Effect of DNA lesions on transcription elongation

Biochimie

Volumn 81, Issue 1-2, 1999, Pages 139-146

  Tornaletti, Silvia ^a   Hanawalt, Philip C ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

RNA polymerase; Transcription coupled repair; Ultraviolet light

Indexed keywords

CELL DNA; DNA POLYMERASE; RNA POLYMERASE; TRANSCRIPTION FACTOR;

ANIMAL CELL; ARTICLE; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; EXCISION REPAIR; HUMAN; HUMAN CELL; NONHUMAN;

ANIMALIA; MAMMALIA;

EID: 0032738023     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0300-9084(99)80046-7     Document Type: Article

References (86)

1. 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. USA. 91:1994;8502-8506.
2. 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. 25:1997;787-793.
3. Wood R.D. DNA repair in eukaryotes. Annu. Rev. Biochem. 65:1996;135-167.
4. Sancar A. DNA excision repair. Annu. Rev. Biochem. 65:1996;43-81.
5. Friedberg E.C., Walker G.C., Siede W. DNA repair and mutagenesis. 1995;ASM Press, Washington D.C.
6. Friedberg E.C. Relationships between DNA repair and transcription. Annu. Rev. Biochem. 65:1996;15-42.
7. 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.
8. 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.
9. Christians F.C., Hanawalt P.C. Lack of transcription-coupled repair in mammalian ribosomal RNA genes. Biochemistry. 32:1993;10512-10518.
10. Vos J.M.H., Wauthier E.L. Differential introduction of DNA damage and repair in mammalian genes transcribed by RNA polymerases I and II. Mol. Cell. Biol. 11:1991;2245-2252.
11. Fritz L.K., Smerdon M.J. Repair of UV damage in actively transcribed ribosomal genes. Biochemistry. 34:1995;13117-13124.
12. Dammann R., Pfeifer G.P. Lack of gene and strand-specific DNA repair in RNA polymerase III-transcribed human tRNA genes. Mol. Cell. Biol. 17:1997;219-229.
13. Carreau M., Hunting D. Transcription-dependent and independent DNA excision repair pathways in human cells. Mutat. Res. 274:1992;57-64.
14. Christians F.C., Hanawalt P.C. Inhibition of transcription and strand-specific DNA repair by α-amanitin in Chinese hamster ovary cells. Mutat. Res. 274:1992;93-101.
15. Leadon S.A., Lawrence D.A. Preferential repair of DNA damage on the transcribed strand of the human metallothionein genes requires RNA polymerase II. Mutat. Res. 255:1991;67-78.
16. 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.
17. 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.
18. Lommel L., Carswell-Crumpton C., Hanawalt P.C. Preferential repair of the transcribed DNA strand in the dihydrofolate reductase gene throughout the cell cycle in UV-irradiated human cells. Mutat. Res. 336:1995;181-192.
19. Ford J.M., Hanawalt P.C. expression of wildtype p53 is required for efficient global genomic nucleotide excision repair in the nontranscribed strand of an active gene. J. Biol. Chem. 272:1997;28073-28080.
20. Hwang B.J., Ford J.M., Hanawalt P.C., Chu G. Expression of the p48 xeroderma pigmentosum gene is p53 dependent and involved in global genomic repair. Proc. Natl. Acad. Sci. USA. 96:1998;447-452.
21. Yamaizumi M., Sugano T. U. V.-induced nuclear accumulation of p53 is evoked through DNA damage of actively transcribed genes independent of the cell cycle. Oncogene. 9:1994;2775-2784.
22. Ljungman M., Zhang F. Blockage of RNA polymerase as a possible trigger for u.v. light-induced apoptosis. Oncogene. 13:1996;823-831.
23. Sugasawa K., Ng J.M.Y., Musutani C., van derSpek P.J., Eker A.P.M., Hanaoka F., Bootsma D., Hoeijmakers J.H.J. Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Mol. Cell. 2:1998;223-232.
24. Bowman K.K., Smith C.A., Hanawalt P.C. Excision-repair patch lengths are similar for transcription-coupled repair and global genome repair in UV-irradiated human-cells. Mutat. Res. 385:1997;95-105.
25. Wood R.D. DNA damage recognition during nucleotide excision repair in mammalian cells. Biochimie. 81:1999;39-44.
26. Mellon I., Bohr V.A., Smith A.C., Hanawalt P.C. Preferential DNA repair of an active gene in human cells. Proc. Natl. Acad. Sci. USA. 83:1986;8878-8882.
27. Mellon I., Hanawalt P.C. Induction of the Escherichia colilactose operon selectively increases repair of its transcribed DNA strand. Nature. 342:1989;95-98.
28. Selby C.B., Witkin E.M., Sancar A. Escherichia coli mfdmutant deficient in 'mutation frequency decline' lacks strand-specific repair: In vitro complementation with purified coupling factor. Proc. Natl. Acad. Sci. USA. 88:1991;11574-11578.
29. Selby C.P., Sancar A. Molecular mechanism of transcription-repair coupling. Science. 260:1993;53-58.
30. Troelstra C., VanGool A., Wit J.D., Vermeulen W., Bootsma D., Hoeijmakers J.H.J. ERCC6a member of a subfamily of putative helicases, is involved in Cockayne's syndrome and preferential repair of active genes. Cell. 71:1992;939-953.
31. Eisen J.A., Sweder K.S., Hanawalt P.C. Evolution of the SNF2 family of proteins: Subfamilies with distinct sequences and functions. Nucleic Acids Res. 23:1995;2715-2723.
32. Liu M., Xie Z., Price D.H. A human RNA polymerase II trascription termination factor is a SW12/SNF2 family member. J. Biol. Chem. 273:1998;25541-25544.
33. Tu Y., Bates S., Pfeifer G.P. Sequence-specific and domain-specific DNA repair in xeroderma pigmentosum and Cockayne syndrome cells. J. Biol. Chem. 272:1997;20747-20755.
34. Tijsterman M., Verhage R.A., van de Putte P., Tasseron-deJong J.G., Brouwer J. Transitions in the coupling of transcription and nucleotide excision repair within RNA polymerase II-transcribed genes of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 94:1997;8027-8032.
35. Tu Y., Bates S., Pfeifer G.P. The transcription-repair coupling factor CSA is required for efficient repair only during the elongation stages of RNA polymerase II transcription. Mutat. Res. 400:1998;143-151.
36. Tantin D. RNA Polymerase II elongation complexes containing the Cockayne Syndrome group B protein interact with a molecular complex containing the transcription factor IIH components xeroderma pigmentosum B and p62. J. Biol. Chem. 273:1998;27794-27799.
37. Mellon I., Champe G.N. Products of DNA mismatch repair genes mutS and mutL are required for transcription-coupled nucleotide-excision repair of the lactose operon in Escherichia coli. Proc. Natl. Acad. Sci. USA. 93:1996;1292-1297.
38. Mellon I., Rajpal D.K., Koi M., Boland C.R., Champe G.N. Transcription-coupled repair deficiency and mutations in human mismatch repair genes. Science. 272:1996;557-560.
39. Sweder K.S., Verhage R.A., Crowley D.J., Crouse G.F., Brouwer J., Hanawalt P.C. Mismatch repair mutants in yeast are not defective in transcription-coupled DNA repair of UV-induced DNA damage. Genetics. 143:1996;1127-1135.
40. Shi Y.B., Gamper H., Hearst J. Interaction of T7 RNA polymerase with DNA in an elongation complex arrested at a specific psoralen adduct site. J. Mol. Biol. 263:1988;527-534.
41. Shi Y.B., Gamper H., Van Houten B., Hearst J.E. Interaction of Escherichia coliRNA polymerase with DNA in an elongation complex arrested at a specific psoralen crosslink site. J. Mol. Biol. 199:1988b;277-293.
42. Hatahet Z., Purmal A.A., Wallace S.S. Oxidative DNA lesions as blocks to in vitro transcription by phage T7 RNA polymerase. Ann. NY Acad. Sci. 726:1994;346-348.
43. Zhou W., Doetsch P.W. Effects of abasic sites and DNA single-strand breaks on prokaryotic RNA polymerases. Proc. Natl. Acad. Sci. USA. 90:1993;6601-6605.
44. Chen Y.H., Bogenhagen D.F. Effects of DNA lesions on transcription elongation by T7 RNA polymerase. J. Biol. Chem. 268:1993;5849-5855.
45. Choi D.J., Roth R.B., Liu T., Geacinkov N.E., Scicchitano D. Incorrect base insertion and prematurely terminated transcripts during T7 RNA polymerase transcription elongation past benzo[a]pyrenediol epoxide-modified DNA. J. Mol. Biol. 264:1996;213-219.
46. Viswanathan A., Doetsch P.W. Effects of nonbulky DNA base damages on Escherichia coliRNA polymerase-mediated elongation and promoter clearance. J. Biol. Chem. 273:1998;21276-21281.
47. Zhou W., Doetsch P.W. Transcription bypass or blockage at single-strand breaks on the DNA template strand: effect of different 3' and 5' flanking groups on the T7 RNA polymerase elongation complex. Biochemistry. 33:1994;14926-14934.
48. Zhou W., Reines D., Doetsch P.W. T7 RNA polymerase bypass of large gaps on the template strand reveals a critical role of the nontemplate strand in elongation. Cell. 82:1995;577-585.
49. Liu J., Doetsch P.W. Template strand gap bypass is a general property of prokaryotic RNA polymerases: implications for elongation mechanisms. Biochemistry. 35:1996;14999-15008.
50. Tornaletti S., Donahue B.A., Reines D., Hanawalt P.C. Nucleotide sequence context effect of a cyclobutane pyrimidine dimer upon RNA polymerase II elongation. J. Biol. Chem. 272:1997;31719-31724.
51. Tommasi S., Swiderski P.M., Tu Y., Kaplan B.E., Pfeifer G.P. Inhibition of transcription factor binding by ultraviolet-induced pyrimidine dimers. Biochemistry. 35:1996;15693-15703.
52. Mann D.B., Springer D.L., Smerdon M.J. DNA damage can alter the stability of nucleosomes: effects are dependent on damage type. Proc. Natl. Acad. Sci. USA. 94:1997;2215-2220.
53. Donahue B.A., Fuchs R.P., Reines D., Hanawalt P.C. Effects of aminofluorene and acetylaminofluorene DNA adducts on transcriptional elongation by RNA polymerase II. J. Biol. Chem. 271:1996;10588-10594.
54. Tang M., Bohr V.A., Zhang X., Pierce J., Hanawalt P.C. Quantification of aminofluorene adduct formation and repair in defined DNA sequences in mammalian cells using the UVRABC nuclease. J. Biol. Chem. 264:1989;14455-14462.
55. Tang M.S., Qian M., Pao A. Formation and repair of antitumor antibiotic CC-1065-induced DNA adducts in the adenine phosphoribosyltransferase and amplified dihydrofolate reductase genes of Chinese hamster ovary cells. Biochemistry. 33:1994;2726-2732.
56. Tang M.S., Pao A., Zhang X.S. Repair of benzo(a)pyrene diol epoxide- and UV-induced DNA damage in dihydrofolate reductase and adeninephosphoribosyltransferase genes of CHO cells. J. Biol. Chem. 269:1994;12749-12754.
57. Chen R.H., Maher V.M., Brouwer J., van de Putte P., McCormick J.J. Preferential repair and strand-specific repair of benzo[a]pyrene diol epoxide adducts in the HPRT gene of diploid human fibroblasts. Proc. Natl. Acad. Sci USA. 89:1992;5413-5417.
58. Uptain S.M., Kane C.M., Chamberlin M.J. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66:1997;117-172.
59. Wang Z., Rana T.M. DNA damage-dependent transcriptional arrest and termination of RNA polymerase II elongation complexes in DNA template containing HIV-1 promoter. Proc. Natl. Acad. Sci USA. 94:1997;6688-6693.
60. Islas A.L., Baker F.J., Hanawalt P.C. Transcription-coupled repair of psoralen cross-links but not monoadducts in Chinese hamster ovary cells. Biochemistry. 33:1994;10794-10799.
61. Scicchitano A., Hanawalt P.C. Repair of N-mehylpurines in specific DNA sequences in Chinese hamster ovary cells: absence of strand specificity in the dihydrofolate reductase gene. Proc. Natl. Acad. Sci. USA. 86:1989;3050-3054.
62. Wang W., Sitaram A., Scicchitano D. 3-Methyladenine and 7-methylguanine exibit no preferential removal from the transcribed strand of the dihydrofolate reductase gene in Chinese hamster ovary B11 cells. Biochemistry. 34:1995;1798-1804.
63. Sitaram A., Plitas G., Wang W., Scicchitano D. Functional nucleotide excision repair is required for the preferential removal of N-ethylpurines from the transcribed strand of the dihydrofolate reductase gene of Chinese hamster ovary cells. Mol. Cell. Biol. 17:1997;564-570.
64. Leadon S.A., Cooper P.K. Preferential repair of ionizing radiation-induced damage in the transcribed strand of an active human gene is defective in Cockayne syndrome. Proc. Natl. Acad. Sci. USA. 90:1993;10499-10503.
65. Cooper P.K., Nouspikel T., Clarkson S.G., Leadon S.A. Defective transcription-coupled repair of oxidative base damage in Cockayne syndrome patients from XP group G. Science. 275:1997;990-993.
66. Kerppola T.K., Kane C.M. Analysis of the signals for transcription termination by purified RNA polymerase II. Biochemistry. 29:1990;269-278.
67. Rice G.A., Kane C.M., Chamberlin M.J. Footprinting analysis of mammalian RNA polymerase II along its transcript: an alternative view of transcription elongation. Proc. Natl. Acad. Sci. USA. 88:1991;4245-4249.
68. Mote J.J., Ghanouni P., Reines D. A DNA minor groove-binding ligand both potentiates and arrests transcription by RNA polymerase II. Elongation factor SII enables readthrough at arrest sites. J. Mol. Biol. 236:1994;725-737.
69. Reines D., Mote J.J. Elongation factor SII-dependent transcription by RNA polymerase II through a sequence-specific DNA-binding protein. Proc. Natl. Acad. Sci. USA. 90:1993;1917-1921.
70. Christie K.R., Awrey D.E., Edwards A.M., Kane C.M. Purified yeast RNA polymerase II reads through intrinsic blocks to elongation in response to the yeast TFIIS analogue, P37. J. Biol. Chem. 269:1994;936-943.
71. Sluder A.E., Greenleaf A., Price D.H. Properties of a DrosophilaRNA polymerase II elongation factor. J. Biol. Chem. 264:1989;8963-8969.
72. Reines D. RNA polymerase II elongation complex. Elongation complexes purified using an anti-RNA antibody do not contain initiation factor alpha. J. Biol. Chem. 266:1991;10510-10517.
73. Izban M.G., Luse D.S. The RNA polymerase II ternary complex cleaves the nascent transcript in a 3'-5' direction in the presence of elongation factor SII. Genes Dev. 6:1992;1342-1356.
74. Wang D., Hawley D.K. Identification of a 3'→5' exonuclease activity associated with human RNA polymerase II. Proc. Natl. Acad. Sci. USA. 90:1993;843-847.
75. Archambault J., Lacroute F., Ruet A., Friesen J.D. Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II. Mol. Cell. Biol. 12:1992;4142-4152.
76. Thomas M.J., Platas A.A., Hawley D.K. Transcriptional fidelity and proofreading by RNA polymerase II. Cell. 93:1998;627-637.
77. Gu W., Powell W., Mote J.J., Reines D. Nascent RNA cleavage by arrested RNA polymerase II does not require upstream translocation of the elongation complex on DNA. J. Biol. Chem. 268:1993;25604-25616.
78. Chamberlin M.J. New models for the mechanism of transcription elongation and its regulation. Harvey Lect. Series. 88:1995;1-21.
79. Nudler E., Goldfarb A., Kashlev M. Discontinuous mechanism of transcription elongation. Science. 265:1994;793-796.
80. Wang D., Meier T.I., Chan C.L., Feng G., Lee D.N., Landick R. Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex. Cell. 81:1995;341-350.
81. Landick R. RNA polymerase slides home: pause and termination site recognition. Cell. 88:1997;741-744.
82. Hanawalt P.C. Transcription-coupled repair and human diseases. Science. 266:1994;1957-1958.
83. Verhage R.A., Heyn J., van de Putte P. Brouwer, Transcription elongation factor S-II is not required for transcription-coupled repair in yeast. Mol. Gen. Genet. 254:1997;284-290.
84. Bregman D.B., Halaban R., VanGool A.J., Henning K.A., Friedberg E.C., Warren S.L. UV-induced ubiquitubation if RNA polymerase II: a novel modification deficient in Cockayne syndrome cells. Proc. Natl. Acad. Sci. USA. 93:1996;11586-11590.
85. Ratner J.N., Balasubramanian B., Corden J., Warren S.L., Bregman D.B. Ultraviolet-induced ubiquitination and proteasomal degradation of the large subunit of RNA polymerase II. J. Biol. Chem. 273:1998;5184-5189.
86. Selby C.P., Sancar A. Cockayne syndrome group B protein enhances elongation by RNA polymerase II. Proc. Natl. Acad. Sci. USA. 94:1997;11205-11209.