RNA Polymerase II Elongation Complexes Paused after the Synthesis of 15- or 35-Base Transcripts Have Different Structures

REFERENCES

• Bentley, D., and M. Groudine. 1986. A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells. Nature (London) 321:702-706.
   PubMed Web of Science ®Google Scholar
• Bunick, D., R. Zandomeni, S. Ackerman, and R. Weinmann. 1982. Mechanism of RNA polymerase II-specific initiation of transcription in vitro: ATP requirement and uncapped runoff transcripts. Cell 29:877-886.
   PubMed Web of Science ®Google Scholar
• Buratowski, S., S. Hahn, L. Guarente, and P. A. Sharp. 1989. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56:549-561.
   PubMed Web of Science ®Google Scholar
• Cai, H., and D. S. Luse. 1987. Variations in template protection by the RNA polymerase II transcription complex during the initiation process. Mol. Cell. Biol. 7:3371-3379.
   PubMedGoogle Scholar
• Cai, H., and D. S. Luse. 1987. Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation and elongation complexes. J. Biol. Chem. 262:298-304.
   PubMed Web of Science ®Google Scholar
• Carthew, R. W., L. A. Chodosh, and P. A. Sharp. 1985. An RNA polymerase II transcription factor binds to an upstream element in the adenovirus major late promoter. Cell 43:439-448.
   PubMed Web of Science ®Google Scholar
• Coppola, J. A., A. S. Field, and D. S. Luse. 1983. Promoterproximal pausing by RNA polymerase II in vitro: transcripts shorter than 20 nucleotides are not capped. Proc. Natl. Acad. Sci. USA 80:1251-1255.
   PubMed Web of Science ®Google Scholar
• Coppola, J. A., and D. S. Luse. 1984. Purification and characterization of ternary complexes containing accurately initiated RNA polymerase II and less than 20 nucleotides of RNA. J. Mol. Biol. 178:415-437.
   PubMedGoogle Scholar
• Crothers, D. M., T. E. Haran, and J. G. Nadeau. 1990. Intrinsically bent DNA. J. Biol. Chem. 265:7093-7096.
   PubMed Web of Science ®Google Scholar
• Dignam, J. D., R. M. Lebovitz, and R. G. Roeder. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11:1475-1489.
   PubMed Web of Science ®Google Scholar
• Gariglio, P., J. Buss, and M. H. Green. 1974. Sarkosyl activation of RNA polymerase activity in mitotic mouse cells. FEBS Lett. 44:330-333.
   PubMedGoogle Scholar
• Izban, M., and D. Luse. Unpublished data.
   Google Scholar
• Krummel, B., and M. J. Chamberlin. 1989. RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry 28:7829-7842.
   PubMedGoogle Scholar
• Krummel, B. M. 1990. Ph.D. thesis. University of California, Berkeley.
   Google Scholar
• Kuwabara, M. D., and D. S. Sigman. 1987. Footprinting DNAprotein complexes in situ following gel retardation assays using 1,10-phenanthroline-copper ion: Escherichia coli RNA polymerase-lac promoter complexes. Biochemistry 26:7234-7238.
   PubMedGoogle Scholar
• Laybourn, P. J., and M. E. Dahmus. 1990. Phosphorylation of RNA polymerase IIA occurs subsequent to interaction with the promoter and before the initiation of transcription. J. Biol. Chem. 265:13165-13173.
   PubMedGoogle Scholar
• Lewis, M. K., and R. R. Burgess. 1980. Transcription of simian virus 40 DNA by wheat germ RNA polymerase II. Priming of RNA synthesis by the 3′-hydroxyl of DNA at single strand nicks. J. Biol. Chem. 255:4928-4936.
   PubMedGoogle Scholar
• Luse, D. S., and G. A. Jacob. 1987. Abortive initiation by RNA polymerase II in vitro at the adenovirus 2 major late promoter. J. Biol. Chem. 262:14990-14997.
   PubMedGoogle Scholar
• Luse, D. S., T. Kochel, E. D. Kuempel, J. A. Coppola, and H. Cai. 1987. Transcription initiation by RNA polymerase II in vitro. At least two nucleotides must be added to form a stable ternary complex. J. Biol. Chem. 262:289-297.
   PubMed Web of Science ®Google Scholar
• Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual, p. 454. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Nakajima, N., M. Horikoshi, and R. G. Roeder. 1988. Factors involved in specific transcription by mammalian RNA polymerase II: purification, genetic specificity, and TATA box-promoter interactions of TFIID. Mol. Cell. Biol. 8:4028-4040.
   PubMed Web of Science ®Google Scholar
• Pope, L., and D. S. Sigman. 1984. Secondary structure specificity of the nuclease activity of the 1,10-phenanthroline-copper complex. Proc. Natl. Acad. Sci. USA 81:3-7.
   PubMed Web of Science ®Google Scholar
• Price, D. H., A. E. Sluder, and A. L. Greenleaf. 1989. Dynamic interaction between a Drosophila transcription factor and RNA polymerase II. Mol. Cell. Biol. 9:1465-1475.
   PubMedGoogle Scholar
• Reinberg, D., M. Horikoshi, and R. G. Roeder. 1987. Factors involved in specific transcription in mammalian RNA polymerase II. Functional analysis of initiation factors IIA and IID and identification of a new factor operating at sequences downstream of the initiation site. J. Biol. Chem. 262:3322-3330.
   PubMed Web of Science ®Google Scholar
• Reines, D., M. J. Chamberlin, and C. M. Kane. 1989. Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a block to transcription in a human gene in vitro. J. Biol. Chem. 264:10799-10809.
   PubMed Web of Science ®Google Scholar
• Roeder, R. G. 1976. Eukaryotic nuclear RNA polymerases, p. 285-329. In R. Losick and M. Chamberlin (ed.), RNA polymerase. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Rougvie, A. E., and J. T. Lis. 1988. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54:795-804.
   PubMed Web of Science ®Google Scholar
• Sawadogo, M., and R. G. Roeder. 1984. Energy requirement for specific transcription initiation by the human RNA polymerase II system. J. Biol. Chem. 259:5321-5326.
   PubMed Web of Science ®Google Scholar
• Shi, Y. B., H. Gamper, B. Van Houten, and J. E. Hearst. 1988. Interaction of Escherichia coli RNA polymerase with DNA in an elongation complex arrested at a specific psoralen crosslink site. J. Mol. Biol. 199:277-293.
   PubMedGoogle Scholar
• Sigman, D. S. 1986. Nuclease activity of 1,10-phenanthroline-copper ion. Acc. Chem. Res. 19:180-186.
   Web of Science ®Google Scholar
• Sigman, D. S. 1990. Chemical nucleases. Biochemistry 29:9097-9105.
   PubMed Web of Science ®Google Scholar
• Smale, S. T., and D. Baltimore. 1989. The “initiator” as a transcription control element. Cell 57:103-113.
   PubMed Web of Science ®Google Scholar
• Straney, D. C., and D. M. Crothers. 1985. Intermediates in transcription initiation from the E. coli lac UV5 promoter. Cell 43:449-459.
   PubMed Web of Science ®Google Scholar
• Thederahn, T., A. Spassky, M. D. Kuwahara, and D. S. Sigman. 1990. Chemical nuclease activity of 5-phenyl-l,10-phenanthroline copper ion detects intermediates in transcription initiation by E. coli RNA polymerase. Biochem. Biophys. Res. Commun. 168:756-762.
   PubMed Web of Science ®Google Scholar
• Van Dyke, M. W., R. G. Roeder, and M. Sawadogo. 1988. Physical analysis of transcription preinitiation complex assembly on a class II gene promoter. Science 241:1335-1338.
   PubMed Web of Science ®Google Scholar
• Zock, C., and W. Doerfler. 1990. A mitigator sequence in the downstream region of the major late promoter of adenovirus type 12 DNA. EMBO J. 9:1615-1623.
   PubMedGoogle Scholar