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PMID: 9671455 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Interplay of positive and negative regulators in transcription initiation by RNA polymerase II holoenzyme.

Molecular and cellular biology ·Vol. 18 ·No. 8 ·1998-08-00 ·Pages 4455-62

Lee TI, Wyrick JJ, Koh SS, Jennings EG, Gadbois EL, Young RA

Abstract

Activation of protein-encoding genes involves recruitment of an RNA polymerase II holoenzyme to promoters. Since the Srb4 subunit of the holoenzyme is essential for expression of most class II genes and is a target of at least one transcriptional activator, we reasoned that suppressors of a temperature-sensitive mutation in Srb4 would identify other factors generally involved in regulation of gene expression. We report here that MED6 and SRB6, both of which encode essential components of the holoenzyme, are among the dominant suppressors and that the products of these genes interact physically with Srb4. The recessive suppressors include NCB1 (BUR6), NCB2, NOT1, NOT3, NOT5, and CAF1, which encode subunits of NC2 and the Not complex. NC2 and Not proteins are general negative regulators which interact with TATA box binding protein (TBP). Taken together, these results suggest that transcription initiation involves a dynamic balance between activation mediated by specific components of the holoenzyme and repression by multiple TBP-associated regulators.

MeSH Terms
Alleles Amino Acid Sequence Animals Cell Cycle Proteins/genetics,metabolism Coenzymes/metabolism DNA-Binding Proteins/metabolism Fungal Proteins/genetics,metabolism Gene Expression Regulation, Fungal Mediator Complex Molecular Sequence Data RNA Polymerase II/metabolism Rabbits Ribonucleases Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins TATA-Box Binding Protein Trans-Activators/genetics,metabolism Transcription Factors/genetics,metabolism Transcription, Genetic
Chemicals
CDC39 protein, S cerevisiae Cell Cycle Proteins Coenzymes DNA-Binding Proteins Fungal Proteins MED6 protein, S cerevisiae Mediator Complex NOT5 protein, S cerevisiae SRB4 protein, S cerevisiae SRB6 protein, S cerevisiae Saccharomyces cerevisiae Proteins TATA-Box Binding Protein Trans-Activators Transcription Factors RNA Polymerase II Ribonucleases POP2 protein, S cerevisiae
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Lee T I
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Wyrick J J
Koh S S
Jennings E G
Gadbois E L
Young R A
References (64)
64 references, click to expand
  1. Genetic applications of yeast transformation with linear and gapped plasmids.
    Methods Enzymol. 1983;101:228-45 PMID: 6310326
  2. Functional antagonism between RNA polymerase II holoenzyme and global negative regulator NC2 in vivo.
    Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):3145-50 PMID: 9096360
  3. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics.
    Methods Enzymol. 1987;154:164-75 PMID: 3323810
  4. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase.
    Gene. 1988 Jul 15;67(1):31-40 PMID: 3047011
  5. Nucleosome loss activates yeast downstream promoters in vivo.
    Cell. 1988 Dec 23;55(6):1137-45 PMID: 2849508
  6. Mutations in RNA polymerase II enhance or suppress mutations in GAL4.
    Proc Natl Acad Sci U S A. 1989 Apr;86(8):2794-8 PMID: 2495535
  7. High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier.
    Curr Genet. 1989 Dec;16(5-6):339-46 PMID: 2692852
  8. RNA polymerase II C-terminal repeat influences response to transcriptional enhancer signals.
    Nature. 1990 Oct 4;347(6292):491-4 PMID: 2215664
  9. Histone function in transcription.
    Annu Rev Cell Biol. 1990;6:643-78 PMID: 2275823
  10. Functional differences between yeast and human TFIID are localized to the highly conserved region.
    Cell. 1991 Apr 19;65(2):341-8 PMID: 2015628
  11. Family of proteins that interact with TFIID and regulate promoter activity.
    Cell. 1991 Nov 1;67(3):557-67 PMID: 1934060
  12. RNA polymerase II carboxy-terminal domain contributes to the response to multiple acidic activators in vitro.
    Genes Dev. 1991 Dec;5(12B):2431-40 PMID: 1752437
  13. A presumptive helicase (MOT1 gene product) affects gene expression and is required for viability in the yeast Saccharomyces cerevisiae.
    Mol Cell Biol. 1992 Apr;12(4):1879-92 PMID: 1312673
  14. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae.
    Genes Dev. 1992 Jul;6(7):1319-31 PMID: 1628834
  15. Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription.
    Cell. 1992 Aug 7;70(3):477-89 PMID: 1339312
  16. CDC39, an essential nuclear protein that negatively regulates transcription and differentially affects the constitutive and inducible HIS3 promoters.
    EMBO J. 1993 Jan;12(1):177-86 PMID: 8428577
  17. A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast.
    Cell. 1993 Jul 2;73(7):1361-75 PMID: 8324825
  18. Immunopurification of yeast TATA-binding protein and associated factors. Presence of transcription factor IIIB transcriptional activity.
    J Biol Chem. 1993 Jul 25;268(21):15325-8 PMID: 8340360
  19. Mutations that suppress the deletion of an upstream activating sequence in yeast: involvement of a protein kinase and histone H3 in repressing transcription in vivo.
    Genetics. 1993 Nov;135(3):665-76 PMID: 8293972
  20. An RNA polymerase II holoenzyme responsive to activators.
    Nature. 1994 Mar 31;368(6470):466-9 PMID: 8133894
  21. Histones, nucleosomes and the roles of chromatin structure in transcriptional control.
    Biochem Soc Trans. 1997 May;25(2):354-8 PMID: 9191116
  22. A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans.
    Mol Cell Biol. 1997 Aug;17(8):4622-32 PMID: 9234719
  23. Transcription: in tune with the histones.
    Cell. 1994 Apr 8;77(1):13-6 PMID: 8156588
  24. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II.
    Cell. 1994 May 20;77(4):599-608 PMID: 8187178
  25. Yeast Taf170 is encoded by MOT1 and exists in a TATA box-binding protein (TBP)-TBP-associated factor complex distinct from transcription factor IID.
    J Biol Chem. 1994 Sep 16;269(37):23135-40 PMID: 8083216
  26. NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization.
    Genes Dev. 1994 Mar 1;8(5):525-37 PMID: 7926748
  27. Yeast TAFIIS in a multisubunit complex required for activated transcription.
    Nature. 1994 Oct 6;371(6497):523-7 PMID: 7935765
  28. Differential regulation of RNA polymerases I, II, and III by the TBP-binding repressor Dr1.
    Science. 1994 Oct 21;266(5184):448-50 PMID: 7939686
  29. Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism.
    Genes Dev. 1994 Aug 15;8(16):1920-34 PMID: 7958867
  30. Structure-function analysis of the TBP-binding protein Dr1 reveals a mechanism for repression of class II gene transcription.
    Genes Dev. 1994 Sep 1;8(17):2097-109 PMID: 7958881
  31. A kinase-cyclin pair in the RNA polymerase II holoenzyme.
    Nature. 1995 Mar 9;374(6518):193-6 PMID: 7877695
  32. The RNA polymerase II holoenzyme and its implications for gene regulation.
    Trends Biochem Sci. 1995 Mar;20(3):113-6 PMID: 7709429
  33. RNA polymerase II C-terminal domain required for enhancer-driven transcription.
    Nature. 1995 Apr 13;374(6523):660-2 PMID: 7715709
  34. General requirement for RNA polymerase II holoenzymes in vivo.
    Proc Natl Acad Sci U S A. 1995 May 9;92(10):4587-90 PMID: 7753848
  35. Association of an activator with an RNA polymerase II holoenzyme.
    Genes Dev. 1995 Apr 15;9(8):897-910 PMID: 7774808
  36. Yeast histone H3 and H4 N termini function through different GAL1 regulatory elements to repress and activate transcription.
    Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5664-8 PMID: 7777566
  37. A mammalian RNA polymerase II holoenzyme containing all components required for promoter-specific transcription initiation.
    Cell. 1995 Oct 6;83(1):137-46 PMID: 7553866
  38. The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization.
    Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):11170-4 PMID: 7479959
  39. A mammalian SRB protein associated with an RNA polymerase II holoenzyme.
    Nature. 1996 Mar 7;380(6569):82-5 PMID: 8598913
  40. Requirement of a corepressor for Dr1-mediated repression of transcription.
    Genes Dev. 1996 Apr 15;10(8):1033-48 PMID: 8608938
  41. A human RNA polymerase II complex associated with SRB and DNA-repair proteins.
    Nature. 1996 May 2;381(6577):86-9 PMID: 8609996
  42. Functional analysis of histones H2A and H2B in transcriptional repression in Saccharomyces cerevisiae.
    Mol Cell Biol. 1996 Jun;16(6):2545-53 PMID: 8649361
  43. Transcriptional corepression in vitro: a Mot1p-associated form of TATA-binding protein is required for repression by Leu3p.
    Mol Cell Biol. 1996 Apr;16(4):1641-8 PMID: 8657139
  44. A mechanism for repression of class II gene transcription through specific binding of NC2 to TBP-promoter complexes via heterodimeric histone fold domains.
    EMBO J. 1996 Jun 17;15(12):3105-16 PMID: 8670811
  45. All four core histone N-termini contain sequences required for the repression of basal transcription in yeast.
    EMBO J. 1996 Aug 1;15(15):3974-85 PMID: 8670902
  46. A negative cofactor containing Dr1/p19 modulates transcription with TFIIA in a promoter-specific fashion.
    J Biol Chem. 1996 Aug 2;271(31):18405-12 PMID: 8702484
  47. Purification of yeast RNA polymerase II holoenzymes.
    Methods Enzymol. 1996;273:176-84 PMID: 8791611
  48. The role of general initiation factors in transcription by RNA polymerase II.
    Trends Biochem Sci. 1996 Sep;21(9):327-35 PMID: 8870495
  49. Interaction of elongation factors TFIIS and elongin A with a human RNA polymerase II holoenzyme capable of promoter-specific initiation and responsive to transcriptional activators.
    J Biol Chem. 1997 Sep 26;272(39):24563-71 PMID: 9305922
  50. Baculoviral transfer vectors for expression of FLAG fusion proteins in insect cells.
    Biotechniques. 1997 Oct;23(4):622-4, 626-7 PMID: 9343676
  51. The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain.
    Genes Dev. 1998 Jan 1;12(1):45-54 PMID: 9420330
  52. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively.
    EMBO J. 1998 Feb 16;17(4):1096-106 PMID: 9463387
  53. Characterization of NOT5 that encodes a new component of the Not protein complex.
    Gene. 1998 Jan 19;207(1):61-9 PMID: 9511744
  54. Regulation of gene expression by TBP-associated proteins.
    Genes Dev. 1998 May 15;12(10):1398-408 PMID: 9585500
  55. An activator target in the RNA polymerase II holoenzyme.
    Mol Cell. 1998 May;1(6):895-904 PMID: 9660972
  56. The NOT, SPT3, and MOT1 genes functionally interact to regulate transcription at core promoters.
    Mol Cell Biol. 1996 Dec;16(12):6668-76 PMID: 8943321
  57. The general transcription factors of RNA polymerase II.
    Genes Dev. 1996 Nov 1;10(21):2657-83 PMID: 8946909
  58. Characterization of the basal inhibitor of class II transcription NC2 from Saccharomyces cerevisiae.
    Nucleic Acids Res. 1996 Nov 15;24(22):4450-5 PMID: 8948634
  59. Functional dissection of a human Dr1-DRAP1 repressor complex.
    Mol Cell Biol. 1997 Jan;17(1):36-45 PMID: 8972183
  60. Histone and histone fold sequences and structures: a database.
    Nucleic Acids Res. 1997 Jan 1;25(1):272-3 PMID: 9016552
  61. The Dr1/DRAP1 heterodimer is a global repressor of transcription in vivo.
    Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):820-5 PMID: 9023340
  62. Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme.
    Mol Cell Biol. 1997 Mar;17(3):1160-9 PMID: 9032243
  63. Saccharomyces cerevisiae BUR6 encodes a DRAP1/NC2alpha homolog that has both positive and negative roles in transcription in vivo.
    Mol Cell Biol. 1997 Apr;17(4):2057-65 PMID: 9121454
  64. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli.
    Gene. 1987;57(2-3):267-72 PMID: 3319781
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/MCB.18.8.4455
Published
1998-08-00
Pages
4455-62
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC109031
Subset
IM
External Links
PubMed source DOI: 10.1128/MCB.18.8.4455 PMC Full Text View journal details
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