Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Oct 1;25(19):3795–3800. doi: 10.1093/nar/25.19.3795

RNA polymerase II transcription inhibits DNA repair by photolyase in the transcribed strand of active yeast genes.

M Livingstone-Zatchej 1, A Meier 1, B Suter 1, F Thoma 1
PMCID: PMC146978  PMID: 9380500

Abstract

Yeast uses nucleotide excision repair (NER) and photolyase (photoreactivation) to repair cyclobutane pyrimidine dimers (CPDs) generated by ultraviolet light. In active genes, NER preferentially repairs the transcribed strand (TS). In contrast, we recently showed that photolyase preferentially repairs the non-transcribed strands (NTS) of the URA3 and HIS3 genes in minichromosomes. To test whether photoreactivation depends on transcription, repair of CPDs was investigated in the transcriptionally regulated GAL10 gene in a yeast strain deficient in NER [AMY3 (rad1Delta)]. In the active gene (cells grown in galactose), photoreactivation was fast in the NTS and slow in the TS demonstrating preferential repair of the NTS. In the inactive gene (cells grown in glucose), both strands were repaired at similar rates. This suggests that RNA polymerases II blocked at CPDs inhibit accessibility of CPDs to photolyase. In a strain in which both pathways are operational [W303-1a (RAD1)], no strand bias was observed either in the active or inactive gene, demonstrating that photoreactivation of the NTS compensates preferential repair of the TS by NER. Moreover, repair of the NTS was more quickly in the active gene than in the repressed gene indicating that transcription dependent disruption of chromatin facilitates repair of an active gene.

Full Text

The Full Text of this article is available as a PDF (131.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Cavalli G., Bachmann D., Thoma F. Inactivation of topoisomerases affects transcription-dependent chromatin transitions in rDNA but not in a gene transcribed by RNA polymerase II. EMBO J. 1996 Feb 1;15(3):590–597. [PMC free article] [PubMed] [Google Scholar]
  2. Cavalli G., Thoma F. Chromatin transitions during activation and repression of galactose-regulated genes in yeast. EMBO J. 1993 Dec;12(12):4603–4613. doi: 10.1002/j.1460-2075.1993.tb06149.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Donahue B. A., Yin S., Taylor J. S., Reines D., Hanawalt P. C. Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template. Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8502–8506. doi: 10.1073/pnas.91.18.8502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Friedberg E. C. Relationships between DNA repair and transcription. Annu Rev Biochem. 1996;65:15–42. doi: 10.1146/annurev.bi.65.070196.000311. [DOI] [PubMed] [Google Scholar]
  5. Gordon L. K., Haseltine W. A. Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus UV-specific endonucleases. J Biol Chem. 1980 Dec 25;255(24):12047–12050. [PubMed] [Google Scholar]
  6. Hanawalt P., Mellon I. Stranded in an active gene. Curr Biol. 1993 Jan;3(1):67–69. doi: 10.1016/0960-9822(93)90156-i. [DOI] [PubMed] [Google Scholar]
  7. Hsu D. S., Zhao X., Zhao S., Kazantsev A., Wang R. P., Todo T., Wei Y. F., Sancar A. Putative human blue-light photoreceptors hCRY1 and hCRY2 are flavoproteins. Biochemistry. 1996 Nov 5;35(44):13871–13877. doi: 10.1021/bi962209o. [DOI] [PubMed] [Google Scholar]
  8. Kassavetis G. A., Geiduschek E. P. RNA polymerase marching backward. Science. 1993 Feb 12;259(5097):944–945. doi: 10.1126/science.7679800. [DOI] [PubMed] [Google Scholar]
  9. Kim S. T., Malhotra K., Taylor J. S., Sancar A. Purification and partial characterization of (6-4) photoproduct DNA photolyase from Xenopus laevis. Photochem Photobiol. 1996 Mar;63(3):292–295. doi: 10.1111/j.1751-1097.1996.tb03028.x. [DOI] [PubMed] [Google Scholar]
  10. Leadon S. A., Lawrence D. A. Strand-selective repair of DNA damage in the yeast GAL7 gene requires RNA polymerase II. J Biol Chem. 1992 Nov 15;267(32):23175–23182. [PubMed] [Google Scholar]
  11. Li Y. F., Kim S. T., Sancar A. Evidence for lack of DNA photoreactivating enzyme in humans. Proc Natl Acad Sci U S A. 1993 May 15;90(10):4389–4393. doi: 10.1073/pnas.90.10.4389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Mellon I., Spivak G., Hanawalt P. C. Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell. 1987 Oct 23;51(2):241–249. doi: 10.1016/0092-8674(87)90151-6. [DOI] [PubMed] [Google Scholar]
  13. Sancar A. DNA excision repair. Annu Rev Biochem. 1996;65:43–81. doi: 10.1146/annurev.bi.65.070196.000355. [DOI] [PubMed] [Google Scholar]
  14. Sancar A. No "End of History" for photolyases. Science. 1996 Apr 5;272(5258):48–49. doi: 10.1126/science.272.5258.48. [DOI] [PubMed] [Google Scholar]
  15. Selby C. P., Drapkin R., Reinberg D., Sancar A. RNA polymerase II stalled at a thymine dimer: footprint and effect on excision repair. Nucleic Acids Res. 1997 Feb 15;25(4):787–793. doi: 10.1093/nar/25.4.787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Selby C. P., Sancar A. Mechanisms of transcription-repair coupling and mutation frequency decline. Microbiol Rev. 1994 Sep;58(3):317–329. doi: 10.1128/mr.58.3.317-329.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Selby C. P., Sancar A. Transcription preferentially inhibits nucleotide excision repair of the template DNA strand in vitro. J Biol Chem. 1990 Dec 5;265(34):21330–21336. [PubMed] [Google Scholar]
  18. Selby C. P., Sancar A. Transcription-repair coupling and mutation frequency decline. J Bacteriol. 1993 Dec;175(23):7509–7514. doi: 10.1128/jb.175.23.7509-7514.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Smerdon M. J., Thoma F. Site-specific DNA repair at the nucleosome level in a yeast minichromosome. Cell. 1990 May 18;61(4):675–684. doi: 10.1016/0092-8674(90)90479-x. [DOI] [PubMed] [Google Scholar]
  20. St John T. P., Davis R. W. The organization and transcription of the galactose gene cluster of Saccharomyces. J Mol Biol. 1981 Oct 25;152(2):285–315. doi: 10.1016/0022-2836(81)90244-8. [DOI] [PubMed] [Google Scholar]
  21. Suter B., Livingstone-Zatchej M., Thoma F. Chromatin structure modulates DNA repair by photolyase in vivo. EMBO J. 1997 Apr 15;16(8):2150–2160. doi: 10.1093/emboj/16.8.2150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Sutherland B. M., Bennett P. V. Human white blood cells contain cyclobutyl pyrimidine dimer photolyase. Proc Natl Acad Sci U S A. 1995 Oct 10;92(21):9732–9736. doi: 10.1073/pnas.92.21.9732. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. 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 U S A. 1992 Nov 15;89(22):10696–10700. doi: 10.1073/pnas.89.22.10696. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Todo T., Ryo H., Yamamoto K., Toh H., Inui T., Ayaki H., Nomura T., Ikenaga M. Similarity among the Drosophila (6-4)photolyase, a human photolyase homolog, and the DNA photolyase-blue-light photoreceptor family. Science. 1996 Apr 5;272(5258):109–112. doi: 10.1126/science.272.5258.109. [DOI] [PubMed] [Google Scholar]
  25. Todo T., Takemori H., Ryo H., Ihara M., Matsunaga T., Nikaido O., Sato K., Nomura T. A new photoreactivating enzyme that specifically repairs ultraviolet light-induced (6-4)photoproducts. Nature. 1993 Jan 28;361(6410):371–374. doi: 10.1038/361371a0. [DOI] [PubMed] [Google Scholar]
  26. Tornaletti S., Pfeifer G. P. Slow repair of pyrimidine dimers at p53 mutation hotspots in skin cancer. Science. 1994 Mar 11;263(5152):1436–1438. doi: 10.1126/science.8128225. [DOI] [PubMed] [Google Scholar]
  27. 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. 1994 Sep;14(9):6135–6142. doi: 10.1128/mcb.14.9.6135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Wood R. D. DNA repair in eukaryotes. Annu Rev Biochem. 1996;65:135–167. doi: 10.1146/annurev.bi.65.070196.001031. [DOI] [PubMed] [Google Scholar]
  29. Yasui A., Eker A. P., Yasuhira S., Yajima H., Kobayashi T., Takao M., Oikawa A. A new class of DNA photolyases present in various organisms including aplacental mammals. EMBO J. 1994 Dec 15;13(24):6143–6151. doi: 10.1002/j.1460-2075.1994.tb06961.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES