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EMBO J. Feb 1988; 7(2): 503–512.
PMCID: PMC454347

Upstream regulatory elements are necessary and sufficient for transcription of a U6 RNA gene by RNA polymerase III.

Abstract

Whereas the genes coding for trimethyl guanosine-capped snRNAs are transcribed by RNA polymerase II, the U6 RNA genes are transcribed by RNA polymerase III. In this study, we have analyzed the cis-regulatory elements involved in the transcription of a mouse U6 snRNA gene in vitro and in frog oocytes. Transcriptional analysis of mutant U6 gene constructs showed that, unlike most known cases of polymerase III transcription, intragenic sequences except the initiation nucleotide are dispensable for efficient and accurate transcription of U6 gene in vitro. Transcription of 5' deletion mutants in vitro and in frog oocytes showed that the upstream region, within 79 bp from the initiation nucleotide, contains elements necessary for U6 gene transcription. Transcription studies were carried out in frog oocytes with U6 genes containing 5' distal sequence; these studies revealed that the distal element acts as an orientation-dependent enhancer when present upstream to the gene, while it is orientation-independent but distance-dependent enhancer when placed down-stream to the U6 gene. Analysis of 3' deletion mutants showed that the transcription termination of U6 RNA is dependent on a T cluster present on the 3' end of the gene, thus providing further support to other lines of evidence that U6 genes are transcribed by RNA polymerase III. These observations suggest the involvement of a composite of components of RNA polymerase II and III transcription machineries in the transcription of U6 genes by RNA polymerase III.

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Selected References

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  • Ares M, Jr, Mangin M, Weiner AM. Orientation-dependent transcriptional activator upstream of a human U2 snRNA gene. Mol Cell Biol. 1985 Jul;5(7):1560–1570. [PMC free article] [PubMed]
  • Bark C, Weller P, Zabielski J, Janson L, Pettersson U. A distant enhancer element is required for polymerase III transcription of a U6 RNA gene. Nature. 1987 Jul 23;328(6128):356–359. [PubMed]
  • Bogenhagen DF, Brown DD. Nucleotide sequences in Xenopus 5S DNA required for transcription termination. Cell. 1981 Apr;24(1):261–270. [PubMed]
  • Bogenhagen DF, Sakonju S, Brown DD. A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3' border of the region. Cell. 1980 Jan;19(1):27–35. [PubMed]
  • Bohmann D, Keller W, Dale T, Schöler HR, Tebb G, Mattaj IW. A transcription factor which binds to the enhancers of SV40, immunoglobulin heavy chain and U2 snRNA genes. Nature. 1987 Jan 15;325(6101):268–272. [PubMed]
  • Brownlee GG, Sanger F, Barrell BG. The sequence of 5 s ribosomal ribonucleic acid. J Mol Biol. 1968 Jun 28;34(3):379–412. [PubMed]
  • Carbon P, Murgo S, Ebel JP, Krol A, Tebb G, Mattaj LW. A common octamer motif binding protein is involved in the transcription of U6 snRNA by RNA polymerase III and U2 snRNA by RNA polymerase II. Cell. 1987 Oct 9;51(1):71–79. [PubMed]
  • Chambon P. Eukaryotic nuclear RNA polymerases. Annu Rev Biochem. 1975;44:613–638. [PubMed]
  • Chen EY, Seeburg PH. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. [PubMed]
  • Ciliberto G, Castagnoli L, Melton DA, Cortese R. Promoter of a eukaryotic tRNAPro gene is composed of three noncontiguous regions. Proc Natl Acad Sci U S A. 1982 Feb;79(4):1195–1199. [PMC free article] [PubMed]
  • Ciliberto G, Castagnoli L, Cortese R. Transcription by RNA polymerase III. Curr Top Dev Biol. 1983;18:59–88. [PubMed]
  • Das G, Henning D, Reddy R. Structure, organization, and transcription of Drosophila U6 small nuclear RNA genes. J Biol Chem. 1987 Jan 25;262(3):1187–1193. [PubMed]
  • Epstein P, Reddy R, Henning D, Busch H. The nucleotide sequence of nuclear U6 (4.7 S) RNA. J Biol Chem. 1980 Sep 25;255(18):8901–8906. [PubMed]
  • Falkner FG, Zachau HG. Correct transcription of an immunoglobulin kappa gene requires an upstream fragment containing conserved sequence elements. Nature. 1984 Jul 5;310(5972):71–74. [PubMed]
  • Fowlkes DM, Shenk T. Transcriptional control regions of the adenovirus VAI RNA gene. Cell. 1980 Nov;22(2 Pt 2):405–413. [PubMed]
  • Guo LH, Wu R. New rapid methods for DNA sequencing based in exonuclease III digestion followed by repair synthesis. Nucleic Acids Res. 1982 Mar 25;10(6):2065–2084. [PMC free article] [PubMed]
  • Hernandez N. Formation of the 3' end of U1 snRNA is directed by a conserved sequence located downstream of the coding region. EMBO J. 1985 Jul;4(7):1827–1837. [PMC free article] [PubMed]
  • Hernandez N, Weiner AM. Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements. Cell. 1986 Oct 24;47(2):249–258. [PubMed]
  • Kenney S, Natarajan V, Strike D, Khoury G, Salzman NP. JC virus enhancer-promoter active in human brain cells. Science. 1984 Dec 14;226(4680):1337–1339. [PubMed]
  • Korn LJ, Brown DD. Nucleotide sequence of Xenopus borealis oocyte 5S DNA: comparison of sequences that flank several related eucaryotic genes. Cell. 1978 Dec;15(4):1145–1156. [PubMed]
  • Krol A, Carbon P, Ebel JP, Appel B. Xenopus tropicalis U6 snRNA genes transcribed by Pol III contain the upstream promoter elements used by Pol II dependent U snRNA genes. Nucleic Acids Res. 1987 Mar 25;15(6):2463–2478. [PMC free article] [PubMed]
  • Kunkel GR, Maser RL, Calvet JP, Pederson T. U6 small nuclear RNA is transcribed by RNA polymerase III. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8575–8579. [PMC free article] [PubMed]
  • Laimins LA, Gruss P, Pozzatti R, Khoury G. Characterization of enhancer elements in the long terminal repeat of Moloney murine sarcoma virus. J Virol. 1984 Jan;49(1):183–189. [PMC free article] [PubMed]
  • Mangin M, Ares M, Jr, Weiner AM. Human U2 small nuclear RNA genes contain an upstream enhancer. EMBO J. 1986 May;5(5):987–995. [PMC free article] [PubMed]
  • Mattaj IW, Lienhard S, Jiricny J, De Robertis EM. An enhancer-like sequence within the Xenopus U2 gene promoter facilitates the formation of stable transcription complexes. Nature. 1985 Jul 11;316(6024):163–167. [PubMed]
  • Maxam AM, Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. [PubMed]
  • McKnight S, Tjian R. Transcriptional selectivity of viral genes in mammalian cells. Cell. 1986 Sep 12;46(6):795–805. [PubMed]
  • Miller JR, Melton DA. A transcriptionally active pseudogene in xenopus laevis oocyte 5S DNA. Cell. 1981 Jun;24(3):829–835. [PubMed]
  • Moreau P, Hen R, Wasylyk B, Everett R, Gaub MP, Chambon P. The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. Nucleic Acids Res. 1981 Nov 25;9(22):6047–6068. [PMC free article] [PubMed]
  • Mosthaf L, Pawlita M, Gruss P. A viral enhancer element specifically active in human haematopoietic cells. Nature. 1985 Jun 13;315(6020):597–600. [PubMed]
  • Murphy S, Di Liegro C, Melli M. The in vitro transcription of the 7SK RNA gene by RNA polymerase III is dependent only on the presence of an upstream promoter. Cell. 1987 Oct 9;51(1):81–87. [PubMed]
  • Myers RM, Tilly K, Maniatis T. Fine structure genetic analysis of a beta-globin promoter. Science. 1986 May 2;232(4750):613–618. [PubMed]
  • de Vegvar HE, Lund E, Dahlberg JE. 3' end formation of U1 snRNA precursors is coupled to transcription from snRNA promoters. Cell. 1986 Oct 24;47(2):259–266. [PubMed]
  • Ohshima Y, Okada N, Tani T, Itoh Y, Itoh M. Nucleotide sequences of mouse genomic loci including a gene or pseudogene for U6 (4.8S) nuclear RNA. Nucleic Acids Res. 1981 Oct 10;9(19):5145–5158. [PMC free article] [PubMed]
  • Parslow TG, Blair DL, Murphy WJ, Granner DK. Structure of the 5' ends of immunoglobulin genes: a novel conserved sequence. Proc Natl Acad Sci U S A. 1984 May;81(9):2650–2654. [PMC free article] [PubMed]
  • Ptashne M. Gene regulation by proteins acting nearby and at a distance. Nature. 1986 Aug 21;322(6081):697–701. [PubMed]
  • Reddy R, Busch H. Small nuclear RNAs and RNA processing. Prog Nucleic Acid Res Mol Biol. 1983;30:127–162. [PubMed]
  • Reddy R, Henning D, Das G, Harless M, Wright D. The capped U6 small nuclear RNA is transcribed by RNA polymerase III. J Biol Chem. 1987 Jan 5;262(1):75–81. [PubMed]
  • Sakonju S, Bogenhagen DF, Brown DD. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region. Cell. 1980 Jan;19(1):13–25. [PubMed]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [PMC free article] [PubMed]
  • Selker EU, Morzycka-Wroblewska E, Stevens JN, Metzenberg RL. An upstream signal is required for in vitro transcription of Neurospora 5S RNA genes. Mol Gen Genet. 1986 Oct;205(1):189–192. [PubMed]
  • Sergeant A, Bohmann D, Zentgraf H, Weiher H, Keller W. A transcription enhancer acts in vitro over distances of hundreds of base-pairs on both circular and linear templates but not on chromatin-reconstituted DNA. J Mol Biol. 1984 Dec 15;180(3):577–600. [PubMed]
  • Sharp SJ, Schaack J, Cooley L, Burke DJ, Söll D. Structure and transcription of eukaryotic tRNA genes. CRC Crit Rev Biochem. 1985;19(2):107–144. [PubMed]
  • Singh H, Sen R, Baltimore D, Sharp PA. A nuclear factor that binds to a conserved sequence motif in transcriptional control elements of immunoglobulin genes. Nature. 1986 Jan 9;319(6049):154–158. [PubMed]
  • Sive HL, Roeder RG. Interaction of a common factor with conserved promoter and enhancer sequences in histone H2B, immunoglobulin, and U2 small nuclear RNA (snRNA) genes. Proc Natl Acad Sci U S A. 1986 Sep;83(17):6382–6386. [PMC free article] [PubMed]
  • Takahashi K, Vigneron M, Matthes H, Wildeman A, Zenke M, Chambon P. Requirement of stereospecific alignments for initiation from the simian virus 40 early promoter. Nature. 1986 Jan 9;319(6049):121–126. [PubMed]
  • Thimmappaya B, Jones N, Shenk T. A mutation which alters initiation of transcription by RNA polymerase III on the Ad5 chromosome. Cell. 1979 Dec;18(4):947–954. [PubMed]
  • Ullu E, Weiner AM. Upstream sequences modulate the internal promoter of the human 7SL RNA gene. Nature. 318(6044):371–374. [PubMed]
  • Weil PA, Segall J, Harris B, Ng SY, Roeder RG. Faithful transcription of eukaryotic genes by RNA polymerase III in systems reconstituted with purified DNA templates. J Biol Chem. 1979 Jul 10;254(13):6163–6173. [PubMed]
  • Wildeman AG, Sassone-Corsi P, Grundström T, Zenke M, Chambon P. Stimulation of in vitro transcription from the SV40 early promoter by the enhancer involves a specific trans-acting factor. EMBO J. 1984 Dec 20;3(13):3129–3133. [PMC free article] [PubMed]
  • Yuo CY, Ares M, Jr, Weiner AM. Sequences required for 3' end formation of human U2 small nuclear RNA. Cell. 1985 Aug;42(1):193–202. [PubMed]

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