pnas.74.6.2475] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Murine erythroleukemic cells accumulate cytoplasmic globin mRNA during differentiation induced in tissue culture by dimethyl sulfoxide. Cellular accumulation of globin RNA may reflect transcriptional activation of the globin genes and/or posttranscriptional stabilization of globin RNA during differentiation. To evaluate possible transcriptional controls directly; globin RNA synthesis by isolated erythroleukemic cell nuclei was studied. Conditions were established for optimal nuclear RNA synthesis in vitro in the presence of a mercurinucleotide (Hg-CTP). Mercurated RNA synthesized in vitro was purified free of endogenous RNA by affinity chromatography on sulfhydryl-Sepharose, and analyzed for the presence of newly synthesized globin RNA sequences by molecular hybridization to globin complementary [32P]DNA. The results demonstrate markedly increased synthesis of globin RNA by nuclei isolated from dimethyl sulfoxide-treated cells, even within 5 min of nuclear transcription in vitro. These findings are most consistent with transcriptional activation of the globin genes upon induction of differentiation.
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Towle HC, Tsai MJ, Tsai SY, O'Malley BW. Effect of estrogen on gene expression in the chick oviduct. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40567-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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McCarty KS, McCarty KS. Steroid hormone receptors in the regulation of differentiation. A review. THE AMERICAN JOURNAL OF PATHOLOGY 1977; 86:705-44. [PMID: 190892 PMCID: PMC2032117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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37
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38
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Slater RJ, Grierson D. Ribonucleic acid synthesis by chromatin isolated from Phaseolus aureus Roxb. : The effect of endogenous ribonuclease. PLANTA 1977; 137:153-157. [PMID: 24420632 DOI: 10.1007/bf00387552] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/1977] [Accepted: 07/19/1977] [Indexed: 06/03/2023]
Abstract
Chromatin was isolated from the hypocotyls of Phaseolus aureus Roxb. and assayed for endogenous RNA polymerase (EC 2.7.7.6) activity in vitro. The molecular size of the RNA product, measured by polyacrylamide gel electrophoresis, was found to be much smaller than that known to be synthesised in vivo and was affected by the assay temperature. Although conventional enzyme assays provided no evidence for the presence of ribonuclease in chromatin, a more sensitive technique revealed sufficient ribonuclease activity to degrade high-molecular weight RNA to smaller fragments. The inclusion of unlabelled exogenous RNA in the media for chromatin preparation and RNA polymerase assay substantially increased the molecular-weight of the RNA products synthesised in vitro.
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Affiliation(s)
- R J Slater
- Department of Physiology and Environmental Studies, School of Agriculture, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, UK
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