Home LiteratureArticle Details
PMID: 12582242 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Rap1p and other transcriptional regulators can function in defining distinct domains of gene expression.

Nucleic acids research ·Vol. 31 ·No. 4 ·2003-02-15 ·Pages 1224-33

Yu Q, Qiu R, Foland TB, Griesen D, Galloway CS, Chiu YH, Sandmeier J, Broach JR, Bi X

Abstract

Barrier elements that are able to block the propagation of transcriptional silencing in yeast are functionally similar to chromatin boundary/insulator elements in metazoans that delimit functional chromosomal domains. We show that the upstream activating sequences of many highly expressed ribosome protein genes and glycolytic genes exhibit barrier activity. Analyses of these barriers indicate that binding sites for transcriptional regulators Rap1p, Abf1p, Reb1p, Adr1p and Gcn4p may participate in barrier function. We also present evidence suggesting that Rap1p is directly involved in barrier activity, and its barrier function correlates with local changes in chromatin structure. We further demonstrate that tethering the transcriptional activation domain of Rap1p to DNA is sufficient to recapitulate barrier activity. Moreover, targeting the activation domain of Adr1p or Gcn4p also establishes a barrier to silencing. These results support the notion that transcriptional regulators could also participate in delimiting functional domains in the genome.

MeSH Terms
Binding Sites/genetics Chromatin/genetics,metabolism DNA-Binding Proteins/genetics Gene Expression Regulation, Fungal Gene Silencing Mutation Peptide Elongation Factor 1/genetics Protein Kinases/genetics Saccharomyces cerevisiae Proteins/genetics,metabolism Shelterin Complex Telomere-Binding Proteins/genetics,metabolism Transcription Factors/genetics,metabolism Transcription, Genetic
Chemicals
ADR1 protein, S cerevisiae Chromatin DNA-Binding Proteins Peptide Elongation Factor 1 RAP1 protein, S cerevisiae Saccharomyces cerevisiae Proteins Shelterin Complex Telomere-Binding Proteins Transcription Factors Protein Kinases
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Yu Qun
Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
Qiu Runxiang
Foland Travis B
Griesen Dan
Galloway Carl S
Chiu Ya-Hui
Sandmeier Joseph
Broach James R
Bi Xin
References (53)
53 references, click to expand
  1. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase.
    Mol Cell. 2000 Dec;6(6):1297-307 PMID: 11163204
  2. Silencers are required for inheritance of the repressed state in yeast.
    Genes Dev. 1996 Apr 15;10(8):1021-32 PMID: 8608937
  3. An activation-independent role of transcription factors in insulator function.
    EMBO Rep. 2001 Feb;2(2):124-32 PMID: 11258704
  4. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association.
    Nat Genet. 2001 Aug;28(4):327-34 PMID: 11455386
  5. Activation mechanism of the multifunctional transcription factor repressor-activator protein 1 (Rap1p).
    Mol Cell Biol. 1996 Jun;16(6):3187-96 PMID: 8649429
  6. C-terminal domains of general regulatory factors Abf1p and Rap1p in Saccharomyces cerevisiae display functional similarity.
    Mol Microbiol. 1996 Feb;19(3):535-43 PMID: 8830244
  7. Global regulators of ribosome biosynthesis in yeast.
    Biochem Cell Biol. 1995 Nov-Dec;73(11-12):825-34 PMID: 8721998
  8. ADR1 activation domains contact the histone acetyltransferase GCN5 and the core transcriptional factor TFIIB.
    J Biol Chem. 1996 Dec 13;271(50):32359-65 PMID: 8943299
  9. Characterization of the yeast transcriptome.
    Cell. 1997 Jan 24;88(2):243-51 PMID: 9008165
  10. Telomere length regulation: getting the measure of chromosome ends.
    Biol Chem. 1997 Jul;378(7):591-7 PMID: 9278138
  11. DNA in transcriptionally silent chromatin assumes a distinct topology that is sensitive to cell cycle progression.
    Mol Cell Biol. 1997 Dec;17(12):7077-87 PMID: 9372939
  12. Yeast heterochromatin: regulation of its assembly and inheritance by histones.
    Cell. 1998 May 1;93(3):325-8 PMID: 9590166
  13. Yeast carbon catabolite repression.
    Microbiol Mol Biol Rev. 1998 Jun;62(2):334-61 PMID: 9618445
  14. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes.
    Nature. 1998 Jul 30;394(6692):498-502 PMID: 9697775
  15. Dividing the empire: boundary chromatin elements delimit the territory of enhancers.
    EMBO J. 1999 Jan 4;18(1):1-8 PMID: 9878044
  16. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae.
    Genes Dev. 1999 Mar 15;13(6):698-708 PMID: 10090726
  17. Cohabitation of insulators and silencing elements in yeast subtelomeric regions.
    EMBO J. 1999 May 4;18(9):2522-37 PMID: 10228166
  18. DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences.
    Bioinformatics. 1999 Apr;15(4):267-77 PMID: 10320394
  19. UASrpg can function as a heterochromatin boundary element in yeast.
    Genes Dev. 1999 May 1;13(9):1089-101 PMID: 10323861
  20. The yeast HML I silencer defines a heterochromatin domain boundary by directional establishment of silencing.
    Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11934-9 PMID: 10518554
  21. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase.
    Nature. 2000 Feb 17;403(6771):795-800 PMID: 10693811
  22. Saccharomyces cerevisiae RAP1 binds to telomeric sequences with spatial flexibility.
    Nucleic Acids Res. 2000 Jun 15;28(12):2292-301 PMID: 10871358
  23. Understanding the growth phenotype of the yeast gcr1 mutant in terms of global genomic expression patterns.
    J Bacteriol. 2000 Sep;182(17):4970-8 PMID: 10940042
  24. RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae.
    EMBO J. 2001 Feb 1;20(3):520-31 PMID: 11157758
  25. RAP, RAP, open up! New wrinkles for RAP1 in yeast.
    Trends Genet. 2000 Feb;16(2):51-3 PMID: 10652526
  26. SAGA is an essential in vivo target of the yeast acidic activator Gal4p.
    Genes Dev. 2001 Aug 1;15(15):1935-45 PMID: 11485988
  27. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4.
    Genes Dev. 2001 Aug 1;15(15):1946-56 PMID: 11485989
  28. Common themes in mechanisms of gene silencing.
    Mol Cell. 2001 Sep;8(3):489-98 PMID: 11583612
  29. Insulators: many functions, many mechanisms.
    Genes Dev. 2002 Feb 1;16(3):271-88 PMID: 11825869
  30. Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3.
    J Biol Chem. 2002 Feb 15;277(7):4778-81 PMID: 11714726
  31. Braking the silence: how heterochromatic gene repression is stopped in its tracks.
    Bioessays. 2002 Apr;24(4):344-9 PMID: 11948620
  32. Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast.
    Mol Cell. 2002 Apr;9(4):823-33 PMID: 11983173
  33. Chromatin boundaries in budding yeast: the nuclear pore connection.
    Cell. 2002 May 31;109(5):551-62 PMID: 12062099
  34. General regulatory factors (GRFs) as genome partitioners.
    J Biol Chem. 2002 Nov 1;277(44):41736-43 PMID: 12200417
  35. LexA protein is a repressor of the colicin E1 gene.
    J Biol Chem. 1983 Nov 10;258(21):13258-61 PMID: 6355108
  36. Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure.
    Cell. 1985 Oct;42(3):799-808 PMID: 2996776
  37. The 87A7 chromomere. Identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains.
    J Mol Biol. 1985 Sep 20;185(2):341-58 PMID: 2997449
  38. Histone acetylation reduces nucleosome core particle linking number change.
    Cell. 1989 May 5;57(3):449-57 PMID: 2541913
  39. Multiple factors bind the upstream activation sites of the yeast enolase genes ENO1 and ENO2: ABFI protein, like repressor activator protein RAP1, binds cis-acting sequences which modulate repression or activation of transcription.
    Mol Cell Biol. 1990 Sep;10(9):4872-85 PMID: 2201905
  40. Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway.
    Microbiol Rev. 1991 Sep;55(3):349-70 PMID: 1943992
  41. Multifunctional yeast high-copy-number shuttle vectors.
    Gene. 1992 Jan 2;110(1):119-22 PMID: 1544568
  42. A REB1-binding site is required for GCN4-independent ILV1 basal level transcription and can be functionally replaced by an ABF1-binding site.
    Mol Cell Biol. 1992 Dec;12(12):5516-26 PMID: 1448083
  43. Concerted action of the transcriptional activators REB1, RAP1, and GCR1 in the high-level expression of the glycolytic gene TPI.
    Mol Cell Biol. 1993 Jan;13(1):543-50 PMID: 8417350
  44. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation.
    Genes Dev. 1993 Apr;7(4):592-604 PMID: 8458576
  45. Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites.
    J Mol Biol. 1993 May 20;231(2):293-310 PMID: 8510148
  46. Mammalian Ras interacts directly with the serine/threonine kinase Raf.
    Cell. 1993 Jul 16;74(1):205-14 PMID: 8334704
  47. A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila.
    Cell. 1993 Aug 13;74(3):505-14 PMID: 8348617
  48. Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1.
    Genes Dev. 1994 Oct 1;8(19):2257-69 PMID: 7958893
  49. RAP1: a protean regulator in yeast.
    Trends Genet. 1994 Nov;10(11):408-12 PMID: 7809947
  50. Transcription activation of yeast ribosomal protein genes requires additional elements apart from binding sites for Abf1p or Rap1p.
    Nucleic Acids Res. 1995 May 11;23(9):1475-80 PMID: 7784199
  51. Control of glycolytic gene expression in the budding yeast (Saccharomyces cerevisiae).
    Curr Genet. 1995 Dec;29(1):1-9 PMID: 8595651
  52. The multifunctional transcription factors Abf1p, Rap1p and Reb1p are required for full transcriptional activation of the chromosomal PGK gene in Saccharomyces cerevisiae.
    Mol Gen Genet. 1996 Feb 25;250(3):348-56 PMID: 8602150
  53. Chromosomal boundaries in S. cerevisiae.
    Curr Opin Genet Dev. 2001 Apr;11(2):199-204 PMID: 11250144
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkg200
Published
2003-02-15
Pages
1224-33
Language
English
Region
England
NLM ID
0411011
PMCID
PMC150219
Subset
IM
Grants
NIGMS NIH HHS · R01 GM062484 · United States
NIGMS NIH HHS · GM 62484 · United States
External Links
PubMed source DOI: 10.1093/nar/gkg200 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