Template Topology and Transcription: Chromatin Templates Relaxed by Localized Linearization Are Transcriptionally Active in Yeast

REFERENCES

• Bjorkroth, B., C. Ericsson, M. M. Lamb, and B. Daneholt. 1988. Structure of the chromatin axis during transcription. Chromosoma 96:333–340.
   Google Scholar
• Brill, J. S., and R. Sternglanz. 1988. Transcription-dependent DNA super-coiling in yeast DNA topoisomerase mutants. Cell 54:403–411.
   PubMed Web of Science ®Google Scholar
• Church, G. M., and W. Gilbert. 1984. Genomic sequencing. Proc. Natl. Acad. Sci. USA 81:1991–1995.
   PubMed Web of Science ®Google Scholar
• Cockerill, P. N. 1990. Nuclear matrix attachment occurs in several regions of the IgH locus. Nucleic Acids Res. 18:2643–2648.
   PubMedGoogle Scholar
• Duttweiler, H., D. S. Gross, and W. T. Garrard. Unpublished results.
   Google Scholar
• Eng, W.-K., L. Faucette, R. K. Johnson, and R. Sternglanz. 1988. Evidence that DNA topoisomerase I is necessary for the cytotoxic effects of camptothecin. Mol. Pharmacol. 34:755–760.
   PubMed Web of Science ®Google Scholar
• Fleischmann, G., G. Pflugfelder, E. K. Steiner, K. Javaherian, G. C. Howard, J. C. Wang, and S. C. R. Elgin. 1984. Drosophila DNA topoisomerase I is associated with transcriptionally active regions of the genome. Proc. Natl. Acad. Sci. USA 81:6958–6962.
   PubMedGoogle Scholar
• Freeman, L. A., and W. T. Garrard. 1992. DNA supercoiling in chromatin structure and gene expression. Crit. Rev. Eukaryotic Gene Expr. 2:165–209.
   PubMedGoogle Scholar
• Furst, P., S. Hu, R. Hackett, and D. Hamer. 1988. Copper activates metal-lothionein gene transcription by altering the conformation of a specific DNA binding protein. Cell 55:705–717.
   PubMed Web of Science ®Google Scholar
• Giaever, G. N., and J. C. Wang. 1988. Supercoiling of intracellular DNA can occur in eukaryotic cells. Cell 55:849–856.
   PubMed Web of Science ®Google Scholar
• Goodrich, J. A., and R. Tjian. 1994. Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell 77:145–156.
   PubMedGoogle Scholar
• Harland, R. M., H. Weintraub, and S. L. McKnight. 1983. Transcription of DNA injected into Xenopus oocytes is influenced by template topology. Nature (London) 302:38–43.
   PubMed Web of Science ®Google Scholar
• Hoffman, C. S. 1993. Preparation of yeast DNA, p. 13.11.1–13.11.4. In K. Janssen (ed.), Current protocols in molecular biology, vol. 2. John Wiley & Sons, New York, N.Y.
   Google Scholar
• Horton, R. M. 1993. In vitro recombination and mutagenesis of DNA: SOEing together tailor-made genes. Methods Mol. Biol. 15:251–261.
   PubMedGoogle Scholar
• Ito, H., Y. Fukuda, K. Murata, and A. Kimura. 1983. Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 53:163–168.
   Google Scholar
• Izban, M. G., and D. S. Luse. 1991. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev. 5:683–696.
   PubMed Web of Science ®Google Scholar
• Izban, M. G., and D. S. Luse. 1992. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem. 267:13647–13655.
   PubMed Web of Science ®Google Scholar
• Izban, M. G., I. Samkurashvili, and D. S. Luse. 1995. RNA polymerase II ternary complexes may become arrested after transcribing to within 10 bases of the end of linear templates. J. Biol. Chem. 270:2290–2297.
   PubMedGoogle Scholar
• Jenuwein, T., W. C. Forrester, R. G. Qiu, and R. Grosschedl. 1993. The immunoglobulin µ, enhancer core establishes local factor access in nuclear chromatin independent of transcriptional stimulation. Genes Dev. 7:2016–2032.
   PubMedGoogle Scholar
• Jupe, E. R., R. R. Sinden, and I. L. Cartwright. 1993. Stably maintained microdomain of localized unrestrained supercoiling at a Drosophila heat shock gene locus. EMBO J. 3:1067–1075.
   Google Scholar
• Kostriken, R., J. N. Strathern, A. J. S. Klar, J. B. Hicks, and F. Heffron. 1983. A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae. Cell 35:167–174.
   PubMed Web of Science ®Google Scholar
• Landsman, D. 1996. Histone H1 in Saccharomyces cerevisiae: a double mystery solved? Trends Biochem. Sci. 21:287–288.
   Google Scholar
• Lee, M.-S., and W. T. Garrard. 1991. Positive DNA supercoiling generates a chromatin conformation characteristic of highly active genes. Proc. Natl. Acad. Sci. USA 88:9675–9679.
   PubMedGoogle Scholar
• Lee, M.-S., and W. T. Garrard. 1991. Transcription-induced nucleosome splitting: an underlying structure for DNase I sensitive chromatin. EMBO J. 10:607–615.
   PubMedGoogle Scholar
• Lehmann, A. R. 1995. Nucleotide excision repair and the link with transcription. Trends Biochem. Sci. 20:402–405.
   PubMed Web of Science ®Google Scholar
• Liao, X., W. C. Small, P. A. Srere, and R. A. Butow. 1991. Intramitochondrial functions regulate nonmitochondrial citrate synthase (CIT2) expression in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:38–46.
   PubMedGoogle Scholar
• Lin, C.-M., and D. J. Kosman. 1990. Copper uptake in wild type and copper metallothionein-deficient Saccharomyces cerevisiae: kinetics and mechanism. J. Biol. Chem. 265:9194–9200.
   PubMedGoogle Scholar
• Ljungman, M., and P. C. Hanawalt. 1992. Localized torsional tension in the DNA of human cells. Proc. Natl. Acad. Sci. USA 89:6055–6059.
   PubMed Web of Science ®Google Scholar
• Luchnik, A. N., T. A. Hisamutdinov, and G. P. Georgiev. 1988. Inhibition of transcription in eukaryotic cells by X-irradiation: relation to the loss of topological constraint in closed DNA loops. Nucleic Acids Res. 16:5175–5190.
   PubMedGoogle Scholar
• Mizutani, M., T. Ohta, H. Watanabe, H. Handa, and S. Hirose. 1991. Negative supercoiling of DNA facilitates an interaction between transcription factor IID and the fibroin gene promoter. Proc. Natl. Acad. Sci. USA 88:718–722.
   PubMed Web of Science ®Google Scholar
• Mizutani, M., K. Ura, and S. Hirose. 1991. DNA superhelicity affects the formation of transcription preinitiation complex on eukaryotic genes differently. Nucleic Acids Res. 19:2907–2911.
   PubMedGoogle Scholar
• Morse, R. H., D. S. Peterson, A. Dean, and R. T. Simpson. 1987. Yeast nucleosomes allow thermal untwisting of DNA. Nucleic Acids Res. 15:10311–10330.
   PubMed Web of Science ®Google Scholar
• O’Neill, T. E., G. Meersseman, S. Pennings, and E. M. Bradbury. 1995. Deposition of histone H1 onto reconstituted nucleosome arrays inhibits both initiation and elongation of transcripts by T7 RNA polymerase. Nucleic Acids Res. 23:1075–1082.
   PubMedGoogle Scholar
• Osborne, B. I., and L. Guarante. 1988. Transcription by RNA polymerase II induces changes of DNA topology in yeast. Genes Dev. 2:766–772.
   PubMedGoogle Scholar
• Parvin, J. D., and P. A. Sharp. 1993. DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell 73:533–540.
   PubMed Web of Science ®Google Scholar
• Parvin, J. D., R. J. McCormick, P. A. Sharp, and D. E. Fisher. 1995. Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor. Nature (London) 373:724–727.
   PubMed Web of Science ®Google Scholar
• Pedone, F., and P. Ballario. 1984. Stimulation of yeast RNA polymerase II transcription by critical values of supercoiling. Biochemistry 23:69–73.
   PubMedGoogle Scholar
• Piña, B., R. J. G. Haché, J. Arnemann, G. Chalepakis, E. P. Slater, and M. Beato. 1990. Hormonal induction of transfected genes depends on DNA topology. Mol. Cell. Biol. 10:625–633.
   PubMed Web of Science ®Google Scholar
• Pruitt, S. C., and R. H. Reeder. 1984. Effect of topological constraint on transcription of ribosomal DNA in Xenopus oocytes. J. Mol. Biol. 174:121–139.
   PubMedGoogle Scholar
• Raghuraman, M. K., B. J. Brewer, and W. L. Fangman. 1994. Activation of a yeast replication origin near a double-stranded DNA break. Genes Dev. 8:554–562.
   PubMed Web of Science ®Google Scholar
• Rudin, N., and J. E. Haber. 1988. Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences. Mol. Cell. Biol. 8:3918–3928.
   PubMedGoogle Scholar
• Ryoji, M., and A. Worcel. 1984. Chromatin assembly in Xenopus oocytes: in vivo studies. Cell 37:21–32.
   PubMed Web of Science ®Google Scholar
• Sandell, L. L., and V. A. Zakian. 1993. Loss of a yeast telomere: arrest, recovery, and chromosome loss. Cell 75:729–739.
   PubMed Web of Science ®Google Scholar
• Schaack, J., Y.-W. Ho, P. Freimuth, and T. Shenk. 1990. Adenovirus terminal protein mediates both nuclear matrix association and efficient transcription of adenovirus DNA. Genes Dev. 4:1197–1208.
   PubMedGoogle Scholar
• Schmitt, M. E., T. A. Brown, and B. L. Trumpower. 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18:3091.
   PubMed Web of Science ®Google Scholar
• Schultz, M. C., S. J. Brill, Q. D. Ju, R. Sternglanz, and R. H. Reeder. 1992. Topoisomerases and yeast rRNA transcription: negative supercoiling stimulates initiation and topoisomerase activity is required for elongation. Genes Dev. 6:1332–1341.
   PubMed Web of Science ®Google Scholar
• Sherman, F. 1991. Getting started with yeast. Methods Enzymol. 194:3–21.
   PubMed Web of Science ®Google Scholar
• Sikorski, R. S., and J. D. Boeke. 1991. In vitro mutagenesis and plasmid shuffling: from cloned gene to mutant yeast. Methods Enzymol. 194:302–318.
   PubMed Web of Science ®Google Scholar
• Sinden, R. R., J. O. Carlson, and D. E. Pettijohn. 1980. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell 21:773–783.
   PubMed Web of Science ®Google Scholar
• Studitsky, V. M., D. J. Clark, and G. Felsenfeld. 1995. Overcoming a nu-cleosomal barrier to transcription. Cell 83:19–27.
   PubMed Web of Science ®Google Scholar
• Thiele, D. J. 1988. ACE1 regulates expression of the Saccharomyces cerevisiae metallothionein gene. Mol. Cell. Biol. 8:2745–2752.
   PubMed Web of Science ®Google Scholar
• Weintraub, H., P. F. Chenk, and K. Conrad. 1986. Expression of transfected DNA depends on DNA topology. Cell 46:115–122.
   PubMed Web of Science ®Google Scholar