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

Journal of Molecular Biology

Volumn 267, Issue 2, 1997, Pages 324-337

  Teng, Yumin ^a   Li, Shisheng ^a   Waters, Raymond ^a   Reed, Simon H ^b  

^a SWANSEA UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

DNA repair; MFA2; Nucleotide resolution; RAD16; Saccharomyces cerevisiae

Indexed keywords

CYCLOBUTANE DERIVATIVE; ENDONUCLEASE; FUNGAL DNA; NUCLEOTIDE; PYRIMIDINE DIMER; RNA POLYMERASE II;

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA DETERMINATION; DNA TRANSCRIPTION; EXCISION REPAIR; FUNGUS MUTANT; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SOUTHERN BLOTTING; ULTRAVIOLET RADIATION;

FUNGI; SACCHAROMYCES CEREVISIAE;

EID: 0031588941     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0908     Document Type: Article

References (48)

1. Bang D. D., Timmermans V., Verhage R., Zeeman A. M., van de Putte P., Brouwer J. Regulation of the Saccharomyces cerevisiae DNA repair gene RAD 16. Nucl. Acids Res. 23:1995;1679-1685.
2. Bohr V. A., Smith C. A., Okumoto D. S., Hanawalt P. C. DNA repair in an active gene: removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall. Cell. 40:1985;359-369.
3. Chen-Cleland T. A., Smith M. M., Le S. Y., Sternglanz R., Allfrey V. G. Nucleosome structural-changes during derepression of silent mating-type loci in yeast. J. Biol. Chem. 268:1993;1118-1124.
4. Croston G. E., Kerrigan L. A., Lira L. M., Marshak D. R., Kadonaga J. T. Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science. 251:1991;643-649.
5. Dolan J. W., Kirkman C., Fields S. The yeast STE12 protein binds to the DNA sequence mediating pheromone induction. Proc. Natl Acad. Sci. USA. 86:1989;5703-5707.
6. Feaver W. J., Svejstrup J. Q., Bardwell L., Bardwell A. J., Buratowski S., Gulyas K. D., Donahue T. F., Friedberg E. C., Kornberg R. D. Dual roles of a multiprotein complex from S. cerevisiae in transcription and DNA repair. Cell. 75:1993;1379-1387.
7. Gao S., Drouin R., Holmquist G. P. DNA repair rates mapped along the human PGK 1 gene at nucleotide resolution. Science. 263:1994;1438-1440.
8. Grimaldi K. A., McAdam S. R., Souhami R. L., Hartley J. A. DNA damage by anti-cancer agents resolved at the nucleotide level of a single copy gene: evidence for a novel binding site for cisplatin in cells. Nucl. Acids Res. 22:1994;2311-2317.
9. Grunstein M. Histone function in transcription. Annu. Rev. Cell Biol. 6:1990;643-678.
10. Han M., Grunstein M. Nucleosome loss activates yeast downstream promoters in vivo. Cell. 55:1988;1137-1145.
11. Hartwell L. H., Weinert T. A. Checkpoints: controls that ensire the order of cell cycle events. Science. 246:1987;629-634.
12. Hirschhorn J. N., Brown S. A., Clark C. D., Winston F. Evidence that SNF2/SW12 and SNF5 active transcription in yeast by altering chromatin structure. Genes Dev. 6:1992;2288-2298.
13. Johnson A. D., Herskowitz I. A repressor (MAT alpha 2 Product) and its operator control expression of a set of cell type specific genes in yeast. Cell. 42:1985;237-247.
14. Jones E. W., Pringle J. R., Broach J. R. The Molecular and Cellular Biology of the Yeast Saccharomyces. 1992;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
15. Kalinoswki D. P., Illenye S., Van Houten B. Analysis of DNA damage and repair in murine leukemia L1210 cells using a quantitative polymerase chain reaction assay. Nucl. Acids Res. 20:1992;3485-3494.
16. Keleher C. A., Goutte C., Johnson A. D. The yeast cell-type-specific repressor alpha 2 acts cooperatively with a non-cell-type-specific protein. Cell. 53:1988;927-936.
17. Kunala S., Brash D. E. Excision repair at individual bases of the Escherichia coli lacI gene: relation to mutation hot spots and transcription coupling activity. Proc. Natl Acad. Sci. USA. 89:1992;11031-11035.
18. Kunala S., Brash D. E. Intragenic domains of strand-specific repair in Escherichia coli. J. Mol. Biol. 246:1995;264-272.
19. Kurjan J. The pheromone response in yeast. Annu. Rev. Biochem. 61:1992;1097-1129.
20. Laurenson P., Rine J. Silencers, silencing, and heritable transcriptional states. Microbiol. Rev. 56:1992;543-560.
21. Laybourn P. J., Kadonaga J. T. Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science. 254:1991;238-245.
22. Leadon S. A., Lawrence D. A. Strand-selective repair of DNA damage in the yeast GAL7 gene requires RNA polymerase II. J. Biol. Chem. 267:1992;23175-23182.
23. Li S., Waters R. Nucleotide level detection of cyclobutane pyrimidine dimers using oligonucleotides and magnetic beads to facilitate labelling of DNA fragments incised at the dimers and chemical sequencing reference ladders. Carcinogenesis. 17:1996;1549-1552.
24. Mallet L., Bussereau F., Jacquet M. A 43.5Kb segment of yeast chromosome XIV, which contains MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FRP1/RBP1, MOM22 and CPT1, predicts an adenosine deaminase gene and 14 new open reading frames. Yeast. 11:1995;1195-1209.
25. Mellon I., Spivak G., Hanawalt P. C. Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell. 51:1987;241-249.
26. Paranjape S. M., Kamakaka R. T., Kadonaga J. T. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu. Rev. Biochem. 63:1994;265-297.
27. Patterton H. G., Simpson R. T. Nucleosomal location of the STE6 TATA box and Mat alpha 2p-mediated repression. Mol. Cell. Biol. 14:1994;4002-4010.
28. Pfeifer G. P., Drouin R., Riggs A. D., Holmquist G. P. In vivo mapping of a DNA adduct at nucleotide resolution: detection of pyrimidine (6-4) pyrimidone photoproducts by ligation-mediated polymerase chain reaction. Proc. Natl Acad. Sci. USA. 88:1991;1374-1378.
29. Pfeifer G. P., Drouin R., Riggs A. D., Holmquist G. P. Binding of transcription factors creates hot spots for UV photoproducts in vivo. Mol. Cell. Biol. 12:1992;1798-1804.
30. Pfeifer G. P., Drouin R., Holmquist G. P. Detection of DNA adducts at the DNA sequence level by ligation-mediated PCR. Mutat. Res. 288:1993;39-46.
31. Prakash S., Sung P., Prakash L. DNA repair genes and proteins of Saccharomyces cerevisiae. Annu. Rev. Genet. 27:1993;33-70.
32. Prelich G., Winston F. 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. 135:1993;665-676.
33. Reed S. H., Boiteux S., Waters R. 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 HMLα Mol. Gen. Genet. 250:1996;505-514.
34. Roth S. Y., Shimizu M., Johnson L., Grurstein M., Simpson R. T. Stable nucleosome positioning and complete repression by the yeast alpha 2 repressor are disrupted by amino-terminal mutations in histone H4. Genes Dev. 6:1992;411-425.
35. Sancar G. B., Sancar A. Structure and function of DNA photolyases. Trends Biochem. Sci. 12:1987;259-261.
36. Shimizu M., Roth S. Y., Szent-Gyorgyi C., Simpson R. T. Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae. EMBO J. 10:1991;3033-3041.
37. Stevenson B. J., Rhodes N., Errede B., Sprague G. F. Genes Dev. 6:1992;1293-1304.
38. St John T. P., Davis R. W. The organization and transcription of the galactose gene cluster of Saccharomyces cerevisiae. J. Mol. Biol. 152:1981;285-315.
39. Sweder K. S., Hanawalt P. C. Preferential repair of cyclobutane pyrimidine dimers in the transcribed strand of a gene in yeast chromosomes and plasmids is dependent on transcription. Proc. Natl Acad. Sci. USA. 89:1992;10696-10700.
40. Terleth C., van Sluis C. A., van de Putte P. Differential repair of UV damage in Saccharomyces cerevisiae. Nucl. Acids Res. 17:1989;4433-4439.
41. Terleth C., Schenk P., Poot R., Brouwer J., van de Putte P. Differential repair of UV damage in rad mutants of Saccharomyces cerevisiae: a possible function of G2 arrest upon UV irradiation. Mol. Cell. Biol. 10:1990;4678-4684.
42. Thompson J. S., Hecht A., Grunstein M. Histones and the regulation of heterochromatin in yeast. Cold Spring Harbor Symp. Quant. Bio. 58:1993;247-256.
43. Thompson J. S., Ling X., Grunstein M. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature. 369:1994;245-247.
44. Tijsterman M., Tasseron-de Jong J. G., van de Putte P., Brouwer J. Transcription-coupled and global genome repair in the Saccharomyces cerevisiae RPB2 gene at nucleotide resolution. Nucl. Acids Res. 24:1996;3499-3506.
45. Tu Y., Tornaletti S., Pfiefer G. P. DNA repair domains within a human gene: selective repair of sequences near the transcription initiation site. EMBO J. 15:1996;675-683.
46. van Gool A. J., Verhage R., Swagemakers S. M., van de Putte P., Brouwer J., Troelstra C., Bootsma D., Hoeijmakers J. H. RAD26, the function S. cerevisiae homolog of the Cockayne syndrome B gene ERCC6. EMBO J. 13:1994;5361-5369.
47. Verhage R., Zeeman A. M., de Groot N., Gleig F., Bang D. D., van de Putte P., Brouwer J. The RAD7 and RAD16 genes, which are essential for pyrimidine dimer removal from the silent mating type loci, are also required for repair of the nontranscribed strand of an active gene in Saccharomyces cerevisiae. Mol. Cell. Biol. 14:1994;6135-6161.
48. Waters R., Zhang R., Jones N. J. Inducible removal of UV-induced pyrimidine dimers from transcriptionally active and inactive genes of Saccharomyces cerevisiae. Mol. Gen. Genet. 239:1993;28-32.