Cbf1p modulates chromatin structure, transcription and repair at the Saccharomyces cerevisiae MET16 locus

Nucleic Acids Research

Volumn 32, Issue 5, 2004, Pages 1617-1626

  Ferreiro, J A ^c,d   Powell, N G ^c   Karabetsou, N ^a   Kent, N A ^a   Mellor, J ^a   Waters, R ^b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c SWANSEA UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF OVIEDO   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLYLSULFATE KINASE; DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CBF1P; UNCLASSIFIED DRUG; ADENYLYLSULFATE REDUCTASE; BASIC HELIX LOOP HELIX LEUCINE ZIPPER TRANSCRIPTION FACTOR; CBF1 PROTEIN, S CEREVISIAE; OXIDOREDUCTASE; PYRIMIDINE DIMER; SACCHAROMYCES CEREVISIAE PROTEIN; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

AMINO ACID SEQUENCE; ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; EXCISION REPAIR; GENE LOCUS; GENE REPRESSION; GENETIC CODE; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOSOME; PERIODICITY; PRIORITY JOURNAL; PROMOTER REGION; RESTRICTION FRAGMENT; SACCHAROMYCES CEREVISIAE; WILD TYPE; BIOSYNTHESIS; CHEMISTRY; CHROMATIN; DNA REPAIR; FUNGAL GENE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MUTATION; PHYSIOLOGY; ULTRASTRUCTURE;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

BASIC HELIX-LOOP-HELIX LEUCINE ZIPPER TRANSCRIPTION FACTORS; CHROMATIN; DEOXYRIBONUCLEASE HPAII; DNA REPAIR; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; MUTATION; NUCLEOSOMES; OXIDOREDUCTASES ACTING ON SULFUR GROUP DONORS; PYRIMIDINE DIMERS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

EID: 3042624480     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh324     Document Type: Article

References (40)

1. Wolffe,A. (1998) Chromatin: Structure and Function. Academic Press, San Diego, USA.
2. Meijer,M. and Smerdon,M.J. (1999) Accessing DNA damage in chromatin: insights from transcription. BioEssays, 21, 596-603.
3. Meyer,P. (2001) Chromatin remodelling. Curr. Opin. Plant Biol., 4, 457-462.
4. Pfeifer,G.P. (1997) Formation and processing of UV photoproducts: effects of DNA sequence and chromatin environment. Photochem. Photobiol., 65, 270-283.
5. Smerdon,M.J. and Conconi,A. (1999) Modulation of DNA damage and DNA repair in chromatin. Prog. Nucleic Acid Res. Mol. Biol., 62, 227-255.
6. Mann,D.B., Springer,D.L. and Smerdon,M.J. (1997) DNA damage can alter the stability of nucleosomes: effects are dependent on damage type. Proc. Natl Acad. Sci. USA, 94, 2215-2220.
7. Wellinger,R.E. and Thoma,F. (1997) Nucleosome structure and positioning modulate nucleotide excision repair in the non-transcribed strand of an active gene. EMBO J., 16, 5046-5056.
8. Tijsterman,M., De Pril,R., Tasseron-de Jong,J.G. and Brouwer,J. (1999) RNA polymerase II transcription suppresses nucleosomal modulation of UV-induced (6-4) photoproduct and cyclobutane pyrimidine dimer repair in yeast. Mol. Cell. Biol., 19, 934-940.
9. Hara,R., Mo,J. and Sancar,A. (2000) DNA damage in the nucleosome core is refractory to repair by human excision nuclease. Mol. Cell. Biol., 20, 9173-9181.
10. Ura,K., Araki,M., Saeki,H., Masutani,C., Ito,T., Iwai,S., Mizukoshi,T., Kaneda,Y. and Hanaoka,F. (2001) ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes. EMBO J., 20, 2004-2014.
11. Powell,N.G., Ferreiro,J., Karabetsou,N., Mellor,J., and Waters,R. (2003) Transcription, nucleosome positioning and protein binding modulate nucleotide excision repair of the Saccharomyces cerevisiae MET17 promoter. DNA Repair (Amst.), 2, 375-386.
12. O'Connell,K.F., Surdin-Kerjan,Y. and Baker,R.E. (1995) Role of the Saccharomyces cerevisiae general regulatory factor CP1 in methionine biosynthetic gene transcription. Mol. Cell. Biol., 15, 1879-1888.
13. Kuras,L., Chérest,H., Surdin-Kerjan,Y. and Thomas,D. (1996) A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediates the transcription activation of yeast sulfur metabolism. EMBO J., 15, 2519-2529.
14. Thomas,D., Barbey,R. and Surdin-Kedan,Y. (1990) Gene-enzyme relationship in the sulfate assimilation pathway of Saccharomyces cerevisiae. Study of the 3′-phosphoadenylylsulfate reductase structural gene. J. Biol. Chem., 265, 15518-15524.
15. Wang,Y., Liu,C.L., Storey,J.D., Tibshirani,R.J., Herschlag,D. and Brown,P.O. (2002) Precision and functional specificity in mRNA decay. Proc. Natl Acad. Sci. USA, 99, 5860-5865.
16. Cai,M. and Davis,R.W. (1990) Yeast centromere binding protein CBF1, of the helix-loop-helix protein family, is required for chromosome stability and methionine prototrophy. Cell, 61, 437-446.
17. Mellor,J., Jiang,W., Funk,M., Rathjen,J., Barnes,C.A., Hinz,T., Hegemann,J.H. and Philippsen,P. (1990) CPF1, a yeast protein which functions in centromeres and promoters. EMBO J., 9, 4017-4026.
18. McKenzie,E.A., Kent,N.A., Dowell,S.J., Moreno,F., Bird,L.E. and Mellor,J. (1993) The centromere and promoter factor 1, CPF1, of Saccharomyces cerevisiae modulates gene activity through a family of factors including SPT21, RPD1 (SIN3), RPD3 and CCR4. Mol. Gen. Genet., 240, 374-386.
19. Kent,N.A., Tsang,J.S., Crowther,D.J. and Mellor,J. (1994) Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1. Mol. Cell. Biol., 14, 5229-5241.
20. Reed,S.H., Boiteux,S. and Waters,R. (1996) UV-induced endonuclease III-sensitive sites at the mating type loci in Saccharomyces cerevisiae are repaired by nucleotide excision repair: RAD7 and RAD16 are not required for their removal from HML alpha. Mol. Gen. Genet., 250, 505-514.
21. Teng,Y., Li,S., Waters,R. and Reed,S.H. (1997) Excision repair at the level of the nucleotide in the Saccharomyces cerevisiae MFA2 gene: mapping of where enhanced repair in the transcribed strand begins or ends and identification of only a partial rad16 requisite for repairing upstream control sequences. J. Mol. Biol., 267, 324-337.
22. Ausubel,F.M. (1989) Current Protocols in Molecular Biology. Wiley, New York, NY.
23. Kent,N.A. and Mellor,J. (1995) Chromatin structure snap-shots: rapid nuclease digestion of chromatin in yeast. Nucleic Acids Res., 23, 3786-3787.
24. Teng,Y., Yu,S. and Waters,R. (2001) The mapping of nucleosomes and regulatory protein binding sites at the Saccharomyces cerevisiae MFA2 gene: a high resolution approach. Nucleic Acids Res., 29, e64.
25. Morillon,A., Karabetsou,N., O'Sullivan,J., Kent,N., Proudfoot,N. and Mellor,J. (2003) Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA Polymerase II. Cell, 115, 425-435.
26. Teng,Y. and Waters,R. (2000) Excision repair at the level of the nucleotide in the upstream control region, the coding sequence and in the region where transcription terminates of the Saccharomyces cerevisiae MFA2 gene and the role of RAD26. Nucleic Acids Res., 28, 1114-1119.
27. Dutnall,R.N. and Ramakrishnan,V. (1997) Twists and turns of the nucleosome: tails without ends. Structure, 5, 1255-1259.
28. Luger,K., Mader,A.W., Richmond,R.K., Sargent,D.F. and Richmond,T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 231-233.
29. Studitsky,V.M., Kassavetis,G.A., Geiduschek,E.P. and Felsenfeld,G. (1997) Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science, 278, 1960-1963.
30. Cote,J., Peterson,C.L. and Workman,J.L. (1998) Perturbation of nucleosome core structure by the SWI/SNF complex persists after its detachment, enhancing subsequent transcription factor binding. Proc. Natl Acad. Sci. USA, 95, 4947-4952.
31. Tse,C., Sera,T., Wolffe,A.P. and Hansen,J.C. (1998) Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol. Cell. Biol., 18, 4629-4638.
32. Bednar,J., Studitsky,V.M., Grigoryev,S.A., Felsenfeld,G. and Woodcock,C.L. (1999) The nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryomicroscopy. Mol. Cell, 4, 377-386.
33. Wolffe,A.P. and Hayes,J.J. (1999) Chromatin disruption and modification. Nucleic Acids Res., 27, 711-720.
34. Workman,J.L. and Kingston,R.E. (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem., 67, 545-579.
35. Brower-Toland,B.D., Smith,C.L., Yeh,R.C., Lis,J.T., Peterson,C.L. and Wang,M.D. (2002) Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl Acad. Sci. USA, 99, 1960-1965.
36. Hayes,J.J. and Wolffe,A.P. (1992) Histones H2A/H2B inhibit the interaction of transcription factor IIIA with the Xenopus borealis somatic 5S RNA gene in a nucleosome. Proc. Natl Acad. Sci. USA, 89, 1229-1233.
37. Hansen,J.C. and Wolffe,A.P. (1994) A role for histones H2A/H2B in chromatin folding and transcriptional repression. Proc. Natl Acad. Sci. USA, 91, 2339-2343.
38. Spangenberg,C., Eisfeld,K., Stunkel,W., Luger,K., Flaus,A., Richmond,T.J., Truss,M. and Beato,M. (1998) cAMP-dependent phosphorylation sites and macroscopic activity of recombinant cardiac L-type calcium channels. J. Mol. Biol., 278, 725-739.
39. Hu,W., Feng,Z., Chasin,L.A. and Tang,M. (2002) Transcription-coupled and transcription-independent repair of cyclobutane pyrimidine dimers in the dihydrofolate reductase gene. J. Biol. Chem., 277, 38305-38310.
40. Zheng,Y., Pao,A., Adair,G.M. and Tang,M. (2001) Cyclobutane pyrimidine dimers and bulky chemical DNA adducts are efficiently repaired in both strands of either a transcriptionally active or promoter-deleted APRT gene. J. Biol. Chem., 276, 16786-16796.