Transcriptional effects on double-strand break-induced gene conversion tracts

Mutation Research - DNA Repair

Volumn 461, Issue 2, 2000, Pages 119-132

  Weng, Yi shin ^a   Xing, Dongxia ^a   Clikeman, Jennifer A ^b   Nickoloff, Jac A ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

Author keywords

Heteroduplex DNA; Homologous recombination; Mismatch repair; Saccharomyces cerevisiae

Indexed keywords

HETERODUPLEX;

ALLELE; BASE MISPAIRING; DNA REPAIR; DNA STRAND BREAKAGE; GENE CONVERSION; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; NONHUMAN; PLASMID; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 0034676225     PISSN: 09218777     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0921-8777(00)00043-4     Document Type: Article

References (80)

1. T.D. Petes, R.E. Malone, L.S. Symington, Recombination in yeast, in: J.R. Broach, J.R. Pringle, E.W. Jones (Eds.), The Molecular and Cellular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1991, pp. 407-521.
2. Bhattacharyya N.P., Maher V.M., McCormick J.J. Effect of nucleotide excision repair in human cells on intrachromosomal homologous recombination induced by UV and 1-nitrosopyrene. Mol. Cell. Biol. 10:1990;3945-3951.
3. Deng W.P., Nickoloff J.A. Preferential repair of UV damage in highly transcribed DNA diminishes UV-induced intrachromosomal recombination in mammalian cells. Mol. Cell. Biol. 14:1994;391-399.
4. Nairn R.S., Adair G.M., Christmann C.B., Humphrey R.M. Ultraviolet stimulation of intermolecular homologous recombination in Chinese hamster ovary cells. Mol. Carcinog. 4:1991;519-526.
5. Tsujimura T., Maher V.M., Godwin A.R., Liskay R.M., McCormick J.J. Frequency of intrachromosomal homologous recombination induced by UV radiation in normally repairing and excision repair-deficient human cells. Proc. Natl. Acad. Sci. U. S. A. 87:1990;1566-1570.
6. Resnick M.A. The induction of molecular and genetic recombination in eukaryotic cells. Adv. Radiat. Biol. 8:1979;175-217.
7. Benjamin M.B., Little J.B. X rays induce interallelic homologous recombination at the human thymidine kinase gene. Mol. Cell. Biol. 12:1992;2730-2738.
8. Nickoloff J.A., Singer J.D., Hoekstra M.F., Heffron F. Double-strand breaks stimulate alternative mechanisms of recombination repair. J. Mol. Biol. 207:1989;527-541.
9. Ray A., Machin N., Stahl F.W. A DNA double chain break stimulates triparental recombination in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 86:1989;6225-6229.
10. Lin F.-L., Sperle K., Sternberg N. Repair of double-stranded breaks by homologous fragments during transfer of DNA into mouse L cells. Mol. Cell. Biol. 10:1990;113-119.
11. Rouet P., Smith F., Jasin M. Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 91:1994;6064-6068.
12. Choulika A., Perrin A., Dujon B., Nicolas J.-F. Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol. Cell. Biol. 15:1995;1968-1973.
13. Droge P. Transcription-driven site-specific DNA recombination in vitro. Proc. Natl. Acad. Sci. U. S. A. 90:1993;2759-2763.
14. Nault C., Veilleux S., Delbecchi L., Bourgaux-Ramoisy D., Bourgaux P. Intramolecular recombination in polyomavirus DNA is controlled by promoter elements. Nucleic Acids Res. 22:1994;485-491.
15. Klar A.J.S., Strathern J.N., Hicks J.B. A position-effect control for gene transposition: state of the expression of yeast mating-type genes affects their ability to switch. Cell. 25:1981;517-524.
16. Alt F.W., Blackwell T.K., Yancopoulos G.D. Development of the primary antibody repertoire. Science. 238:1987;1079-1087.
17. Blackwell T.K., Moore M.W., Yancopoulos G.D., Suh H., Lutzker S., Selsing E., Alt F.W. Recombination between immunoglobulin variable region gene segments is enhanced by transcription. Nature. 324:1986;585-589.
18. Bottaro A., Lansford R., Xu L., Zhang J., Rothman P., Alt F.W. S region transcription per se promotes basal IgE class switch recombination but additional factors regulate the efficiency of the process. EMBO J. 13:1994;665-674.
19. Leung H., Maizels N. Transcriptional regulatory elements stimulate recombination in extrachromosomal substrates carrying immunoglobulin switch-region sequences. Proc. Natl. Acad. Sci. U. S. A. 89:1992;4154-4158.
20. Xu L., Gorham B., Li S.C., Bottaro A., Alt F.W., Rothman P. Replacement of germ-line epsilon promoter by gene targeting alters control of immunoglobulin heavy chain class switching. Proc. Natl. Acad. Sci. U. S. A. 90:1993;3705-3709.
21. McArthur J.G., Beitel L.K., Chamberlain J.W., Stanners C.P. Elements which stimulate gene amplification in mammalian cells: role of recombinogenic sequences/structures and transcriptional activation. Nucleic Acids Res. 19:1991;2477-2484.
22. J.D. Boeke, S.B. Sandmeyer, Yeast transposable elements, in: J.R. Broach, J.R. Pringle, E.W. Jones (Eds.), The Molecular and Cellular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1991, pp. 193-261.
23. Branciforte D., Martin S.L. Developmental and cell type specificity of LINE-1 expression in mouse testis: implications for transposition. Mol. Cell. Biol. 14:1994;2584-2592.
24. Melamed C., Nevo Y., Kupiec M. Involvement of cDNA in homologous recombination between Ty elements in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:1992;1613-1620.
25. Derr L.K., Strathern J.N. A role for reverse transcripts in gene conversion. Nature. 361:1993;170-173.
26. Nevo-Caspi Y., Kupiec M. Transcriptional induction of Ty recombination in yeast. Proc. Natl. Acad. Sci. U. S. A. 91:1994;12711-12715.
27. Voelkel-Meiman K., Roeder G.S. Gene conversion tracts stimulated by HOT1-promoted transcription are long and continuous. Genetics. 126:1990;851-867.
28. Voelkel-Meiman K., Roeder G.S. A chromosome containing HOT1 preferentially receives information during mitotic interchromosomal gene conversion. Genetics. 124:1990;561-572.
29. Thomas B.J., Rothstein R. Elevated recombination rates in transcriptionally active DNA. Cell. 56:1989;619-630.
30. Nickoloff J.A. Transcription enhances intrachromosomal homologous recombination in mammalian cells. Mol. Cell. Biol. 12:1992;5311-5318.
31. Nickoloff J.A., Reynolds R.J. Transcription stimulates homologous recombination in mammalian cells. Mol. Cell. Biol. 10:1990;4837-4845.
32. White M.A., Detloff P., Strand M., Petes T.D. A promoter deletion reduces the rate of mitotic, but not meiotic, recombination at the HIS4 locus in yeast. Curr. Genet. 21:1992;109-116.
33. Grimm C., Schaer P., Munz P., Kohli J. The strong ADH1 promoter stimulates mitotic and meiotic recombination at the ADE6 gene of Schizosaccharomyces pombe. Mol. Cell. Biol. 11:1991;289-298.
34. Bratty J., Ferbeyre G., Molinaro C., Cedergren R. Stimulation of mitotic recombination upon transcription from the yeast GAL1 promoter but not from other RNA polymerase I, II and III promoters. Curr. Genet. 30:1996;381-388.
35. Piruat J.I., Aguilera A. A novel yeast gene, THO2, is involved in RNA POLII transcription and provides new evidence for transcriptional elongation-associated recombination. EMBO J. 17:1998;4859-4872.
36. Chavez S., Aguilera A. The yeast HPR1 gene has a functional role in transcriptional elongation that uncovers a novel source of genome instability. Genes Dev. 11:1997;3459-3470.
37. Ikeda H., Matsumoto T. Transcription promotes recA-independent recombination mediated by DNA-dependent RNA polymerase in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 76:1979;4571-4575.
38. McCormack W.T., Thompson C.B. Chicken IgL variable region gene conversions display pseudogene donor preference and 5′ to 3′ polarity. Genes Dev. 4:1990;548-558.
39. Kotani H., Kmiec E.B. A role for RNA synthesis in homologous pairing events. Mol. Cell. Biol. 14:1994;6097-6106.
40. Kotani H., Kmiec E.B. Transcription activates RecA-promoted homologous pairing of nucleosomal DNA. Mol. Cell. Biol. 14:1994;1949-1955.
41. White M.A., Dominska M., Petes T.D. Transcription factors are required for the meiotic recombination hotspot at the HIS4 locus in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 90:1993;6621-6625.
42. White M.A., Wierdl M., Detloff P., Petes T.D. DNA-binding protein RAP1 stimulates meiotic recombination at the HIS4 locus in yeast. Proc. Natl. Acad. Sci. U. S. A. 88:1991;9755-9759.
43. Kon N., Krawchuk M.D., Warren B.G., Smith G.R., Wahls W.P. Transcription factor Mts1/Mts2 (Atf1/Pcr1, Gad7/Pcr1) activates the M26 meiotic recombination hotspot in Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. U. S. A. 94:1997;13765-13770.
44. Kirkpatrick D.T., Fan Q.P., Petes T.D. Maximal stimulation of meiotic recombination by a yeast transcription factor requires the transcription activation domain and a DNA-binding domain. Genetics. 152:1999;101-115.
45. Maldonado E., Shiekhattar R., Sheldon M., Cho H., Drapkin R., Rickert P., Lees E., Anderson C.W., Linn S., Reinberg D. A human RNA polymerase II complex associated with SRB and DNA repair proteins. Nature. 381:1996;86-89.
46. Scully R., Anderson S.F., Chao D.M., Wei W.J., Ye L.Y., Young R.A., Livingston D.M., Parvin J.D. BRCA1 is a component of the RNA polymerase II holoenzyme. Proc. Natl. Acad. Sci. U. S. A. 94:1997;5605-5610.
47. Hannan R.D., Cavanaugh A., Hempel W.M., Moss T., Rothblum L. Identification of a mammalian RNA polymerase I holoenzyme containing components of the DNA repair/replication system. Nucleic Acids Res. 27:1999;3720-3727.
48. deLaat W.L., Jaspers N.G.J., Hoeijmakers J.H.J. Molecular mechanism of nucleotide excision repair. Genes Dev. 13:1999;768-785.
49. Gowen L.C., Avrutskaya A.V., Latour A.M., Koller B.H., Leadon S.A. BRCA1 required for transcription-coupled repair of oxidative DNA damage. Science. 281:1998;1009-1012.
50. Taghian D.G., Nickoloff J.A. Chromosomal double-strand breaks induce gene conversion at high frequency in mammalian cells. Mol. Cell. Biol. 17:1997;6386-6393.
51. Nag D.K., Petes T.D. Meiotic recombination between dispersed repeated genes is associated with heteroduplex formation. Mol. Cell. Biol. 10:1990;4420-4423.
52. Nag D.K., Petes T.D. Physical detection of heteroduplexes during meiotic recombination in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 13:1993;2324-2331.
53. Ray B.L., White C.I., Haber J.E. Heteroduplex formation and mismatch repair of the 'stuck' mutation during mating-type switching in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:1991;5372-5380.
54. Weng Y.-s., Nickoloff J.A. Evidence for independent mismatch repair processing on opposite sides of a double-strand break in Saccharomyces cerevisiae. Genetics. 148:1998;59-70.
55. Nickoloff J.A., Sweetser D.B., Clikeman J.A., Khalsa G.J., Wheeler S.L. Multiple heterologies increase mitotic double-strand break-induced allelic gene conversion tract lengths in yeast. Genetics. 153:1999;665-679.
56. 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. U. S. A. 93:1996;1292-1297.
57. 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.
58. Leadon S.A., Avrutskaya A.V. Differential involvement of the human mismatch repair proteins, hMLH1 and hMSH2, in transcription-coupled repair. Cancer Res. 57:1997;3784-3791.
59. 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 repair of UV-induced DNA damage. Genetics. 143:1996;1127-1135.
60. Leadon S.A., Avrutskaya A.V. Requirement for DNA mismatch repair proteins in the transcription-coupled repair of thymine glycols in Saccharomyces cerevisiae. Mutat. Res. 407:1998;177-187.
61. Sweetser D.B., Hough H., Whelden J.F., Arbuckle M., Nickoloff J.A. Fine-resolution mapping of spontaneous and double-strand break-induced gene conversion tracts in Saccharomyces cerevisiae reveals reversible mitotic conversion polarity. Mol. Cell. Biol. 14:1994;3863-3875.
62. Cho J.W., Khalsa G.J., Nickoloff J.A. Gene conversion tract directionality is influenced by the chromosome environment. Curr. Genet. 34:1998;269-279.
63. Nickoloff J.A., Reynolds R.J. Subcloning with new ampicillin and kanamycin resistant analogs of pUC9. Biotechniques. 10:1991;469-472.
64. Rothstein R.J. One-step gene disruption in yeast. Methods Enzymol. 101:1983;202-211.
65. Scherer S., Davis R.W. Replacement of chromosome segments with altered DNA sequences constructed in vitro. Proc. Natl. Acad. Sci. U. S. A. 76:1979;4951-4955.
66. Kohrer K., Domday H. Preparation of high molecular weight RNA. Methods Enzymol. 194:1991;398-405.
67. Weng Y.-s., Whelden J., Gunn L., Nickoloff J.A. Double-strand break-induced gene conversion: examination of tract polarity and products of multiple recombinational repair events. Curr. Genet. 29:1996;335-343.
68. Hill A., Bloom K. Genetic manipulation of centromere function. Mol. Cell. Biol. 7:1987;2397-2405.
69. Nickoloff J.A., Chen E.Y.C., Heffron F. A 24-base-pair sequence from the MAT locus stimulates intergenic recombination in yeast. Proc. Natl. Acad. Sci. U. S. A. 83:1986;7831-7835.
70. Ray A., Siddiqi I., Kolodkin A.L., Stahl F.W. Intrachromosomal gene conversion induced by a DNA double-strand break in Saccharomyces cerevisiae. J. Mol. Biol. 201:1988;247-260.
71. Nickoloff J.A., Singer J.D., Heffron F. In vivo analysis of the Saccharomyces cerevisiae HO nuclease recognition site by site-directed mutagenesis. Mol. Cell. Biol. 10:1990;1174-1179.
72. Rudin N., Haber J.E. Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences. Mol. Cell. Biol. 8:1988;3918-3928.
73. Rudin N., Sugarman E., Haber J.E. Genetic and physical analysis of double-strand break repair and recombination in Saccharomyces cerevisiae. Genetics. 122:1989;519-534.
74. McGill C.B., Shafer B.K., Derr L.K., Strathern J.N. Recombination initiated by double-strand breaks. Curr. Genet. 23:1993;305-314.
75. J.A. Nickoloff, M.F. Hoekstra, Double-strand break and recombinational repair in Saccharomyces cerevisiae, in: J.A. Nickoloff, M.F. Hoekstra (Eds.), DNA Damage and Repair, Vol. 1, DNA Repair in Prokaryotes and Lower Eukaryotes, Humana Press, Totowa, NJ, 1998, pp. 335-362.
76. Gilbertson L.A., Stahl F.W. A test of the double-strand break repair model for meiotic recombination in Saccharomyces cerevisiae. Genetics. 144:1996;27-41.
77. Nelson H.H., Sweetser D.B., Nickoloff J.A. Effects of terminal nonhomology and homeology on double-strand break-induced gene conversion tract directionality. Mol. Cell. Biol. 16:1996;2951-2957.
78. Ahn B.-Y., Dornfeld K.J., Fagrelius T.J., Livingston D.M. Effect of limited homology on gene conversion in a Saccharomyces cerevisiae plasmid recombination system. Mol. Cell. Biol. 8:1988;2442-2448.
79. Haber J.E., Ray B.L., Kolb J.M., White C.I. Rapid kinetics of mismatch repair of heteroduplex DNA that is formed during recombination in yeast. Proc. Natl. Acad. Sci. U. S. A. 90:1993;3363-3367.
80. McGill C., Shafer B., Strathern J. Coconversion of flanking sequences with homothallic switching. Cell. 57:1989;459-467.