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Song MK, Hunt JA. Specific role of manganese and magnesium on RNA synthesis in rabbit bone marrow erythroid cell nuclei. Biol Trace Elem Res 1988; 16:203-19. [PMID: 2484549 DOI: 10.1007/bf02797136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Specific roles of manganese (Mn) and magnesium (Mg) on the activities of DNA-dependent RNA polymerases I and II isolated from rabbit bone marrow erythroid cell nuclei were investigated. Three main polymerases were separated from the cell nuclei. When RNA polymerase I and Mg were added to the RNA synthesis assay mixture containing erythroid cell DNA as template, RNA transcription activity was highest, but when Mg was replaced with Mn, denatured calf thymus DNA formed a better template than erythroid cell DNA. In contrast, nucleoplasmic DNA from erythroid cell and liver DNA were the best templates to stimulate RNA transcription when RNA polymerase II and Mn were added to the assay mixture. However, if Mn was replaced with Mg, RNA synthesis activity was drastically reduced when the template was nucleoplasmic DNA of erythroid cell. RNA polymerase I and Mg synthesized GC rich RNA, whereas RNA polymerase II and Mn synthesized AU rich RNA. Sedimentation analysis showed that the molecular weights of the RNA produced by polymerase I were larger when the enzyme was activated with Mg than with Mn, whereas those of the RNA produced by polymerase II were larger with Mn than with Mg. Furthermore, RNA produced by polymerase I and Mg using chromatin as a template hybridized better with nucleolar DNA than with nucleoplasmic DNA, whereas that produced by polymerase II and Mn hybridized better with nucleoplasmic DNA than with nucleolar DNA. These results suggest that RNA synthesis is dependent on the activity of specific RNA polymerases and the presence of specific divalent cations and templates, and that the cofactor and template for RNA polymerase I are, respectively, Mg and the nucleolar DNA of cell nuclei, whereas those for RNA polymerase II are Mn and nucleoplasmic DNA.
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Affiliation(s)
- M K Song
- Research Service, Veterans Administration Medical Center, Sepulveda, CA 91343
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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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Gasaryan KG. Genome activity and gene expression in avian erythroid cells. INTERNATIONAL REVIEW OF CYTOLOGY 1982; 74:95-126. [PMID: 6181005 DOI: 10.1016/s0074-7696(08)61170-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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5
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Shenk T. Transcriptional control regions: nucleotide sequence requirements for initiation by RNA polymerase II and III. Curr Top Microbiol Immunol 1981; 93:25-46. [PMID: 7026181 DOI: 10.1007/978-3-642-68123-3_3] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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6
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Palmiter R, Lee D. Regulation of gene transcription by estrogen and progesterone. Lack of hormonal effects on transcription by Escherichia coli RNA polymerase. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(18)43448-5] [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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Abstract
(1) Globin gene regulatory factors, and the DNA sites on which they act, are being sought. (2) Positive and negative regulatory factors that influence globin gene expression have been identified. The positive factor(s) is globin gene specific. (3) Assays are being developed using cloned globin genes to (a) purify the positive globin regulatory factor(s) in a cell-free transcription assay, and (b) identify the DNA sites that act as control regions by microinjection of "full-length" and shortened genomic genes into MEL cells. (4) Globin genes from mouse and human thalassemia cells are being studied as models of abnormal globin gene expression.
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Gazit B, Panet A, Cedar H. Reconstitution of a deoxyribonuclease I-sensitive structure on active genes. Proc Natl Acad Sci U S A 1980; 77:1787-90. [PMID: 6929520 PMCID: PMC348592 DOI: 10.1073/pnas.77.4.1787] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Chicken erythrocyte nuclei have been labeled in the active regions of the chromosome by using the nick translation reaction. In this procedure, accessible areas of the genome are preferentially nicked by the action of pancreatic DNase I and subsequently labeled by using DNA polymerase I from Escherichia coli. These nuclei were employed as a substrate for studying the factors responsible for maintaining the special chromatin conformation of the overall population of active genes. Treatment of nuclei with 0.35 M NaCl resulted in the loss of DNase I sensitivity in the active genes, but this sensitivity could be restored when nuclei were reconstituted with the NaCl eluate. Further purification of the released factors revealed that the HMG (high-mobility group) proteins HMG-14 and HMG-17 are involved in maintaining the conformation of the active regions. These factors are not tissue specific and seem to be involved in the chromosomal structure of most of the active genes.
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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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Ueno K, Sekimizu K, Mizuno D, Natori S. Antibody against a stimulatory factor of RNA polymerase II inhibits nuclear RNA synthesis. Nature 1979; 277:145-6. [PMID: 366437 DOI: 10.1038/277145a0] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Winter WP, Hanash SM, Rucknagel DL. Genetic mechanisms contributing to the expression of the human hemoglogin loci. ADVANCES IN HUMAN GENETICS 1979; 9:229-91, 361-7. [PMID: 393093 DOI: 10.1007/978-1-4615-8276-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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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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Crouse GF, Fodor EJ, Doty P. The specificity of in vitro chromatin transcription. Nucleic Acids Res 1979; 6:371-83. [PMID: 370786 PMCID: PMC327694 DOI: 10.1093/nar/6.1.371] [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: 12/14/2022] Open
Abstract
The in vitro transcription of chicken reticulocyte chromatin with E. coli RNA polymerase has been studied in several different ways. The amount of globin RNA sequences has been measured by hybridizing the transcript with globin cDNA; we show that under the proper conditions mercurated transcript RNA can be separated from endogenous RNA on sulfhydryl affinity columns. The amount of globin RNA in the transcript is approximately 20 fold greater than that from erythrocyte chromatin or reticulocyte DNA. Although these data could be used to support the hypothesis of specific transcription, we show by RNA/RNA self hybridization of the transcript (which is at least 50% symmetric) and by hybridization of the transcript to unique DNA in vast RNA excess that the bulk of the chromatin transcript differs little from the transcript of naked DNA. Several explanations for these apparently contradictory results are offered with the most likely one being compatible with random transcription of at least most of the sequences in the chromatin.
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Nakanishi Y, Sekimizu K, Mizuno D, Natori S. Apparent difference in the way of RNA synthesis stimulation by two stimulatory factors of RNA polymerase II. FEBS Lett 1978; 93:357-60. [PMID: 568564 DOI: 10.1016/0014-5793(78)81139-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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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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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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Johnson L, Baxter J. Regulation of gene expression by glucocorticoid hormones. Early effects preserved in isolated chromatin. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(19)62345-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Grundmann U, Knochel W. Sequences coding for proteins expressed in liver and for globin in poly(A)+ and poly(A)- RNA fractions from nuclei and cytoplasm of chicken immature red blood cells. Mol Biol Rep 1978; 4:39-44. [PMID: 642941 DOI: 10.1007/bf00775179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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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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Orkin SH. Differentiation of murine erythroleukemic (Friend) cells: an in vitro model of erythropoiesis. IN VITRO 1978; 14:146-54. [PMID: 342390 DOI: 10.1007/bf02618181] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Normal erythropoiesis involves differentiation of uncommitted stem cells through committed erythroid precursors into cells specialized for hemoglobin synthesis. Several aspects of this developmental sequence may be studied in murine erythroleukemic cells infected with Friend virus complex. These cells are arrested at the proerythroblast stage, yet capable of continuous growth in vitro. Maturation along an erythroid pathway is induced after treatment with a variety of agents (e.g. dimethylsulfoxide, butyric acid, hemin, ouabain). Following induction, the cells morphologically resemble normoblasts, accumulate globin mRNAs and strain-specific globins, increase heme synthesis and acquire erythrocyte membrane antigens. Cloned populations of erythroleukemic cells mature in a nonhomogeneous fashion upon induction, indicative of a stochastic response in the inductive process. This "probability of differentiation" phenotype is formally analogous to stem cell development in which hematopoietic precursor cells form a constant, dividing population from which cells are continuously maturing. Although the sequence of events involved in triggering differentiation is uncertain, cloning and cell hybridization experiments demonstrate that this phenotype is under rather stable genetic (or epigenetic) control. Recent molecular analysis shows that induced differentiation is accompanied by transcriptional activation of the globin genes rather than posttranscriptional stabilization of the globin RNAs. Further application of cellular, molecular and genetic approaches in this system may help to define specific control mechanisms in erythroid development.
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Wilson GN, Streggles AW, Anderson WF, Nienhuis AW. Transcription of chromatin with prokaryotic and eukaryotic polymerases. Methods Cell Biol 1978; 19:339-57. [PMID: 357917 DOI: 10.1016/s0091-679x(08)60034-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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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Wallace RB, Dube SK, Bonner J. Localization of the globin gene in the template active fraction of chromatin of Friend leukemia cells. Science 1977; 198:1166-8. [PMID: 270812 DOI: 10.1126/science.270812] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Friend leukemia cell chromatin has been fractionated into template active and inactive components. The globin gene sequence is associated with the template active component both prior to and after the cells are induced with dimethyl sulfoxide to synthesize hemoglobin and therefore appears to be in an active configuration in uninduced as well as in induced Friend leukemia cells. In cells which have lost the ability to produce hemoglobin, the globin gene sequence is not associated with the template active fraction of chromatin. These results demonstrate the success of the fractionation procedure.
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Nienhuis AW, Benz EJ. Regulation of hemoglobin synthesis during the development of the red cell (first of three parts). N Engl J Med 1977; 297:1318-28. [PMID: 335250 DOI: 10.1056/nejm197712152972404] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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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Yamamoto M, Jonas D, Seifart K. Transcription of ribosomal k-S RNA by RNA polymerase C in isolated chromatin from HeLa cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 80:243-53. [PMID: 336366 DOI: 10.1111/j.1432-1033.1977.tb11876.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Avvedimento VE, Acquaviva AM, Varrone S. Repetitive and non-repetitive sequences in the transcript in vitro of porcine thyroid chromatin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 78:1-10. [PMID: 913390 DOI: 10.1111/j.1432-1033.1977.tb11707.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Purified pig thyroid chromatin has been transcribed in vitro with Escherichia coli RNA polymerase. The transcript, analyzed by DNA-RNA hybridization, shows two major kinetic components: 40% of the transcript is copied by repetitive sequences present 100 times per haploid genome; another 25% anneals to DNA with a rate constant Kh 10-4 M - S-1, typical of single-copy sequences. The transcript annealed at cot = 40 M - S to fractions of 2000-nucleotide DNA, when banded in neutral CsCl gradient only hybridizes to the heavy side of the main band. At cot = 3000 M - S, another hybridizing fraction appears on the light side of the main band of the gradient. The reassociation properties of these fractions show that the heavy DNA fraction is reiterated about 100 times per haploid genome, whereas the light DNA appears as a unique sequence, associated to small repetitive elements. The transcript, analyzed by formamide/sucrose gradient, shows two peaks with sedimentation coefficients of 10 S and 4 S, respectively. The 10-S RNA, hybridized to native 2000-nucleotide-length DNA, has a Kh of 10-4 M - S-1 and a cot1/2 of 10(3) M - S, typical of single-copy sequences.
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Knöchel W, Kohnert-Stavenhagen E. Are globin coding sequences expressed in nuclear RNA of chick embryo brain? HOPPE-SEYLER'S ZEITSCHRIFT FUR PHYSIOLOGISCHE CHEMIE 1977; 358:835-42. [PMID: 561018 DOI: 10.1515/bchm2.1977.358.2.835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The content of globin coding sequences in nuclear RNA from chicken embryo red blood cells and chicken embryo brain was determined by hybridization with globin cDNA to be 0.27% for embryonic red blood cells and 0.001% for embryo brain, i.e. 0.37% of globin coding sequences relative to embryonic red blood cells. By transfusion of [3H]uridine labelled red blood cells it could be shown that the brain nuclear RNA preparation was contaminated by 0.41% RNA originating from blood cells. As this value is in the same range as the hybridization rate there is no evidence for globin transcripts in brain nuclear RNA. It has also not been possible to detect a short-lived globin mRNA precursor in pulse labelled brain nuclear RNA. In further experiments the RNAs were translated in an Ehrlich ascites cell-free system. No globin synthesis could be observed with brain RNA.
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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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Sridhara S, Daillie J. Preparation and properties of chromatin from the silk glands of the silkworm Bombyx mori. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 75:107-19. [PMID: 862612 DOI: 10.1111/j.1432-1033.1977.tb11509.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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31
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Weiss GB, Anderson WF. The problem of nuclease activity in nucleic acid hybridization reactions. Theoretical considerations. Biophys Chem 1977; 6:337-44. [PMID: 880345 DOI: 10.1016/0301-4622(77)85014-x] [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: 12/24/2022]
Abstract
The presence of nuclease during DNA-DNA or DNA-RNA hybridization reactions alters the kinetics of hybrid formation. Unfortunately, while the effect (even of small amounts of nucleas) on the Cot curve may be large, it may not be readily detectable. The effect of various types of nuclease is shown. As many nucleases cause a shift in the position rather than a change in shape of the curve, all studies involving nucleic acid hybridization should assay for the presence of nucleases and care must be taken to avoid their presence as contaminants.
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32
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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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Levy B, Dixon GH. Renaturation kinetics of cDNA complementary to cytoplamic polyadenylated RNA from rainbow trout testis. Accessibility of transcribed genes to pancreatic DNase. Nucleic Acids Res 1977; 4:883-98. [PMID: 866196 PMCID: PMC342492 DOI: 10.1093/nar/4.4.883] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We have determined the fraction of polyadenylated cytoplasmic RNA from trout testis complementary to unique and repetitive DNA. Some 21% of the cDNA probe representative of this RNA population renatures with rapid kinetics, characteristics of repetitive sequences. The major proportion of the cDNA renatures with unique sequence DNA. Experiments with fractionated cDNA probes allow us to conclude that, in trout testis, the most abundant polyadenylated mRNAs are not preferentially transcribed from repetitive DNA, as it has shown to be the case in two eukaryotic cell lines. Treatment of trout testis nuclei with DNase I, under conditions in which 10% of the total DNA is digested, preferentially depletes the DNA of sequences being transcribed into polyadenylated mRNA. These data confirm the results of H. Weintraub and M. Groundine [(1976) Science 193, 848-856] and those of A. Garel and R. Axel [(1976) Proc. Natl. Acad. Sci. U.S.A. 73, 3966-3970] and suggest that the conformation of DNA in the active genes of chromatin is such that it is more susceptible to digestion by DNaseI.
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Benz EJ, Geist CE, Steggles AW, Barker JE, Nienhuis AW. Hemoglobin switching in sheep and goats. Preparation and characterization of complementary DNAs specific for the alpha-, beta-, and gamma-globin messenger RNAs of sheep. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(18)71844-9] [Citation(s) in RCA: 19] [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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36
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Holland MJ, Hager GL, Rutter WJ. Transcription of yeast DNA by homologous RNA polymerases I and II: selective transcription of ribosomal genes by RNA polymerase I. Biochemistry 1977; 16:16-24. [PMID: 318852 DOI: 10.1021/bi00620a003] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purified yeast DNA was transcribed by homologous RNA polymerases I and II and Escherichia coli RNA polymerase. Transcripts synthesized in vitro were analyzed by molecular hybridization with complementary DNA (cDNA) synthesized from yeast poly(A)-containing mRNA with viral reverse transcriptase and ribosomal DNA labeled in vitro by nick translation with E. coli DNA polymerase I. RNA synthesized by polymerase I and II in the presence of Mn2+ contained sequences complementary to cDNA and rDNA at a frequency consistent with random transcription of the template. Similarly, E. coli RNA polymerase synthesized an apparently random transcript in the presence of either Mn2+ or Mg2+. In contrast to these results, RNA polymerase I but not polymerase II transcripts were markedly enriched in sequences complementary to rDNA when transcription was carried out in the presence of Mg2+. The observed enrichment was 15-30-fold higher than observed for polymerase II or E. coli polymerase transcripts and is consistent with the transcript being comprised of 6-10% ribosomal sequences. These data strongly suggest that RNA polymerase I plays a critical role in selective transcription of ribosomal cistrons.
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Axel R. The structure of specific genes in chromatin. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 19:355-71. [PMID: 1019352 DOI: 10.1016/s0079-6603(08)60931-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Garel A, Axel R. Selective digestion of transcriptionally active ovalbumin genes from oviduct nuclei. Proc Natl Acad Sci U S A 1976; 73:3966-70. [PMID: 1069279 PMCID: PMC431285 DOI: 10.1073/pnas.73.11.3966] [Citation(s) in RCA: 396] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Analysis of the DNA of isolated nucleosomes suggests that virtually all genomic DNA sequences are organized in this basic chromatin subunit. In this report, we demonstrate that although histones reside on the transcriptionally active ovalbumin genes in the oviduct, the organization of proteins about this gene renders it highly sensitive to deoxyribonuclease I (deoxyribonucleate 5'-oligonucleotidohydrolase, EC 3.1.4.5). Treatment of oviduct nuclei from the laying hen with pancreatic deoxyribonuclease I results in the preferential digestion of over 70% of the ovalbumin sequences when only 10% of the total nuclear DNA has been solubilized. Treatment of liver nuclei does not reveal selective sensitivity of these genes to DNase I. Furthermore, regions of DNA not actively transcribed, such as the endogenous leukosis virus genes in the oviduct, are not selectively degraded by this enzyme. Similar digestions with micrococcal nuclease, however, reveal no specific digestion of transcriptionally active chromatin. These data confirm the observations of H. Weintraub and M. Groudine [(1976) Science 193, 848-856] and suggest we are dealing with an aspect of structure that may be necessary to permit transcription of the chromatin complex.
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Abstract
Ten percent digestion of isolated nuclei by pancreatic deoxyribonuclease I preferentially removes globin DNA sequences from nuclei obtained from chick red blood cells but not from nuclei obtained from fibroblasts, from brain, or from a population of red blood cell precursors. Moreover, the nontranscribed ovalbumin sequences in nuclei isolated from red blood cells and fibroblasts are retained after mild deoxyribonuclease I digestion. This suggests that active genes are preferentially digested by deoxyribonuclease I. In contrast, treatment of red cell nuclei with staphylococcal nuclease results in no preferential digestion of active globin genes. When the 11S monomers obtained after staphylococcal nuclease digestion of nuclei are then digested with deoxyribonuclease I, the active globin genes are again preferentially digested. The results indicate that active genes are probably associated with histones in a subunit conformation in which the associated DNA is particularly sensitive to digestion by deoxyribonuclease I.
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Tsai SY, Harris SE, Tsai MJ, O'Malley BW. Effects of estrogen on gene expression in chick oviduct. The role of chromatin proteins in regulating transcription of the ovalbumin gene. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33261-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Abstract
Analysis of RNA transcription from isolated mouse liver chromatin has been undertaken by means of RNA-excess hybridizations with small amounts of radioactive DNA. This analysis indicates that mouse liver chromatin is a restricted template for the in vitro synthesis of RNA complements to repetitive DNA, but more RNA species are synthesized than are found in the RNA isolated from mouse liver nuclei. Extraction with 0.5 M NaC1 destroys the template restriction of isolated chromatin. RNA synthesized in vitro from DNA or chromatin templates by Escherichia coli RNA polymerase, as well as in vivo mouse liver nuclear RNA, were each hybridized to 125I-labeled DNA of high, intermediate, or low reiteration frequency. Chromatin-primed and nuclear RNA saturate a smaller portion of each DNA fraction than does DNA-primed RNA. However, chromatin-primed RNA saturates more high and low reiteration frequency DNA than does nuclear RNA. Simultaneous hybridization of nuclear-and chromatin-primed RNA with 125I-labeled DNA indicates that chromatin-primed RNA contains all of the sequences present in nuclear RNA. Extraction of chromatin with 0.5 MNaC1 leads to removal of histone F1, as well as a wide variety of non-histone proteins. When used as a template for in vitro RNA synthesis, such salt-extracted chromatin produced RNAs that hybridize as large a portion of each DNA fraction as does DNA-primed RNA.
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Deisseroth A, Velez R, Burk RD, Minna J, Anderson WF, Nienhuis A. Extinction of globin gene expression in human fibroblast x mouse erythroleukemia cell hybrids. SOMATIC CELL GENETICS 1976; 2:373-84. [PMID: 1071909 DOI: 10.1007/bf01538841] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have chosen human fibroblast x mouse erythroleukemia hybrid cells as a model system to examine regulation of unique genes. The globin genes were studied as a marker of erythroid differentiation. Three separate hybrid cell lines were incubated in 2% dimethylsulfoxide, an agent which induces erythroid differentiation of the parental erythroleukemia cells. Neither human nor mouse globin mRNA sequences could be detected by a sensitive molecular hybridization assay which utilized globin complementary D N A. However, td n a from one of the cell lines was shown to contain both the mouse and humand globin genes. Thus, loss of the genes by chromosomal segregation did not account for their failure to be expressed. Cocultivation of the mouse erythroleukemia cells with excess human fibroblasts did not prevent erythroid differentiation of the erythroleukemia cells in the presence of dimethylsulfoxide. Similarly globin gene expression was preserved in tetraploid cells generated by fusion of two erythroleukemia lines. Thus, extinction of globin geneated by fusion of two erythroleukemia lines. Thus, extinction of blobin gene expression in the human fibroblast x erythroleukemia hybrids occurred at the level of mRNA production and appeared to be due to the presence of the fibroblast genome within the hybrial cell.
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Abstract
The effect of chromatin proteins on template activity has been studied. Using both E. coli RNA polymerase and calf thymmus polymerase B we have measured the number of initiation sites on chromatin and various histone-DNA complexes. Chromatin can be reconstituted with histone proteins alone and this complex is still a restricted template for RNA synthesis. The removal of histone f1 causes a large increase in the template activity. Chromatin is then treated with Micrococcal nuclease and the DNA fragments protected from nuclease attack ("covered DNA") are isolated. Alternatively, the chromatin is titrated with poly-D-lysine, and by successive treatment with Pronase and nuclease, the DNA regions accessible to polylysine are isolated ("open DNA"). Both fractions were tested for template activity. It was found that RNA polymerase initiation sites are distributed equally in open and covered region DNA.
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Crouse GF, Fodor JB, Doty P. In vitro transcription of chromatin in the presence of a mercurated nucleotide. Proc Natl Acad Sci U S A 1976; 73:1564-7. [PMID: 1064024 PMCID: PMC430338 DOI: 10.1073/pnas.73.5.1564] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mercurated uridine triphosphate has been used to label transcripts of chicken reticulocyte chromatin made with Escherichia coli RNA polymerase. The mercury-labeled RNA product can be completely separated from endogenous RNA sequences in the chromatin by passage through a sulfhydryl Sepharose column. Globin cDNA hybridization to the transcript shows that only 2.6 x 10-5 of the transcript is globin RNA. In contrast to this result, erythrocte chromatin transcript contains less than one tenth as many globin RNA sequences.
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Pays E. Double-stranded RNA in chromatin transcripts formed by exogenous RNA polymerase. Proc Natl Acad Sci U S A 1976; 73:1121-5. [PMID: 772679 PMCID: PMC430212 DOI: 10.1073/pnas.73.4.1121] [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: 12/24/2022] Open
Abstract
RNA transcribed in vitro at low ionic strength, from either rat liver chromatin or DNA, contains a significant amount of structure resistant to RNase in high salt buffer. This is observed with rat liver (form B polymerase) as well as with Escherichia coli RNA polymerase (RNA nucleotidyltransferase; nucleoside triphosphate: RNA nucleotidyltransferase; EC 2.7.7.6). Treatment with RNases specific for either double-stranded or hybrid RNA indicates that resistance to RNase is due to the presence of double-stranded RNA sequences. Denaturation kinetics in the presence or absence of RNase suggest that these sequences are formed by intramolecular base pairing. Their mean length is about 20 to 30 nucleotides, but 15-20% are more than 100 nucleotides long. They contain 60-65% G-C base pairs. The proportion of double-stranded segments is higher in chromatin transcripts than in DNA-templated RNA, and is higher with homologous RNA polymerase than with the bacterial enzyme. On the other hand, chromatin endogenous RNA polymerase, which is unable to initiate transcription, does not synthesize double-stranded RNA. The problem of the location of these sequences is discussed; preliminary results suggest that the 5' end of the RNA transcripts could be enriched in complementary sequences.
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Smith MM, Huang RC. Transcription in vitro of immunoglobulin kappa light chain genes in isolated mouse myeloma nuclei and chromatin. Proc Natl Acad Sci U S A 1976; 73:775-9. [PMID: 815908 PMCID: PMC336001 DOI: 10.1073/pnas.73.3.775] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Messenger RNA sequences for immunoglobulin kappa light chain were synthesized in vitro in isolated mouse myeloma nuclei using bound endogenous RNA polymerase (RNA nucleotidyltransferase; nucleoside triphosphate:RNA nucleotidyltransferase; EC 2.7.7.6) and from isolated myeloma chromatin using exogenous Escherichia coli RNA polymerase. The in vitro RNA was transcribed using 5-mercuriuridine triphosphate and separated from in vivo RNA by chromatography on an agarose sulfhydryl affinity column. Template restriction is retained in vitro since synthesis of kappa chain messenger RNA, As determined by hybridization with complementary DNA, was much more efficient in nuclei and chromatin isolated from myeloma 66.2 tissue culture cells, a kappa-chain-producing cell line, than from MOPC 315 tissue culture cells, a lambda-chain-producing cell line. Transcription of kappa chain messenger RNA was 25 times more efficient in myeloma 66.2 nuclei than in myeloma 66.2 chromatin.
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Hirose M, Tsai MJ, O'Malley BW. Effect of estrogen on gene expression in the chick oviduct. Kinetics of initiation of in vitro transcription on chromatin. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33811-5] [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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50
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Harris SE, Schwartz RJ, Tsai MJ, O'Malley BW, Roy AK. Effect of estrogen on gene expression in the chick oviduct. In vitro transcription of the ovalbumin gene in chromatin. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33911-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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