Journal articles: 'DNA topoisomerasa II beta'

1

Sharma, Kaushal K., Brijendra Singh, Somdutt Mujwar, and Prakash S. Bisen. "Molecular Docking Based Analysis to Elucidate the DNA Topoisomerase IIβ as the Potential Target for the Ganoderic Acid; A Natural Therapeutic Agent in Cancer Therapy." Current Computer-Aided Drug Design 16, no. 2 (March 25, 2020): 176–89. http://dx.doi.org/10.2174/1573409915666190820144759.

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Introduction: Intermediate covalent complex of DNA-Topoisomerase II enzyme is the most promising target of the anticancer drugs to induce apoptosis in cancer cells. Currently, anticancer drug and chemotherapy are facing major challenges i.e., drug resistance, chemical instability and, dose-limiting side effect. Therefore, in this study, natural therapeutic agents (series of Ganoderic acids) were used for the molecular docking simulation against Human DNATopoisomerase II beta complex (PDB ID:3QX3). Methods: Molecular docking studies were performed on a 50 series of ganoderic acids reported in the NCBI-PubChem database and FDA approved anti-cancer drugs, to find out binding energy, an interacting residue at the active site of Human DNA-Topoisomerase II beta and compare with the molecular arrangements of the interacting residue of etoposide with the Human DNA topoisomerase II beta. The autodock 4.2 was used for the molecular docking and pharmacokinetic and toxicity studies were performed for the analysis of physicochemical properties and to check the toxicity effects. Discovery studio software was used for the visualization and analysis of docked pose. Results and Conclusion: Ganoderic acids (GS-1, A and DM) were found to be a more suitable competitor inhibitor among the ganoderic acid series with appropriate binding energy, pharmacokinetic profile and no toxicity effects. The interacting residue (Met782, DC-8, DC-11 and DA-12) shared a chemical resemblance with the interacting residue of etoposide present at the active site of human topoisomerase II beta receptor.

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Bernard, F. X., S. Sablé, B. Cameron, J. Provost, J. F. Desnottes, J. Crouzet, and F. Blanche. "Glycosylated flavones as selective inhibitors of topoisomerase IV." Antimicrobial Agents and Chemotherapy 41, no. 5 (May 1997): 992–98. http://dx.doi.org/10.1128/aac.41.5.992.

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Three flavonoids which promoted Escherichia coli topoisomerase IV-dependent DNA cleavage were isolated from cottonseed flour and identified as quercetin 3-O-beta-D-glucose-[1,6]-O-alpha-L-rhamnose (rutin), quercetin 3-O-beta-D-galactose-[1,6]-O-alpha-L-rhamnose, and quercetin 3-O-beta-D-glucose (isoquercitrin). The most active one (rutin) also inhibited topoisomerase IV-dependent decatenation activity (50% inhibitory concentration, 64 microg/ml) and induced the SOS response of a permeable E. coli strain. Derivatives of quercetin glycosylated at position C-3 were shown to induce two site-specific DNA cleavages of pBR322 DNA, which were mapped by DNA sequence analysis to the gene encoding resistance to tetracycline. Cleavage at these sites was hardly detectable in cleavage reactions with quercetin or fluoroquinolones. None of the three flavonoids isolated from cottonseeds had any stimulatory activity on E. coli DNA gyrase-dependent or calf thymus topoisomerase II-dependent DNA cleavage, and they were therefore specific to topoisomerase IV. These results show that selective inhibitors of topoisomerase IV can be derived from the flavone structure. This is the first report on a DNA topoisomerase inhibitor specific for topoisomerase IV.

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Strehl, Sabine, Karin Nebral, Helmut H. Schmidt, and Oskar A. Haas. "Topoisomerase (DNA) II Beta 180 kDa TOP2B) - A New NUP98 Fusion Partner." Blood 106, no. 11 (November 16, 2005): 2849. http://dx.doi.org/10.1182/blood.v106.11.2849.2849.

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Abstract The nucleoporin 98 kDa (NUP98) gene has been reported to be fused to 18 different partner genes in various hematological malignancies with 11p15 aberrations. The most frequently observed fusion partners of NUP98 belong to the homeobox family of transcription factors, whereas the non-HOX NUP98 fusion partners comprise a heterogeneous group of genes that are associated with a wide range of biological functions. Cytogenetic analysis of an adult de novo acute myeloid leukemia (AML-M5a) revealed a t(3;11)(p24;p15) indicating fusion of NUP98 with a novel partner gene. Fluorescence in situ hybridization (FISH) analysis with the NUP98-specific clone 1173K1 showed a split signal, suggesting that NUP98 was indeed disrupted. Selection of possible NUP98 partner genes was performed by computer-aided analysis of the 3p24 region using the University of California Santa Cruz genome browser. Out of the genes located at 3p24, TOP2B was selected as a fusion partner candidate gene. Dual-color fusion gene-specific FISH and RT-PCR analyses verified that NUP98 was indeed fused to TOP2B. In addition to the reciprocal NUP98-TOP2B and TOP2B-NUP98 in-frame fusion transcripts, an alternatively spliced out-of-frame TOP2B-NUP98 transcript that resulted in a premature stop codon was detected. Analysis of the genomic breakpoints revealed typical signs of non-homologous end joining resulting from error-prone DNA repair. TOP2B encodes a type II topoisomerase, which is involved in DNA transcription, replication, recombination, and mitosis. Type II DNA topoisomerases exist as homodimers, with each subunit consisting of three functional domains: an N-terminal ATPase domain, a central DNA breakage-rejoining domain, which contains a nucleotide-binding motif and the catalytic tyrosine, and a relatively poorly conserved C-terminal domain. The C-termini of the two TOP2 isoforms seem to be important for subcellular localization and functional bipartite nuclear localization signal (NLS) sequences as well as nuclear export signals (NES) are located in these domains. The NUP98-TOP2B fusion transcript fuses the N-terminal FG repeat and GLEBs motifs of NUP98 with the C-terminal domain of TOP2B, thereby retaining the functional NLS but eliminating the NES. Consequently, the putative reciprocal TOP2B-NUP98 chimeric protein retains the ATPase, the DNA breakage-rejoining, and the NES domains of TOP2B that are fused to the ribonucleoprotein-binding and the NLS domains of NUP98. The shorter out-of-frame TOP2Bexon24-NUP98exon14 fusion transcript might encode a truncated TOP2B isoform that consists of the ATPase, the DNA breakage-rejoining, and NES domains, which are fused to 18 fusion partner-unrelated amino acids. All proteins encoded by non-HOX NUP98 fusion partners described to date contain regions with a significant probability to adopt a coiled-coil conformation, and protein analysis with the COILS 2.2 and the MULTICOIL programs revealed this remarkable feature also in the C-terminal region of TOP2B. Intriguingly, this is only the second description of a chromosomal rearrangement that involves a topoisomerase and both TOP1 and TOP2B are fused to NUP98. This suggests that the choice of partner genes for NUP98 is not random, and that NUP98-TOP fusions may represent a distinct group, similar to the NUP98-HOX fusions.

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Biersack, H., S. Jensen, I. Gromova, I. S. Nielsen, O. Westergaard, and A. H. Andersen. "Active heterodimers are formed from human DNA topoisomerase II alpha and II beta isoforms." Proceedings of the National Academy of Sciences 93, no. 16 (August 6, 1996): 8288–93. http://dx.doi.org/10.1073/pnas.93.16.8288.

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5

Jenkins, J. R., M. J. Pocklington, and E. Orr. "The F1 ATP synthetase beta-subunit: a major yeast novobiocin binding protein." Journal of Cell Science 96, no. 4 (August 1, 1990): 675–82. http://dx.doi.org/10.1242/jcs.96.4.675.

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Novobiocin affects DNA metabolism in both prokaryotes and eukaryotes, resulting in cell death. In prokaryotes, the drug is a specific inhibitor of DNA gyrase, a type II topoisomerase that can be purified on a novobiocin-Sepharose column. The yeast type II topoisomerase is neither the biochemical, nor the genetic target of the antibiotic. We have purified the major yeast novobiocin binding proteins and identified one of them as the beta-subunit of the yeast mitochondrial F1 ATP synthetase, a protein highly conserved throughout evolution. The inactivation of this protein might explain the toxic effects of novobiocin on higher eukaryotic cells.

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LONN, Ulf, and Sigrid LONN. "5,6-Dichloro-1-beta-O-ribofuranosylbenzimidazole induces DNA damage by interfering with DNA topoisomerase II." European Journal of Biochemistry 164, no. 3 (May 1987): 541–45. http://dx.doi.org/10.1111/j.1432-1033.1987.tb11160.x.

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Khazeem, Mushtaq M., Ian G. Cowell, Lauren F. Harkin, John W. Casement, and Caroline A. Austin. "Transcription of carbonyl reductase 1 is regulated by DNA topoisomerase II beta." FEBS Letters 594, no. 20 (August 30, 2020): 3395–405. http://dx.doi.org/10.1002/1873-3468.13904.

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8

Vassetzky, Y. S., Q. Dang, P. Benedetti, and S. M. Gasser. "Topoisomerase II forms multimers in vitro: effects of metals, beta-glycerophosphate, and phosphorylation of its C-terminal domain." Molecular and Cellular Biology 14, no. 10 (October 1994): 6962–74. http://dx.doi.org/10.1128/mcb.14.10.6962.

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We present a novel assay for the study of protein-protein interactions involving DNA topoisomerase II. Under various conditions of incubation we observe that topoisomerase II forms complexes at least tetrameric in size, which can be sedimented by centrifugation through glycerol. The multimers are enzymatically active and can be visualized by electron microscopy. Dephosphorylation of topoisomerase II inhibits its multimerization, which can be restored at least partially by rephosphorylation of multiple sites within its 200 C-terminal amino acids by casein kinase II. Truncation of topoisomerase II just upstream of the major phosphoacceptor sites reduces its aggregation, rendering the truncated enzyme insensitive to either kinase treatments or phosphatase treatments. This is consistent with a model in which interactions involving the phosphorylated C-terminal domain of topoisomerase II aid either in chromosome segregation or in chromosome condensation.

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9

Vassetzky, Y. S., Q. Dang, P. Benedetti, and S. M. Gasser. "Topoisomerase II forms multimers in vitro: effects of metals, beta-glycerophosphate, and phosphorylation of its C-terminal domain." Molecular and Cellular Biology 14, no. 10 (October 1994): 6962–74. http://dx.doi.org/10.1128/mcb.14.10.6962-6974.1994.

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We present a novel assay for the study of protein-protein interactions involving DNA topoisomerase II. Under various conditions of incubation we observe that topoisomerase II forms complexes at least tetrameric in size, which can be sedimented by centrifugation through glycerol. The multimers are enzymatically active and can be visualized by electron microscopy. Dephosphorylation of topoisomerase II inhibits its multimerization, which can be restored at least partially by rephosphorylation of multiple sites within its 200 C-terminal amino acids by casein kinase II. Truncation of topoisomerase II just upstream of the major phosphoacceptor sites reduces its aggregation, rendering the truncated enzyme insensitive to either kinase treatments or phosphatase treatments. This is consistent with a model in which interactions involving the phosphorylated C-terminal domain of topoisomerase II aid either in chromosome segregation or in chromosome condensation.

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10

Muller, M. T., and V. B. Mehta. "DNase I hypersensitivity is independent of endogenous topoisomerase II activity during chicken erythrocyte differentiation." Molecular and Cellular Biology 8, no. 9 (September 1988): 3661–69. http://dx.doi.org/10.1128/mcb.8.9.3661.

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Endogenous topoisomerase II cleavage sites were mapped in the chicken beta A-globin gene of 12- to 14-day embryonic erythrocytes. A major topoisomerase II catalytic site was mapped to the 5' end of the globin gene which contained a nucleosome-free and DNase I-hypersensitive site and additional but minor sites were mapped to the second intron and 3' of the gene to a tissue-specific enhancer. Cleavage sites, mapped in situ by indirect end labeling, were aligned to single-base-pair resolution by comparison to a consensus sequence derived for vertebrate topoisomerase II catalytic sites. In contrast to embryonic erythrocytes, endogenous topoisomerase II cleavages were not detected in erythrocytes from peripheral blood of adult chickens; therefore, as the transcriptional activity of the beta A-globin gene declines during terminal differentiation of erythrocytes, the activity of topoisomerase II in situ declines as well, despite the fact that DNase I hypersensitivity persists. The results showed that DNase I-hypersensitive chromatin can be maintained in the absence of topoisomerase II activity and suggested that topoisomerase II acts at hypersensitive sites because of an inherent attraction to some preexisting combination of DNA sequence or chromatin structure associated with DNase I-hypersensitive regions.

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Muller, M. T., and V. B. Mehta. "DNase I hypersensitivity is independent of endogenous topoisomerase II activity during chicken erythrocyte differentiation." Molecular and Cellular Biology 8, no. 9 (September 1988): 3661–69. http://dx.doi.org/10.1128/mcb.8.9.3661-3669.1988.

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Endogenous topoisomerase II cleavage sites were mapped in the chicken beta A-globin gene of 12- to 14-day embryonic erythrocytes. A major topoisomerase II catalytic site was mapped to the 5' end of the globin gene which contained a nucleosome-free and DNase I-hypersensitive site and additional but minor sites were mapped to the second intron and 3' of the gene to a tissue-specific enhancer. Cleavage sites, mapped in situ by indirect end labeling, were aligned to single-base-pair resolution by comparison to a consensus sequence derived for vertebrate topoisomerase II catalytic sites. In contrast to embryonic erythrocytes, endogenous topoisomerase II cleavages were not detected in erythrocytes from peripheral blood of adult chickens; therefore, as the transcriptional activity of the beta A-globin gene declines during terminal differentiation of erythrocytes, the activity of topoisomerase II in situ declines as well, despite the fact that DNase I hypersensitivity persists. The results showed that DNase I-hypersensitive chromatin can be maintained in the absence of topoisomerase II activity and suggested that topoisomerase II acts at hypersensitive sites because of an inherent attraction to some preexisting combination of DNA sequence or chromatin structure associated with DNase I-hypersensitive regions.

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12

Burden, D. A., L. J. Goldsmith, and D. M. Sullivan. "Cell-cycle-dependent phosphorylation and activity of Chinese-hamster ovary topoisomerase II." Biochemical Journal 293, no. 1 (July 1, 1993): 297–304. http://dx.doi.org/10.1042/bj2930297.

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Cell-cycle-dependent protein levels and phosphorylation of DNA topoisomerase II in relation to its catalytic and cleavage activities were studied in Chinese-hamster ovary cells. Immunoreactive topoisomerase II protein levels were maximal in G2-phase cells, intermediate in S- and M-phase cells, and minimal in a predominantly G1-phase population. When the phosphorylation of topoisomerase II in vivo was corrected for differences in specific radioactivity of intracellular ATP, the apparent phosphorylation of S- and M-phase topoisomerase II was altered significantly. Relative phosphorylation in vivo was found to be greatest in M-phase cells and decreased in the other populations in the order: S > G2 > asynchronous. Phosphoserine was detected in every phase of the cell cycle, with a minor contribution of phosphothreonine demonstrated in M-phase cells. Topoisomerase II activity measured in vivo as 9-(4,6-O-ethylidene-beta-D-glucopyranosyl)-4′-demethylepipodophylloto xin (VP-16)-induced DNA double-strand breaks (determined by neutral filter elution) increased in the order: asynchronous < S < G2 < M. Topoisomerase II cleavage activity, assayed in vitro as the formation of covalent enzyme-DNA complexes, was lowest in S phase, intermediate in asynchronous and G2-phase cells, and maximal in M phase. Topoisomerase II decatenation activity was 1.6-1.8-fold greater in S-, G2- and M-phase populations relative to asynchronous cells. Therefore DNA topoisomerase II activity measured both in vivo and in vitro is maximal in M phase, that phase of the cell cycle with an intermediate level of immunoreactive topoisomerase II but the highest level of enzyme phosphorylation. The discordance between immunoreactive topoisomerase II protein levels, adjusted relative phosphorylation, catalytic activity, cleavage activity and amino acid residue(s) modified, suggests that the site of phosphorylation may be cell-cycle-dependent and critical in determining catalytic and cleavage activity.

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Reitman, M., and G. Felsenfeld. "Developmental regulation of topoisomerase II sites and DNase I-hypersensitive sites in the chicken beta-globin locus." Molecular and Cellular Biology 10, no. 6 (June 1990): 2774–86. http://dx.doi.org/10.1128/mcb.10.6.2774.

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We have mapped DNase I-hypersensitive sites and topoisomerase II (topo II) sites in the chicken beta-globin locus, which contains four globin genes (5'-rho-beta H-beta A-epsilon-3'). In the 65 kilobases (kb) mapped, 12 strong hypersensitive sites were found clustered within the 25-kb region from 10 kb upstream of rho to just downstream of epsilon. The strong sites were grouped into several classes based on their tissue distribution, developmental pattern, and location. (i) One site was present in all cells examined, both erythroid and nonerythroid. (ii) Three sites, located upstream of the rho-globin gene, were present at every stage of erythroid development, but were absent from nonerythroid cells. (iii) Four sites at the 5' ends of each of the four globin genes were hypersensitive only in the subset of erythroid cells that were transcribing or had recently transcribed the associated gene. (iv) Another three sites, whose pattern of hypersensitivity also correlated with expression of the associated gene, were found 3' of rho, beta H, and epsilon. (v) A site 3' of beta A and 5' of epsilon was erythroid cell specific and present at all developmental stages, presumably reflecting the activity of this enhancer throughout erythroid development. We also mapped the topo II sites in this locus, as determined by teniposide-induced DNA cleavage. All strong teniposide-induced cleavages occurred at DNase I-hypersensitive sites, while lesser amounts of cleavage were observed in transcribed regions of DNA. Most but not all of the DNase I-hypersensitive sites were topo II sites. These data are consistent with the hypothesis that, in vivo, topo II preferentially acts on nucleosome-free regions of DNA but suggest that additional topo II regulatory mechanisms must exist.

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Reitman, M., and G. Felsenfeld. "Developmental regulation of topoisomerase II sites and DNase I-hypersensitive sites in the chicken beta-globin locus." Molecular and Cellular Biology 10, no. 6 (June 1990): 2774–86. http://dx.doi.org/10.1128/mcb.10.6.2774-2786.1990.

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We have mapped DNase I-hypersensitive sites and topoisomerase II (topo II) sites in the chicken beta-globin locus, which contains four globin genes (5'-rho-beta H-beta A-epsilon-3'). In the 65 kilobases (kb) mapped, 12 strong hypersensitive sites were found clustered within the 25-kb region from 10 kb upstream of rho to just downstream of epsilon. The strong sites were grouped into several classes based on their tissue distribution, developmental pattern, and location. (i) One site was present in all cells examined, both erythroid and nonerythroid. (ii) Three sites, located upstream of the rho-globin gene, were present at every stage of erythroid development, but were absent from nonerythroid cells. (iii) Four sites at the 5' ends of each of the four globin genes were hypersensitive only in the subset of erythroid cells that were transcribing or had recently transcribed the associated gene. (iv) Another three sites, whose pattern of hypersensitivity also correlated with expression of the associated gene, were found 3' of rho, beta H, and epsilon. (v) A site 3' of beta A and 5' of epsilon was erythroid cell specific and present at all developmental stages, presumably reflecting the activity of this enhancer throughout erythroid development. We also mapped the topo II sites in this locus, as determined by teniposide-induced DNA cleavage. All strong teniposide-induced cleavages occurred at DNase I-hypersensitive sites, while lesser amounts of cleavage were observed in transcribed regions of DNA. Most but not all of the DNase I-hypersensitive sites were topo II sites. These data are consistent with the hypothesis that, in vivo, topo II preferentially acts on nucleosome-free regions of DNA but suggest that additional topo II regulatory mechanisms must exist.

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OGAWA, Makoto. "Expression of DNA topoisomerase I and II β in the developing cerebellar plate in rat embryos." Okayama Igakkai Zasshi (Journal of Okayama Medical Association) 111, no. 3-8 (1999): 105–14. http://dx.doi.org/10.4044/joma1947.111.3-8_105.

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Ng, Shu-Wing, Yan Liu, and Lowell E. Schnipper. "Cloning and characterization of the 5′-flanking sequence for the human DNA topoisomerase II beta gene." Gene 203, no. 2 (December 1997): 113–19. http://dx.doi.org/10.1016/s0378-1119(97)00500-3.

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17

Emmons, M., D. Boulware, D. M. Sullivan, and L. A. Hazlehurst. "Topoisomerase II beta levels are a determinant of melphalan-induced DNA crosslinks and sensitivity to cell death." Biochemical Pharmacology 72, no. 1 (June 2006): 11–18. http://dx.doi.org/10.1016/j.bcp.2006.03.017.

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Morse-Gaudio, M., and M. S. Risley. "Topoisomerase II expression and VM-26 induction of DNA breaks during spermatogenesis in Xenopus laevis." Journal of Cell Science 107, no. 10 (October 1, 1994): 2887–98. http://dx.doi.org/10.1242/jcs.107.10.2887.

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The relative content of topoisomerase II (topo II) and the induction of topo-II-mediated DNA damage and cellular abnormalities have been characterized in developing spermatogenic cells of Xenopus laevis to gain an insight into the role of topo II during spermatogenesis. Decatenation assays identified topo II activity in nuclear extracts from spermatocytes and pre-elongate spermatids, but not in extracts from elongate spermatids or sperm. Extracts from early-mid spermatids contained 14% (per cell) of the decatenation activity found in spermatocyte extracts. Immunoblots of SDS extracts from whole cells and nuclei from both spermatocytes and pre-elongate spermatids, but not elongate spermatids or sperm, resolved a 180 kDa polypeptide that reacts with polyclonal antisera to Xenopus oocyte topo II, an antipeptide antibody (FHD29) to human topo II alpha and beta, and an antipeptide antibody to human topo II alpha, suggesting homology between Xenopus spermatogenic cell topo II and mammalian topo II alpha. Immunofluorescence microscopy of topo II in testis cryosections revealed the presence of topo II in nuclei of all spermatogenic stages, but not in sperm. The relative levels of topo II estimated from fluorescence intensity were highest in spermatogonia and spermatocytes, then early-mid spermatids, followed by elongate spermatids and somatic cells. Incubation of isolated spermatogenic cells with teniposide (VM-26), a topo II-targetted drug, resulted in a dose-dependent induction of DNA breaks in all spermatocytes and spermatid stages to nuclear elongation stages, as analyzed by alkaline single cell gel electrophoresis. Addition of 0.5-50 microM VM-26 to spermatogenic cell cultures for 27 hours resulted in stage-dependent abnormalities. Mid-late spermatid stages were relatively resistant to VM-26-induced damage. In contrast, meiotic division stages were arrested and spermatogonia B were killed by VM-26, and VM-26 induced abnormal chromosome condensation in pachytene spermatocytes. The results of these studies show that cellular levels of topo II are stage-dependent during spermatogenesis, that most spermatogenic stages are sensitive to topo II-mediated DNA damage, and that spermatogonia B, meiotic divisions and pachytene spermatocytes are particularly sensitive to induction of morphological abnormalities and cell death during acute exposure to topo II-targetted drugs.

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Calderón-Montaño, José Manuel, Estefanía Burgos-Morón, Manuel Luis Orta, Nuria Pastor, Caroline A. Austin, Santiago Mateos, and Miguel López-Lázaro. "Alpha, beta-unsaturated lactones 2-furanone and 2-pyrone induce cellular DNA damage, formation of topoisomerase I- and II-DNA complexes and cancer cell death." Toxicology Letters 222, no. 1 (September 2013): 64–71. http://dx.doi.org/10.1016/j.toxlet.2013.07.007.

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20

Harker, W. Graydon, D. Lynn Slade, Fred H. Drake, and Ryan L. Parr. "Mitoxantrone resistance in HL-60 leukemia cells: reduced nuclear topoisomerase II catalytic activity and drug-induced DNA cleavage in association with reduced expression of the topoisomerase II .beta. isoform." Biochemistry 30, no. 41 (October 1991): 9953–61. http://dx.doi.org/10.1021/bi00105a020.

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Broyles, S. S., and B. Moss. "Sedimentation of an RNA polymerase complex from vaccinia virus that specifically initiates and terminates transcription." Molecular and Cellular Biology 7, no. 1 (January 1987): 7–14. http://dx.doi.org/10.1128/mcb.7.1.7.

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A high-molecular-weight protein complex that is capable of accurate transcription initiation and termination of vaccinia virus early genes without additional factors was demonstrated. The complex was solubilized by disruption of purified virions, freed of DNA by passage through a DEAE-cellulose column, and isolated by glycerol gradient sedimentation. All detectable RNA polymerase activity was associated with the transcription complex, whereas the majority of enzymes released from virus cores including mRNA (nucleoside-2'-O)methyltransferase, poly(A) polymerase, topoisomerase, nucleoside triphosphate phosphohydrolase II, protein kinase, and single-strand DNase sedimented more slowly. Activities corresponding to two enzymes, mRNA guanylyltransferase (capping enzyme) and nucleoside triphosphate phosphohydrolase I (DNA-dependent ATPase), partially sedimented with the complex. Silver-stained polyacrylamide gels, immunoblots, and autoradiographs confirmed the presence of subunits of vaccinia virus RNA polymerase, mRNA guanylyltransferase, and nucleoside triphosphate phosphohydrolase I, as well as additional unidentified polypeptides, in fractions with transcriptase activity. A possible role for the DNA-dependent ATPase was suggested by studies with ATP analogs with gamma-S or nonhydrolyzable beta-gamma-phosphodiester bonds. These analogs were used by vaccinia virus RNA polymerase to nonspecifically transcribe single-stranded DNA templates but did not support accurate transcription of early genes by the complex. Transcription also was sensitive to high concentrations of novobiocin; however, this effect could be attributed to inhibition of RNA polymerase or ATPase activities rather than topoisomerase.

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Broyles, S. S., and B. Moss. "Sedimentation of an RNA polymerase complex from vaccinia virus that specifically initiates and terminates transcription." Molecular and Cellular Biology 7, no. 1 (January 1987): 7–14. http://dx.doi.org/10.1128/mcb.7.1.7-14.1987.

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A high-molecular-weight protein complex that is capable of accurate transcription initiation and termination of vaccinia virus early genes without additional factors was demonstrated. The complex was solubilized by disruption of purified virions, freed of DNA by passage through a DEAE-cellulose column, and isolated by glycerol gradient sedimentation. All detectable RNA polymerase activity was associated with the transcription complex, whereas the majority of enzymes released from virus cores including mRNA (nucleoside-2'-O)methyltransferase, poly(A) polymerase, topoisomerase, nucleoside triphosphate phosphohydrolase II, protein kinase, and single-strand DNase sedimented more slowly. Activities corresponding to two enzymes, mRNA guanylyltransferase (capping enzyme) and nucleoside triphosphate phosphohydrolase I (DNA-dependent ATPase), partially sedimented with the complex. Silver-stained polyacrylamide gels, immunoblots, and autoradiographs confirmed the presence of subunits of vaccinia virus RNA polymerase, mRNA guanylyltransferase, and nucleoside triphosphate phosphohydrolase I, as well as additional unidentified polypeptides, in fractions with transcriptase activity. A possible role for the DNA-dependent ATPase was suggested by studies with ATP analogs with gamma-S or nonhydrolyzable beta-gamma-phosphodiester bonds. These analogs were used by vaccinia virus RNA polymerase to nonspecifically transcribe single-stranded DNA templates but did not support accurate transcription of early genes by the complex. Transcription also was sensitive to high concentrations of novobiocin; however, this effect could be attributed to inhibition of RNA polymerase or ATPase activities rather than topoisomerase.

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23

Tomkins, C. E., S. N. Edwards, and A. M. Tolkovsky. "Apoptosis is induced in post-mitotic rat sympathetic neurons by arabinosides and topoisomerase II inhibitors in the presence of NGF." Journal of Cell Science 107, no. 6 (June 1, 1994): 1499–507. http://dx.doi.org/10.1242/jcs.107.6.1499.

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Sympathetic neurons depend on nerve growth factor (NGF) for their survival and die by apoptosis when NGF is withdrawn, despite their post-mitotic state. Martin et al. (1990, J. Neurosci. 10, 184–193) showed that cytosine arabinoside, but no other arabinofuranosyl nucleoside, could induce cell death in the presence of NGF and they suggested that it may block a critical step in the NGF-signalling pathway. We show that cytosine arabinoside is not the only nucleoside capable of inducing apoptosis in sympathetic neurons in the presence of NGF. In newly isolated neurons from P0 rat pups cultured in the presence of NGF, all the arabinose nucleosides (adenine, cytosine, guanine and thymine) induce apoptosis at 10 microM when combined with 5-fluorodeoxyuridine treatment. Because 1-beta-arabinofuranosylcytosine is associated with double-strand breaks and chromosomal abberrations, we examined whether topoisomerase II inhibitors, which also cause double-strand breaks by stabilising the enzyme-DNA ‘cleavable complex’, were capable of promoting apoptosis in these neurons. Although P0 rat neurons are strictly postmitotic, topoisomerase II inhibitors teniposide and mitoxantrone induced them to die by apoptosis in the presence of NGF with the same apparent time-course as arabinose treatment or NGF withdrawal. By contrast, ICRF 193, a catalytic inhibitor of topoisomerase II, reduced the extent of apoptosis induced by mitoxantrone or teniposide by 80% if added simultaneously with the latter but by 2 hours it had no rescue effect, suggesting that topoisomerase II is highly active in these neurons. ICRF 193 also partially reduced the induction of fluorodeoxyuridine-dependent apoptosis by the arabinose nucleosides.(ABSTRACT TRUNCATED AT 250 WORDS)

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Fleenor, DE, and RE Kaufman. "Characterization of the DNase I hypersensitive site 3' of the human beta globin gene domain." Blood 81, no. 10 (May 15, 1993): 2781–90. http://dx.doi.org/10.1182/blood.v81.10.2781.2781.

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Abstract The members of the human beta globin gene family are flanked by strong DNase I hypersensitive sites. The collection of sites 5' to the epsilon globin gene is able to confer high levels of expression of linked globin genes, but a function has not been assigned to the site 3' to the beta globin gene (3'HS1). Our analysis of this DNase I super hypersensitive site shows that the region is composed of multiple DNase I sites. By examination of the DNA sequence, we have determined that the region is very A/T-rich and contains topoisomerase II recognition sequences, as well as several consensus binding motifs for GATA-1 and AP-1/NF-E2. Gel mobility shift assays indicate that the region can interact in vitro with GATA-1 and AP-1/NF-E2, and functional studies show that the region serves as a scaffold attachment region in both erythroid and nonerythroid cell lines. Whereas many of the physical features of 3'HS1 are shared by 5'HS2 (a component of the 5' locus control region), transient expression studies show that 3' HS1 does not share the erythroid-specific enhancer activity exhibited by 5'HS2.

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25

Fleenor, DE, and RE Kaufman. "Characterization of the DNase I hypersensitive site 3' of the human beta globin gene domain." Blood 81, no. 10 (May 15, 1993): 2781–90. http://dx.doi.org/10.1182/blood.v81.10.2781.bloodjournal81102781.

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The members of the human beta globin gene family are flanked by strong DNase I hypersensitive sites. The collection of sites 5' to the epsilon globin gene is able to confer high levels of expression of linked globin genes, but a function has not been assigned to the site 3' to the beta globin gene (3'HS1). Our analysis of this DNase I super hypersensitive site shows that the region is composed of multiple DNase I sites. By examination of the DNA sequence, we have determined that the region is very A/T-rich and contains topoisomerase II recognition sequences, as well as several consensus binding motifs for GATA-1 and AP-1/NF-E2. Gel mobility shift assays indicate that the region can interact in vitro with GATA-1 and AP-1/NF-E2, and functional studies show that the region serves as a scaffold attachment region in both erythroid and nonerythroid cell lines. Whereas many of the physical features of 3'HS1 are shared by 5'HS2 (a component of the 5' locus control region), transient expression studies show that 3' HS1 does not share the erythroid-specific enhancer activity exhibited by 5'HS2.

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26

Burden, D. Andrew, and Daniel M. Sullivan. "Phosphorylation of the .alpha.- and .beta.-Isoforms of DNA Topoisomerase II Is Qualitatively Different in Interphase and Mitosis in Chinese Hamster Ovary Cells." Biochemistry 33, no. 49 (December 1994): 14651–55. http://dx.doi.org/10.1021/bi00253a001.

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27

Wang, Zhe Qing, Yao Haur Kuo, Dora Schnur, J. Phillip Bowen, Su Ying Liu, Fu Sheng Han, Jang Yang Chang, Yung Chi Cheng, and Kuo Hsiung Lee. "Antitumor agents. 113. New 4.beta.-arylamino derivatives of 4'-O-demethylepipodophyllotoxin and related compounds as potent inhibitors of human DNA topoisomerase II." Journal of Medicinal Chemistry 33, no. 9 (September 1990): 2660–66. http://dx.doi.org/10.1021/jm00171a050.

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28

Hu, Hong, Su Ying Liu, Yung Chi Cheng, Kuo Hsiung Lee, and Zhe Qing Wang. "Antitumor agents. 123. Synthesis and human DNA topoisomerase II inhibitory activity of 2'-chloro derivatives of etoposide and 4.beta.-(arylamino)-4'-O-demethylpodophyllotoxins." Journal of Medicinal Chemistry 35, no. 5 (March 1992): 866–71. http://dx.doi.org/10.1021/jm00083a009.

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29

Jazwinski, S. M. "Participation of ATP in the binding of a yeast replicative complex to DNA." Biochemical Journal 246, no. 1 (August 15, 1987): 213–19. http://dx.doi.org/10.1042/bj2460213.

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The activity that replicates yeast DNA in vitro can be isolated from cells of the budding yeast Saccharomyces in a high-Mr (approximately 2 × 10(6] form. Several lines of evidence indicate that this fraction contains a multiprotein replicative complex. A functional assay has been developed for the analysis of the interaction of the replicating activity with DNA. Binding of the activity required Mg2+, but did not require the addition of ATP or the other ribo- or deoxynucleoside triphosphates. However, the ATP analogues adenosine 5′-[gamma-thio]triphosphate and adenosine 5′-[beta gamma-imido]triphosphate blocked the binding, suggesting that ATP participates in the interaction at some stage. The binding was template (origin)-specific in either the presence or the absence of ATP and the other nucleoside triphosphates; however, ATP stabilized the replicating activity. The preferential inhibition of binding that was observed in the presence of the DNA topoisomerase II inhibitor coumermycin suggests that the requirement for ATP may be at least partially accounted for by the involvement of this enzyme in the initial interaction of the replicating activity with DNA. Finally, the binding was rapid. In contrast, DNA synthesis displayed a lag when assayed directly without first allowing a period for the replicating activity to bind to the DNA. In addition, binding was ‘tight’, as judged by the resistance of the protein–DNA complexes to salt in comparison with the relative sensitivity of binding. The replicating activity was not readily displaced from the complexes by exogenous DNAs, either possessing or lacking yeast origins of replication. The results suggest that the interaction of the replicating activity with the DNA occurs in more than one stage.

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30

Kimura, K., N. Nozaki, M. Saijo, A. Kikuchi, M. Ui, and T. Enomoto. "Identification of the nature of modification that causes the shift of DNA topoisomerase II beta to apparent higher molecular weight forms in the M phase." Journal of Biological Chemistry 269, no. 40 (October 1994): 24523–26. http://dx.doi.org/10.1016/s0021-9258(17)31419-9.

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31

Charron, Martin, and Ronald Hancock. "DNA topoisomerase II is required for formation of mitotic chromosomes in Chinese hamster ovary cells: studies using the inhibitor 4'-demethylepipodophyllotoxin 9-(4,6-O-thenylidene-.beta.-D-glucopyranoside)." Biochemistry 29, no. 41 (October 1990): 9531–37. http://dx.doi.org/10.1021/bi00493a006.

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32

Wang, Zhe-Qing, Hong Hu, Hong-Xin Chen, Yung-Chi Cheng, and Kuo Hsiung Lee. "Antitumor agents. 124. New 4.beta.-substituted aniline derivatives of 6,7-O,O-demethylene-4'-O-demethylpodophyllotoxin and related compounds as potent inhibitors of human DNA topoisomerase II." Journal of Medicinal Chemistry 35, no. 5 (March 1992): 871–77. http://dx.doi.org/10.1021/jm00083a010.

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33

Renzi, L., M. S. Gersch, M. S. Campbell, L. Wu, S. A. Osmani, and G. J. Gorbsky. "MPM-2 antibody-reactive phosphorylations can be created in detergent-extracted cells by kinetochore-bound and soluble kinases." Journal of Cell Science 110, no. 17 (September 1, 1997): 2013–25. http://dx.doi.org/10.1242/jcs.110.17.2013.

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The MPM-2 antibody labels mitosis-specific and cell cycle-regulated phosphoproteins. The major phosphoproteins of mitotic chromosomes recognized by the MPM-2 antibody are DNA topoisomerase II (topoII) alpha and beta. In immunofluorescence studies of PtK1 cytoskeletons, prepared by detergent lysis in the presence of potent phosphatase inhibitors, the MPM-2 antibody labels phosphoproteins found at kinetochores, chromosome arms, midbody and spindle poles of mitotic cells. In cells extracted without phosphatase inhibitors, labeling of the MPM-2 antibodies at kinetochores is greatly diminished. However, in cytoskeletons this epitope can be regenerated through the action of kinases stably bound at the kinetochore. Various kinase inhibitors were tested in order to characterize the endogenous kinase responsible for these phosphorylations. We found that the MPM-2 epitope will not rephosphorylate in the presence of the broad specificity kinase inhibitors K-252a, staurosporine and 2-aminopurine. Several other inhibitors had no effect on the rephosphorylation indicating that the endogenous MPM-2 kinase at kinetochores is not p34cdc2, casein kinase II, MAP kinase, protein kinase A or protein kinase C. The addition of N-ethylmaleimide inactivated the endogenous kinetochore kinase; this allowed testing of several purified kinases in the kinetochore rephosphorylation assay. Active p34cdc2-cyclin B, casein kinase II and MAP kinase could not generate the MPM-2 phosphoepitope. However, bacterially expressed NIMA from Aspergillus and ultracentrifuged mitotic HeLa cell extract were able to catalyze the rephosphorylation of the MPM-2 epitope at kinetochores. Furthermore, fractionation of mitotic HeLa cell extract showed that kinases that create the MPM-2 epitope at kinetochores and chromosome arms are distinct. Our results suggest that multiple kinases (either soluble or kinetochore-bound), including a homolog of mammalian NIMA, can create the MPM-2 phosphoepitope. The kinetochore-bound kinase that catalyzes the formation of the MPM-2 phosphoepitope may play an important role in key events such as mitotic kinetochore assembly and sister chromatid separation at anaphase.

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34

Celada, A., S. McKercher, and R. A. Maki. "Repression of major histocompatibility complex IA expression by glucocorticoids: the glucocorticoid receptor inhibits the DNA binding of the X box DNA binding protein." Journal of Experimental Medicine 177, no. 3 (March 1, 1993): 691–98. http://dx.doi.org/10.1084/jem.177.3.691.

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Glucocorticoids are effective repressors of major histocompatibility complex (MHC) class II gene expression. The repression occurs in B cells, which constitutively express MHC class II, as well as in macrophages, which only express MHC class II after the cells are treated with interferon gamma. For the MHC class II gene IA beta, this negative regulation has been linked to the X box DNA sequence, located with the IA beta promoter. The addition of the glucocorticoid receptor was shown to inhibit the DNA binding of the X box DNA binding protein to the X box. The DNA binding of two other DNA binding proteins that recognize elements within this promoter was unaffected by the addition of glucocorticoid receptor. It is likely that the repression of IA beta gene expression by glucocorticoids occurs because the X box DNA binding protein is prevented from binding to the DNA and activating transcription.

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35

Hagiwara, Kazumi, Hiromi Ito, Takashi Murate, Yasuhiko Miyata, Haruhiko Ohashi, and Hirokazu Nagai. "PROX1 overexpression inhibits protein kinase C beta II transcription through promoter DNA methylation." Genes, Chromosomes and Cancer 51, no. 11 (July 25, 2012): 1024–36. http://dx.doi.org/10.1002/gcc.21985.

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36

Lin, G. C., J. Jaeger, and J. B. Sweasy. "Loop II of DNA polymerase beta is important for polymerization activity and fidelity." Nucleic Acids Research 35, no. 9 (April 16, 2007): 2924–35. http://dx.doi.org/10.1093/nar/gkm126.

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37

Lin, George C., Joachim Jaeger, Kristin A. Eckert, and Joann B. Sweasy. "Loop II of DNA polymerase beta is important for discrimination during substrate binding." DNA Repair 8, no. 2 (February 2009): 182–89. http://dx.doi.org/10.1016/j.dnarep.2008.10.006.

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38

Moi, P., G. Loudianos, J. Lavinha, S. Murru, P. Cossu, R. Casu, L. Oggiano, M. Longinotti, A. Cao, and M. Pirastu. "Delta-thalassemia due to a mutation in an erythroid-specific binding protein sequence 3' to the delta-globin gene." Blood 79, no. 2 (January 15, 1992): 512–16. http://dx.doi.org/10.1182/blood.v79.2.512.bloodjournal792512.

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We have previously described a family of Northern Sardinian descent in which the propositus was affected by thalassemia major resulting from compound heterozygosity for codon 39 nonsense mutation and the beta +IVS II nt 745 mutation and in which all heterozygotes for the beta +IVS II nt 745 mutation had normal hemoglobin (Hb) A2 levels. To define the reasons for normal HbA2 levels in otherwise typical beta- thalassemia heterozygotes, we cloned and sequenced the delta- thalassemia gene in cis to the beta +IVS II nt 745 mutation. The sequence analysis showed a single nucleotide substitution (G----A) at position 69 nts (delta +69) downstream to the polyA addition site. Dot blot analysis with an oligonucleotide probe complementary to the delta +69 mutation detected this mutation in several heterozygotes for the beta +IVS II nt 745 mutation from the proband 's family, but failed to show it either in a group of normal individuals of the same origin or in nonrelated heterozygotes for the beta +IVS II nt 745 mutation of the same or different descent from the proband. The delta +69 (G----A) mutation may be responsible for the low delta-globin output from the beta +IVS II nt 745 chromosome or could be a silent polymorphism not affecting the function of the delta-globin gene. The normal G at position 69 is part of a sequence very similar to the core DNA (A/T)GATA(A/G) motif (GATA box) that is a binding site for the GATA-1 protein. Gel-retardation assay has shown that a DNA fragment containing the GATA motif with the G----A at position +69 has increased binding affinity for erythroid-specific DNA binding protein(s) as compared with the wild-type sequence. These findings may suggest that the delta +69 mutation is responsible for the deficient function of the in cis delta- globin gene.

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39

Wade, W. F., J. H. Freed, and M. Edidin. "Translational diffusion of class II major histocompatibility complex molecules is constrained by their cytoplasmic domains." Journal of Cell Biology 109, no. 6 (December 1, 1989): 3325–31. http://dx.doi.org/10.1083/jcb.109.6.3325.

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Site-directed mutagenesis in vitro was used to introduce stop codons in the genomic DNA of the alpha and beta chains of the murine class II major histocompatibility complex antigen, I-Ak. Mutated DNA was transfected into B lymphoma cells that were then selected by neomycin resistance and for their ability to express I-Ak molecules on their plasma membrane. The translational diffusion coefficient (Dlat) of I-Ak molecules composed of a wild-type beta chain paired with an alpha chain missing either 6 or 12 amino acids from the cytoplasmic domain is on the average threefold higher than the Dlat of wild-type I-Ak molecules as measured by fluorescence photobleaching and recovery. The removal of 12 amino acids from the cytoplasmic domain of the beta chain did not change the Dlat value from that of wild-type I-Ak if the truncated beta chain was paired with a wild-type alpha chain. Removing all amino acids of the cytoplasmic domains of both the alpha and beta chains resulted in a 10-fold increase in the Dlat, the highest value for any of the truncated I-Ak molecules tested. These data indicate that the carboxy-terminal six amino acids of the cytoplasmic domain of the alpha chain and the six plasma membrane-proximal amino acids of the beta chain are important in constraining the translational diffusion of I-Ak molecules in the plasma membrane.

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40

Khalil, N., R. N. O'Connor, K. C. Flanders, W. Shing, and C. I. Whitman. "Regulation of type II alveolar epithelial cell proliferation by TGF-beta during bleomycin-induced lung injury in rats." American Journal of Physiology-Lung Cellular and Molecular Physiology 267, no. 5 (November 1, 1994): L498—L507. http://dx.doi.org/10.1152/ajplung.1994.267.5.l498.

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Three isoforms of transforming growth factor-beta (TGF-beta) are found in mammalian cells and are potent regulators of inflammation, connective tissue synthesis, cellular proliferation, and differentiation. To determine the distribution and regulation of TGF-beta isoforms during pulmonary injury, a rat model of bleomycin-induced lung inflammation and repair was used. Using immunohistochemistry, we demonstrate that TGF-beta 2 and TGF-beta 3 were localized to alveolar macrophages as well as epithelial and smooth muscle cells of both normal rat lungs and rat lungs obtained at all time intervals after bleomycin administration. Early in bleomycin-induced lung injury, when there is active proliferation of type II alveolar epithelial cells, there was an increase in the number of type II alveolar epithelial cells isolated per lung and an increase in DNA synthesis by explanted type II alveolar epithelial cells. At this time, the secretion of biologically active TGF-beta 1–3, which are potent inhibitors of epithelial cell proliferation, was decreased. However, the secretion of TGF-beta 1–3 activity was markedly increased later in the injury response and coincided with a reduction in the number of type II alveolar epithelial cells isolated per lung and DNA synthesis in vitro. Furthermore, the addition of TGF-beta 1, 2, and 3 to cultures of actively proliferating type II alveolar epithelial cells resulted in inhibition of [3H]thymidine incorporation, whereas, in the presence of anti-TGF-beta 1-3 antibody, there was an increase in [3H]thymidine incorporation. Our findings suggest that altered secretion of TGF-beta 1-3 activity by type II alveolar epithelial cells during bleomycin-induced lung injury may regulate pulmonary alveolar epithelial cell proliferation during injury and repair phases.

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41

German, M. S., L. G. Moss, J. Wang, and W. J. Rutter. "The insulin and islet amyloid polypeptide genes contain similar cell-specific promoter elements that bind identical beta-cell nuclear complexes." Molecular and Cellular Biology 12, no. 4 (April 1992): 1777–88. http://dx.doi.org/10.1128/mcb.12.4.1777.

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The pancreatic beta cell makes several unique gene products, including insulin, islet amyloid polypeptide (IAPP), and beta-cell-specific glucokinase (beta GK). The functions of isolated portions of the insulin, IAPP, and beta GK promoters were studied by using transient expression and DNA binding assays. A short portion (-247 to -197 bp) of the rat insulin I gene, the FF minienhancer, contains three interacting transcriptional regulatory elements. The FF minienhancer binds at least two nuclear complexes with limited tissue distribution. Sequences similar to that of the FF minienhancer are present in the 5' flanking DNA of the human IAPP and rat beta GK genes and also the rat insulin II and mouse insulin I and II genes. Similar minienhancer constructs from the insulin and IAPP genes function as cell-specific transcriptional regulatory elements and compete for binding of the same nuclear factors, while the beta GK construct competes for protein binding but functions poorly as a minienhancer. These observations suggest that the patterns of expression of the beta-cell-specific genes result in part from sharing the same transcriptional regulators.

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42

German, M. S., L. G. Moss, J. Wang, and W. J. Rutter. "The insulin and islet amyloid polypeptide genes contain similar cell-specific promoter elements that bind identical beta-cell nuclear complexes." Molecular and Cellular Biology 12, no. 4 (April 1992): 1777–88. http://dx.doi.org/10.1128/mcb.12.4.1777-1788.1992.

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The pancreatic beta cell makes several unique gene products, including insulin, islet amyloid polypeptide (IAPP), and beta-cell-specific glucokinase (beta GK). The functions of isolated portions of the insulin, IAPP, and beta GK promoters were studied by using transient expression and DNA binding assays. A short portion (-247 to -197 bp) of the rat insulin I gene, the FF minienhancer, contains three interacting transcriptional regulatory elements. The FF minienhancer binds at least two nuclear complexes with limited tissue distribution. Sequences similar to that of the FF minienhancer are present in the 5' flanking DNA of the human IAPP and rat beta GK genes and also the rat insulin II and mouse insulin I and II genes. Similar minienhancer constructs from the insulin and IAPP genes function as cell-specific transcriptional regulatory elements and compete for binding of the same nuclear factors, while the beta GK construct competes for protein binding but functions poorly as a minienhancer. These observations suggest that the patterns of expression of the beta-cell-specific genes result in part from sharing the same transcriptional regulators.

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43

Hansmann, Paul. "Daffodil Chromoplast DNA: Comparison with Chloroplast DNA, Physical Map, and Gene Localization." Zeitschrift für Naturforschung C 42, no. 1-2 (February 1, 1987): 118–22. http://dx.doi.org/10.1515/znc-1987-1-219.

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Abstract In daffodil, development of chloroplasts or chromoplasts is not accompanied by plastid DNA modification. This has been shown by comparing the fragment pattern of different restriction endonucleases, and by the lack of methylation of CCGG sequences. A physical map has been constructed for the plastome using the restriction endonucleases Sal I, Pst I, and Bgl I. The fragments containing the genes for the large subunit of ribulose bisphosphate carboxylase/oxygenase (rbcL), the alpha, beta, and epsilon subunits of the ATP synthase complex (atpA , atpB, atpE ), cytochrome f(petA ), and for the 51 kDa chlorophyll apoprotein of photosystem II (psbB) have been identified. The respective gene locations correspond to those on spinach chloroplast DNA.

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44

Rohrbaugh, M. L., J. E. Johnson, M. D. James, and R. C. Hardison. "Transcription unit of the rabbit beta 1 globin gene." Molecular and Cellular Biology 5, no. 1 (January 1985): 147–60. http://dx.doi.org/10.1128/mcb.5.1.147.

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We have hybridized pulse-labeled nuclear transcripts to cloned DNA fragments from the rabbit beta-like globin genes to determine the developmental timing, extent, and asymmetry of their transcription. The fetal-adult gene beta 1 was transcribed in fetal liver but not embryonic nuclei, whereas genes beta 3 and beta 4, which encode embryonic globin polypeptides, were transcribed only in embryonic nuclei. This shows that the switch from embryonic to fetal-adult globin production in rabbits is accomplished primarily by differential transcription of the beta-like globin genes. Gene beta 1 was subdivided into M13 subclones and tested for hybridization to nascent RNA. The nucleotide sequence of the 3' flanking region of gene beta 1 was also determined for 2,447 base pairs past the polyadenylation [poly(A)] site. No transcripts were found 5' to the cap site, but asymmetric transcription of gene beta 1 proceeded at a high level through the gene and past the poly(A) addition site for 603 nucleotides. The level of transcription declined after this, gradually dropping through the next 568 nucleotides. No polymerases were found on a fragment that begins 1,707 nucleotides past the poly(A) site; this fragment was part of a segment of repetitive DNA. These data show that the transcription unit of gene beta 1 begins at or near the cap nucleotide and extends at least 1,171 but no more than 1,706 nucleotides past the poly(A) addition site. The DNA segment that precedes the region of declining transcription contained an inverted repeat and encoded a short RNA transcribed by RNA polymerase II from the strand opposite the beta 1 transcript. These two features may function to attenuate the transcription of gene beta 1. An inverted repeat and a potential polymerase II transcription unit were also found in the homologous segment 3' to the human beta-globin gene. A short DNA segment close to the 3' end of the beta 1 transcription unit was transcribed more actively than the surrounding DNA, and it contained sequences that match the consensus internal control region for RNA polymerase III. This DNA segment may contain a separate polymerase III transcription unit. A member of the D repeat family located 3' to gene beta 1 was not transcribed in its entirety coordinately with beta 1.

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45

Rohrbaugh, M. L., J. E. Johnson, M. D. James, and R. C. Hardison. "Transcription unit of the rabbit beta 1 globin gene." Molecular and Cellular Biology 5, no. 1 (January 1985): 147–60. http://dx.doi.org/10.1128/mcb.5.1.147-160.1985.

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We have hybridized pulse-labeled nuclear transcripts to cloned DNA fragments from the rabbit beta-like globin genes to determine the developmental timing, extent, and asymmetry of their transcription. The fetal-adult gene beta 1 was transcribed in fetal liver but not embryonic nuclei, whereas genes beta 3 and beta 4, which encode embryonic globin polypeptides, were transcribed only in embryonic nuclei. This shows that the switch from embryonic to fetal-adult globin production in rabbits is accomplished primarily by differential transcription of the beta-like globin genes. Gene beta 1 was subdivided into M13 subclones and tested for hybridization to nascent RNA. The nucleotide sequence of the 3' flanking region of gene beta 1 was also determined for 2,447 base pairs past the polyadenylation [poly(A)] site. No transcripts were found 5' to the cap site, but asymmetric transcription of gene beta 1 proceeded at a high level through the gene and past the poly(A) addition site for 603 nucleotides. The level of transcription declined after this, gradually dropping through the next 568 nucleotides. No polymerases were found on a fragment that begins 1,707 nucleotides past the poly(A) site; this fragment was part of a segment of repetitive DNA. These data show that the transcription unit of gene beta 1 begins at or near the cap nucleotide and extends at least 1,171 but no more than 1,706 nucleotides past the poly(A) addition site. The DNA segment that precedes the region of declining transcription contained an inverted repeat and encoded a short RNA transcribed by RNA polymerase II from the strand opposite the beta 1 transcript. These two features may function to attenuate the transcription of gene beta 1. An inverted repeat and a potential polymerase II transcription unit were also found in the homologous segment 3' to the human beta-globin gene. A short DNA segment close to the 3' end of the beta 1 transcription unit was transcribed more actively than the surrounding DNA, and it contained sequences that match the consensus internal control region for RNA polymerase III. This DNA segment may contain a separate polymerase III transcription unit. A member of the D repeat family located 3' to gene beta 1 was not transcribed in its entirety coordinately with beta 1.

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46

Moi, P., G. Loudianos, J. Lavinha, S. Murru, P. Cossu, R. Casu, L. Oggiano, M. Longinotti, A. Cao, and M. Pirastu. "Delta-thalassemia due to a mutation in an erythroid-specific binding protein sequence 3' to the delta-globin gene." Blood 79, no. 2 (January 15, 1992): 512–16. http://dx.doi.org/10.1182/blood.v79.2.512.512.

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Abstract We have previously described a family of Northern Sardinian descent in which the propositus was affected by thalassemia major resulting from compound heterozygosity for codon 39 nonsense mutation and the beta +IVS II nt 745 mutation and in which all heterozygotes for the beta +IVS II nt 745 mutation had normal hemoglobin (Hb) A2 levels. To define the reasons for normal HbA2 levels in otherwise typical beta- thalassemia heterozygotes, we cloned and sequenced the delta- thalassemia gene in cis to the beta +IVS II nt 745 mutation. The sequence analysis showed a single nucleotide substitution (G----A) at position 69 nts (delta +69) downstream to the polyA addition site. Dot blot analysis with an oligonucleotide probe complementary to the delta +69 mutation detected this mutation in several heterozygotes for the beta +IVS II nt 745 mutation from the proband 's family, but failed to show it either in a group of normal individuals of the same origin or in nonrelated heterozygotes for the beta +IVS II nt 745 mutation of the same or different descent from the proband. The delta +69 (G----A) mutation may be responsible for the low delta-globin output from the beta +IVS II nt 745 chromosome or could be a silent polymorphism not affecting the function of the delta-globin gene. The normal G at position 69 is part of a sequence very similar to the core DNA (A/T)GATA(A/G) motif (GATA box) that is a binding site for the GATA-1 protein. Gel-retardation assay has shown that a DNA fragment containing the GATA motif with the G----A at position +69 has increased binding affinity for erythroid-specific DNA binding protein(s) as compared with the wild-type sequence. These findings may suggest that the delta +69 mutation is responsible for the deficient function of the in cis delta- globin gene.

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47

Schmidt, T., and J. S. Heslop-Harrison. "Variability and evolution of highly repeated DNA sequences in the genus Beta." Genome 36, no. 6 (December 1, 1993): 1074–79. http://dx.doi.org/10.1139/g93-142.

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Satellite DNA from wild beet species was separated from restriction endonuclease digested genomic DNA by polyacrylamide gel electrophoresis. Two nonhomologous HaeIII satellite DNA repeats were cloned from the wild beet Beta trigyna. The type I repeat is 140–149 bp long and AT rich, while the type II is 162 bp in size and GC rich. A third repetitive HaeIII element cloned from the related wild beet B. corolliflora was shown to be organized as a HinfI satellite DNA family in the cultivated beet B. vulgaris ssp. vulgaris and the wild beet B. vulgaris ssp. maritima. This type III satellite monomer is 149 bp long and contains a high number of short direct subrepeats. The monomer was found in different genomic organizations and copy numbers in all sections of the genus Beta indicating an amplification early in the phylogeny. The HaeIII repeats from B. trigyna are characterized by a lower variability and form long tandem arrays in the genomes of Corollinae species. The investigation of the distribution of all three sequence families provided data that may contribute to the solution of taxonomic problems of the genus Beta and be useful in the characterization of hybrids and derived lines with alien wild beet chromosomes.Key words: satellite DNA, Beta vulgaris, Beta corolliflora, Beta trigyna, evolution, repetitive DNA.

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48

Lu, H. T., J. L. Riley, G. T. Babcock, M. Huston, G. R. Stark, J. M. Boss, and R. M. Ransohoff. "Interferon (IFN) beta acts downstream of IFN-gamma-induced class II transactivator messenger RNA accumulation to block major histocompatibility complex class II gene expression and requires the 48-kD DNA-binding protein, ISGF3-gamma." Journal of Experimental Medicine 182, no. 5 (November 1, 1995): 1517–25. http://dx.doi.org/10.1084/jem.182.5.1517.

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Interferon (IFN) gamma, a cardinal proinflammatory cytokine, induces expression of the gene products of the class II locus of the major histocompatibility complex (MHC), whereas IFN-alpha or -beta suppresses MHC class II expression. The mechanism of IFN-beta-mediated MHC class II inhibition has been unclear. Recently, a novel factor termed class II transactivator (CIITA) has been identified as essential for IFN-gamma-induced MHC class II transcription. We studied the status of IFN-gamma-induced CIITA messenger RNA (mRNA) accumulation and CIITA-driven transactivation in IFN-beta-treated cells and used cell lines that had defined defects in the type I IFN response pathway to address the roles of IFN signaling components in the inhibition of MHC class II induction. IFN-beta treatment did not suppress IFN-gamma-induced accumulation of CIITA mRNA. After cells were stably transfected with CIITA, endogenous MHC class II genes were constitutively expressed, and MHC class II promoters, delivered by transfection, were actively transcribed in CIITA-expressing cells. Expression of these promoters was significantly impaired by pretreatment with IFN-beta. These results suggest that IFN-beta acts downstream of CIITA mRNA accumulation, and acts in part by reducing the functional competence of CIITA for transactivating MHC class II promoters. IFN stimulated gene factor 3 (ISGF3) gamma was essential for IFN-beta to mediate inhibition of MHC class II induction, regardless of whether MHC class II transcription was stimulated by IFN-gamma or directly by CIITA expression. Results of these experiments suggest that inhibition of MHC class II in IFN-beta-treated cells requires expression of gene(s) directed by the ISGF3-IFN-stimulated response element pathway, and that these gene product(s) may act by blocking CIITA-driven transcription of MHC class II promoters.

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49

Embury, SH, GL Kropp, TS Stanton, TC Warren, PA Cornett, and FF Chehab. "Detection of the hemoglobin E mutation using the color complementation assay: application to complex genotyping." Blood 76, no. 3 (August 1, 1990): 619–23. http://dx.doi.org/10.1182/blood.v76.3.619.619.

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Abstract The color complementation assay (CCA) is a method of allele-specific DNA amplification by which competitive priming and extension of fluorescently labeled oligonucleotide primers determine the color of DNA amplification product. This diagnostic method precludes the need for radioisotopes, electrophoresis, and multiple high-stringency reaction conditions. The multiplicity of mutant globin genes present in Southeast Asians complicates clinical diagnosis and underscores the importance of DNA-based diagnostic methods. We have applied CCA to distinguish beta A and beta E alleles. Competing 15mer primers were a fluorescein-labeled complement to beta A and a rhodamine-labeled complement to beta E, identical except for their central nucleotides. A common unlabeled primer was used to amplify DNA product, the color of which was determined by the perfectly complementary primer. Color photography and spectrofluorometry, as well as a method of black-white photography that we developed to distinguish fluorescein- and rhodamine- labeled DNA, were used to record results. We applied CCA to define the complex genotype of a Thai woman with thalassemia intermedia, 96% HbE, and 4% HbF whose possible genotypes included several permutations of alpha-thalassemia, beta-thalassemia, and beta E genes. zeta-Globin gene mapping of DNA doubly digested with Bg/II and Asp 718 showed the -alpha 3.7/--SEA genotype, and CCA confirmed homozygous beta E/beta E. The CCA is useful for diagnosing the compound hemoglobin genotypes of Southeast Asians and could be applied also to prenatal diagnosis in this population.

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50

Embury, SH, GL Kropp, TS Stanton, TC Warren, PA Cornett, and FF Chehab. "Detection of the hemoglobin E mutation using the color complementation assay: application to complex genotyping." Blood 76, no. 3 (August 1, 1990): 619–23. http://dx.doi.org/10.1182/blood.v76.3.619.bloodjournal763619.

Full text

Abstract:

The color complementation assay (CCA) is a method of allele-specific DNA amplification by which competitive priming and extension of fluorescently labeled oligonucleotide primers determine the color of DNA amplification product. This diagnostic method precludes the need for radioisotopes, electrophoresis, and multiple high-stringency reaction conditions. The multiplicity of mutant globin genes present in Southeast Asians complicates clinical diagnosis and underscores the importance of DNA-based diagnostic methods. We have applied CCA to distinguish beta A and beta E alleles. Competing 15mer primers were a fluorescein-labeled complement to beta A and a rhodamine-labeled complement to beta E, identical except for their central nucleotides. A common unlabeled primer was used to amplify DNA product, the color of which was determined by the perfectly complementary primer. Color photography and spectrofluorometry, as well as a method of black-white photography that we developed to distinguish fluorescein- and rhodamine- labeled DNA, were used to record results. We applied CCA to define the complex genotype of a Thai woman with thalassemia intermedia, 96% HbE, and 4% HbF whose possible genotypes included several permutations of alpha-thalassemia, beta-thalassemia, and beta E genes. zeta-Globin gene mapping of DNA doubly digested with Bg/II and Asp 718 showed the -alpha 3.7/--SEA genotype, and CCA confirmed homozygous beta E/beta E. The CCA is useful for diagnosing the compound hemoglobin genotypes of Southeast Asians and could be applied also to prenatal diagnosis in this population.

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Journal articles on the topic 'DNA topoisomerasa II beta'

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