Additional intragenic promoter elements of the Xenopus 5S RNA genes upstream from the TFIIIA-binding site.

Mol Cell Biol. 1990 October; 10(10): 5166–5176.

PMCID: PMC361192

H J Keller, Q M You, P J Romaniuk, and J M Gottesfeld

Division of Developmental Biology, Medical Biology Institute, La Jolla, California 92037.

This article has been cited by other articles in PMC.

Abstract

The major promoter element of the Xenopus laevis 5S RNA gene is located within the transcribed region of the gene and forms the binding site for the transcription initiation factor TFIIIA. We report an analysis of deletion and substitution mutations within the coding region of the major oocyte-type 5S gene of X. laevis. Our results differ from those of previous mutagenesis studies conducted on the somatic-type genes of Xenopus borealis and X. laevis. Transcription assays in whole oocyte S-150 extracts, with both oocyte- and somatic-type mutants, revealed additional promoter elements between the start site for transcription and the binding site for TFIIIA. These sequences regulate the efficiency of binding TFIIIC, a transcription factor required by the genes transcribed by RNA polymerase III containing intragenic promoters. Under TFIIIC-limiting conditions, the somatic-type gene had a 10-fold-higher affinity for TFIIIC than did the major oocyte-type 5S gene. One mutation in the oocyte-type gene (nucleotides +33 to +39) reduced TFIIIC affinity and transcriptional activity four- to fivefold. Differences in TFIIIC affinity between oocyte- and somatic-type genes may contribute to the differential transcription of these genes observed during Xenopus embryogenesis.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (2.6M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

Andrews, DL; Millstein, L; Hamkalo, BA; Gottesfeld, JM. Competition between Xenopus satellite I sequences and Pol III genes for stable transcription complex formation. Nucleic Acids Res. 1984 Oct 25;12(20):7753–7769. [PubMed]
Bieker, JJ; Martin, PL; Roeder, RG. Formation of a rate-limiting intermediate in 5S RNA gene transcription. Cell. 1985 Jan;40(1):119–127. [PubMed]
Blanco, J; Millstein, L; Razik, MA; Dilworth, S; Cote, C; Gottesfeld, J. Two TFIIIA activities regulate expression of the Xenopus 5S RNA gene families. Genes Dev. 1989 Oct;3(10):1602–1612. [PubMed]
Bogenhagen, DF. The intragenic control region of the Xenopus 5 S RNA gene contains two factor A binding domains that must be aligned properly for efficient transcription initiation. J Biol Chem. 1985 May 25;260(10):6466–6471. [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]
Bogenhagen, DF; Wormington, WM; Brown, DD. Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state. Cell. 1982 Feb;28(2):413–421. [PubMed]
Braun, BR; Riggs, DL; Kassavetis, GA; Geiduschek, EP. Multiple states of protein-DNA interaction in the assembly of transcription complexes on Saccharomyces cerevisiae 5S ribosomal RNA genes. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2530–2534. [PubMed]
Clarkson, SG; Kurer, V; Smith, HO. Sequence organization of a cloned tDNA met fragment from Xenopus laevis. Cell. 1978 Jul;14(3):713–724. [PubMed]
Engelke, DR; Ng, SY; Shastry, BS; Roeder, RG. Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell. 1980 Mar;19(3):717–728. [PubMed]
Fradkin, LG; Yoshinaga, SK; Berk, AJ; Dasgupta, A. Human transcription factor TFIIIC2 specifically interacts with a unique sequence in the Xenopus laevis 5S rRNA gene. Mol Cell Biol. 1989 Nov;9(11):4941–4950. [PubMed]
Geiduschek, EP; Tocchini-Valentini, GP. Transcription by RNA polymerase III. Annu Rev Biochem. 1988;57:873–914. [PubMed]
Ginsberg, AM; King, BO; Roeder, RG. Xenopus 5S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development. Cell. 1984 Dec;39(3 Pt 2):479–489. [PubMed]
Glikin, GC; Ruberti, I; Worcel, A. Chromatin assembly in Xenopus oocytes: in vitro studies. Cell. 1984 May;37(1):33–41. [PubMed]
Hanas, JS; Bogenhagen, DF; Wu, CW. Binding of Xenopus transcription factor A to 5S RNA and to single stranded DNA. Nucleic Acids Res. 1984 Mar 26;12(6):2745–2758. [PubMed]
Lassar, AB; Martin, PL; Roeder, RG. Transcription of class III genes: formation of preinitiation complexes. Science. 1983 Nov 18;222(4625):740–748. [PubMed]
Majowski, K; Mentzel, H; Pieler, T. A split binding site for TFIIIC on the Xenopus 5S gene. EMBO J. 1987 Oct;6(10):3057–3063. [PubMed]
McConkey, GA; Bogenhagen, DF. TFIIIA binds with equal affinity to somatic and major oocyte 5S RNA genes. Genes Dev. 1988 Feb;2(2):205–214. [PubMed]
Miller, J; McLachlan, AD; Klug, A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. [PubMed]
Millstein, L; Eversole-Cire, P; Blanco, J; Gottesfeld, JM. Differential transcription of Xenopus oocyte and somatic-type 5 S genes in a Xenopus oocyte extract. J Biol Chem. 1987 Dec 15;262(35):17100–17110. [PubMed]
Peck, LJ; Millstein, L; Eversole-Cire, P; Gottesfeld, JM; Varshavsky, A. Transcriptionally inactive oocyte-type 5S RNA genes of Xenopus laevis are complexed with TFIIIA in vitro. Mol Cell Biol. 1987 Oct;7(10):3503–3510. [PubMed]
Pelham, HR; Brown, DD. A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4170–4174. [PubMed]
Peterson, RC; Doering, JL; Brown, DD. Characterization of two xenopus somatic 5S DNAs and one minor oocyte-specific 5S DNA. Cell. 1980 May;20(1):131–141. [PubMed]
Pieler, T; Appel, B; Oei, SL; Mentzel, H; Erdmann, VA. Point mutational analysis of the Xenopus laevis 5S gene promoter. EMBO J. 1985 Jul;4(7):1847–1853. [PubMed]
Pieler, T; Hamm, J; Roeder, RG. The 5S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing. Cell. 1987 Jan 16;48(1):91–100. [PubMed]
Pieler, T; Oei, SL; Hamm, J; Engelke, U; Erdmann, VA. Functional domains of the Xenopus laevis 5S gene promoter. EMBO J. 1985 Dec 30;4(13B):3751–3756. [PubMed]
Reynolds, WF; Azer, K. Sequence differences upstream of the promoters are involved in the differential expression of the Xenopus somatic and oocyte 5S RNA genes. Nucleic Acids Res. 1988 Apr 25;16(8):3391–3403. [PubMed]
Reynolds, WF; Gottesfeld, JM. Torsional stress induces an S1 nuclease-hypersensitive site within the promoter of the Xenopus laevis oocyte-type 5S RNA gene. Proc Natl Acad Sci U S A. 1985 Jun;82(12):4018–4022. [PubMed]
Romaniuk, PJ. The role of highly conserved single-stranded nucleotides of Xenopus 5S RNA in the binding of transcription factor IIIA. Biochemistry. 1989 Feb 7;28(3):1388–1395. [PubMed]
Romaniuk, PJ; de Stevenson, IL; Wong, HH. Defining the binding site of Xenopus transcription factor IIIA on 5S RNA using truncated and chimeric 5S RNA molecules. Nucleic Acids Res. 1987 Mar 25;15(6):2737–2755. [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]
Sakonju, S; Brown, DD; Engelke, D; Ng, SY; Shastry, BS; Roeder, RG. The binding of a transcription factor to deletion mutants of a 5S ribosomal RNA gene. Cell. 1981 Mar;23(3):665–669. [PubMed]
Sands, MS; Bogenhagen, DF. TFIIIA binds to different domains of 5S RNA and the Xenopus borealis 5S RNA gene. Mol Cell Biol. 1987 Nov;7(11):3985–3993. [PubMed]
Schneider, HR; Waldschmidt, R; Jahn, D; Seifart, KH. Purification of human transcription factor IIIC and its binding to the gene for ribosomal 5S RNA. Nucleic Acids Res. 1989 Jul 11;17(13):5003–5016. [PubMed]
Segall, J. Assembly of a yeast 5 S RNA gene transcription complex. J Biol Chem. 1986 Sep 5;261(25):11578–11584. [PubMed]
Segall, J; Matsui, T; Roeder, RG. Multiple factors are required for the accurate transcription of purified genes by RNA polymerase III. J Biol Chem. 1980 Dec 25;255(24):11986–11991. [PubMed]
Setzer, DR; Brown, DD. Formation and stability of the 5 S RNA transcription complex. J Biol Chem. 1985 Feb 25;260(4):2483–2492. [PubMed]
Smith, DR; Jackson, IJ; Brown, DD. Domains of the positive transcription factor specific for the Xenopus 5S RNA gene. Cell. 1984 Jun;37(2):645–652. [PubMed]
Vrana, KE; Churchill, ME; Tullius, TD; Brown, DD. Mapping functional regions of transcription factor TFIIIA. Mol Cell Biol. 1988 Apr;8(4):1684–1696. [PubMed]
Wakefield, L; Gurdon, JB. Cytoplasmic regulation of 5S RNA genes in nuclear-transplant embryos. EMBO J. 1983;2(9):1613–1619. [PubMed]
Wolffe, AP. Transcription fraction TFIIIC can regulate differential Xenopus 5S RNA gene transcription in vitro. EMBO J. 1988 Apr;7(4):1071–1079. [PubMed]
Wolffe, AP; Brown, DD. Differential 5S RNA gene expression in vitro. Cell. 1987 Dec 4;51(5):733–740. [PubMed]
Wolffe, AP; Brown, DD. DNA replication in vitro erases a Xenopus 5S RNA gene transcription complex. Cell. 1986 Oct 24;47(2):217–227. [PubMed]
Wolffe, AP; Morse, RH. The transcription complex of the Xenopus somatic 5 S RNA gene. A functional analysis of protein-DNA interactions outside of the internal control region. J Biol Chem. 1990 Mar 15;265(8):4592–4599. [PubMed]
Wormington, WM; Bogenhagen, DF; Jordan, E; Brown, DD. A quantitative assay for Xenopus 5S RNA gene transcription in vitro. Cell. 1981 Jun;24(3):809–817. [PubMed]
Xing, YY; Worcel, A. The C-terminal domain of transcription factor IIIA interacts differently with different 5S RNA genes. Mol Cell Biol. 1989 Feb;9(2):499–514. [PubMed]
Xing, YY; Worcel, A. A 3' exonuclease activity degrades the pseudogene 5S RNA transcript and processes the major oocyte 5S RNA transcript in Xenopus oocytes. Genes Dev. 1989 Jul;3(7):1008–1018. [PubMed]