Home LiteratureArticle Details
PMID: 2677668 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5'-flanking region.

Molecular and cellular biology ·Vol. 9 ·No. 8 ·1989-08-00 ·Pages 3244-52

Huibregtse JM, Engelke DR

Abstract

We have shown by genomic footprinting that the 5'-flanking region of the Saccharomyces cerevisiae tRNASUP53 gene is protected from DNase I digestion. The protected region has a 5' boundary at -40 (relative to the transcription initiation site) and extends into the coding region of the gene, with a 3' boundary at approximately +15. Although the DNase I protection over this region was much greater than at the A- and B-box internal promoters, point mutations within the A or B box that reduced transcription in vitro eliminated the upstream DNase I protection. This implies that formation of a stable complex over the 5'-flanking region is dependent on interaction of the gene with transcription factor IIIC but that stability of the complex may not require continued interaction with this factor. The DNase I protection under varied growth conditions further suggested that the upstream complex is composed of two or more components. The region over the transcription initiation site (approximately +15 to -10) was less protected in stationary-phase cultures, whereas the more upstream region (approximately -10 to -40) was protected in both exponential- and stationary-phase cultures.

MeSH Terms
Base Sequence DNA Mutational Analysis Deoxyribonuclease I Genetic Vectors Molecular Sequence Data Nucleoproteins/metabolism Promoter Regions, Genetic RNA, Fungal/genetics RNA, Transfer/genetics Saccharomyces cerevisiae/genetics Transcription Factors/analysis
Chemicals
Nucleoproteins RNA, Fungal Transcription Factors RNA, Transfer Deoxyribonuclease I
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Huibregtse J M
Department of Biological Chemistry, University of Michigan, Ann Arbor 48109-0606.
Engelke D R
References (57)
57 references, click to expand
  1. Differential binding of a S. cerevisiae RNA polymerase III transcription factor to two promoter segments of a tRNA gene.
    EMBO J. 1984 Apr;3(4):847-53 PMID: 6233142
  2. 5'-flanking sequences that inhibit in vitro transcription of a xenopus laevis tRNA gene.
    Cell. 1983 Oct;34(3):881-90 PMID: 6414719
  3. Copper-induced binding of cellular factors to yeast metallothionein upstream activation sequences.
    Proc Natl Acad Sci U S A. 1989 Jan;86(1):65-9 PMID: 2643107
  4. The 5'-flanking sequences of Drosophila melanogaster tRNA5Asn genes differentially arrest RNA polymerase III.
    J Biol Chem. 1986 Nov 5;261(31):14600-6 PMID: 3095322
  5. Dimeric tRNA precursors in yeast.
    Nature. 1980 Oct 23;287(5784):750-2 PMID: 6253814
  6. Direct identification of small sequence changes in chromosomal DNA.
    Gene. 1986;44(1):151-8 PMID: 2429900
  7. In vivo DNA-binding properties of a yeast transcription activator protein.
    Mol Cell Biol. 1987 Sep;7(9):3260-7 PMID: 3313011
  8. Nucleotide sequence of yeast LEU2 shows 5'-noncoding region has sequences cognate to leucine.
    Cell. 1982 Dec;31(2 Pt 1):319-25 PMID: 6297759
  9. Nucleotide sequence of a yeast tRNAArg3A gene and its transcription in a homologous in vitro system.
    FEBS Lett. 1984 Feb 13;167(1):165-9 PMID: 6321234
  10. Selective proteolysis defines two DNA binding domains in yeast transcription factor tau.
    Nature. 1986 Sep 11-17;323(6084):176-8 PMID: 3528868
  11. Formation of a rate-limiting intermediate in 5S RNA gene transcription.
    Cell. 1985 Jan;40(1):119-27 PMID: 3967290
  12. tRNA gene transcription in yeast: effects of specified base substitutions in the intragenic promoter.
    Cell. 1983 Nov;35(1):117-25 PMID: 6226365
  13. LEU3 of Saccharomyces cerevisiae encodes a factor for control of RNA levels of a group of leucine-specific genes.
    Mol Cell Biol. 1987 Aug;7(8):2708-17 PMID: 2823102
  14. A split binding site for TFIIIC on the Xenopus 5S gene.
    EMBO J. 1987 Oct;6(10):3057-63 PMID: 3691480
  15. A short 5' flanking region containing conserved sequences is required for silkworm alanine tRNA gene activity.
    Proc Natl Acad Sci U S A. 1983 Jun;80(11):3416-20 PMID: 16593326
  16. Assembly of a yeast 5 S RNA gene transcription complex.
    J Biol Chem. 1986 Sep 5;261(25):11578-84 PMID: 3528144
  17. 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 PMID: 7357599
  18. Regulation of eukaryotic ribosomal RNA transcription by RNA polymerase modification.
    Cell. 1986 Nov 7;47(3):445-50 PMID: 3768960
  19. Transcriptional role of yeast deoxyribonucleic acid dependent ribonucleic acid polymerase III.
    Biochemistry. 1978 Feb 21;17(4):750-8 PMID: 341977
  20. Comparison of tRNA gene transcription complexes formed in vitro and in nuclei.
    Mol Cell Biol. 1987 Sep;7(9):3212-20 PMID: 3313009
  21. 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):71-9 PMID: 3652209
  22. Multiple factors are required for the accurate transcription of purified genes by RNA polymerase III.
    J Biol Chem. 1980 Dec 25;255(24):11986-91 PMID: 7440579
  23. Formation of an active transcription complex in the Drosophila melanogaster 5S RNA gene is dependent on an upstream region.
    Mol Cell Biol. 1987 Jun;7(6):2046-51 PMID: 3110601
  24. Transcription by RNA polymerase III.
    Annu Rev Biochem. 1988;57:873-914 PMID: 3052292
  25. A large region controls tRNA gene transcription.
    J Mol Biol. 1985 May 25;183(2):153-63 PMID: 3847510
  26. Transcription of the Drosophila melanogaster 5S RNA gene requires an upstream promoter and four intragenic sequence elements.
    Mol Cell Biol. 1988 Mar;8(3):1266-74 PMID: 3130565
  27. Effects of altered 5'-flanking sequences on the in vivo expression of a Saccharomyces cerevisiae tRNATyr gene.
    Mol Cell Biol. 1984 Apr;4(4):657-65 PMID: 6371493
  28. The yeast tRNATyr gene intron is essential for correct modification of its tRNA product.
    Nature. 1983 Apr 21;302(5910):681-7 PMID: 6339954
  29. In vitro transcription of a silkworm 5S RNA gene requires an upstream signal.
    Proc Natl Acad Sci U S A. 1984 Sep;81(17):5519-22 PMID: 6089209
  30. HeLa cell RNA polymerase III transcription factors. Functional characterization of a fraction identified by its activity in a second template rescue assay.
    J Biol Chem. 1984 Feb 10;259(3):1934-43 PMID: 6229542
  31. Upstream sequences confer distinctive transcriptional properties on genes encoding silkgland-specific tRNAAla.
    Proc Natl Acad Sci U S A. 1986 Jan;83(2):374-8 PMID: 3455775
  32. Factors involved in specific transcription by mammalian RNA polymerase II: purification, genetic specificity, and TATA box-promoter interactions of TFIID.
    Mol Cell Biol. 1988 Oct;8(10):4028-40 PMID: 3185540
  33. Nucleotide sequence of the SUF2 frameshift suppressor gene of Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 1982 Jun;79(11):3565-9 PMID: 7048310
  34. Only one of two closely related yeast suppressor tRNA genes contains an intervening sequence.
    Nature. 1981 Jun 11;291(5815):464-9 PMID: 6262655
  35. A 'hot-spot' for Ty transposition on the left arm of yeast chromosome III.
    Nucleic Acids Res. 1986 Apr 25;14(8):3475-85 PMID: 3010239
  36. Transcription of class III genes: formation of preinitiation complexes.
    Science. 1983 Nov 18;222(4625):740-8 PMID: 6356356
  37. Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements.
    Nature. 1981 Dec 17;294(5842):626-31 PMID: 7312050
  38. A split binding site for transcription factor tau on the tRNA3Glu gene.
    EMBO J. 1985 Feb;4(2):491-500 PMID: 2862029
  39. The yeast repeated element sigma contains a hormone-inducible promoter.
    Mol Cell Biol. 1987 Feb;7(2):749-59 PMID: 3547081
  40. Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo.
    Mol Cell Biol. 1986 Jul;6(7):2663-73 PMID: 3537724
  41. Rho-dependent termination of transcription. I. Identification and characterization of termination sites for transcription from the bacteriophage lambda PR promoter.
    J Biol Chem. 1983 Aug 10;258(15):9553-64 PMID: 6223929
  42. Mutations at the yeast SUP4 tRNATyr locus: DNA sequence changes in mutants lacking suppressor activity.
    Cell. 1980 Jul;20(3):701-9 PMID: 6998562
  43. Analysis of RNA polymerase III transcription complexes by gel filtration.
    J Biol Chem. 1986 Mar 25;261(9):4309-17 PMID: 3633269
  44. Gene size differentially affects the binding of yeast transcription factor tau to two intragenic regions.
    Proc Natl Acad Sci U S A. 1987 Dec;84(24):8768-72 PMID: 2827154
  45. Partial purification and characterization of the Saccharomyces cerevisiae transcription factor TFIIIB.
    J Biol Chem. 1986 Feb 25;261(6):2819-27 PMID: 3512543
  46. Specific DNA binding of GAL4, a positive regulatory protein of yeast.
    Cell. 1985 Apr;40(4):767-74 PMID: 3886158
  47. 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):81-7 PMID: 3652210
  48. Transformation in yeast: development of a hybrid cloning vector and isolation of the CAN1 gene.
    Gene. 1979 Dec;8(1):121-33 PMID: 395029
  49. Identification of a protein factor binding to the 5'-flanking region of a tRNA gene and being involved in modulation of tRNA gene transcription in vivo in Saccharomyces cerevisiae.
    Nucleic Acids Res. 1988 Jul 25;16(14B):6737-52 PMID: 3043375
  50. Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7.
    J Biol Chem. 1987 Nov 25;262(33):16212-23 PMID: 3316214
  51. Resolution of human transcription factor TFIIIC into two functional components.
    Proc Natl Acad Sci U S A. 1987 Jun;84(11):3585-9 PMID: 3473469
  52. An upstream signal is required for in vitro transcription of Neurospora 5S RNA genes.
    Mol Gen Genet. 1986 Oct;205(1):189-92 PMID: 3025558
  53. First position wobble in codon-anticodon pairing: amber suppression by a yeast glutamine tRNA.
    Gene. 1986;49(3):383-8 PMID: 3552889
  54. The properties of a new polymerase III transcription factor reveal that transcription complexes can assemble by more than one pathway.
    EMBO J. 1987 Jul;6(7):1921-7 PMID: 3653074
  55. Transformation of intact yeast cells treated with alkali cations.
    J Bacteriol. 1983 Jan;153(1):163-8 PMID: 6336730
  56. Three regions of a yeast tRNALeu3 gene promote RNA polymerase III transcription.
    J Biol Chem. 1984 May 10;259(9):5990-4 PMID: 6371014
  57. 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):2463-78 PMID: 3031599
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/mcb.9.8.3244-3252.1989
Published
1989-08-00
Pages
3244-52
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC362368
Subset
IM
External Links
PubMed source DOI: 10.1128/mcb.9.8.3244-3252.1989 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2