Involvement of ERCC1/XPF and XPG in oligodeoxynucleotide-directed gene modification

Oligonucleotides

Volumn 16, Issue 1, 2006, Pages 94-104

  Igoucheva, Olga ^a   Alexeev, Vitali ^a   Scharer, Orlando ^b   Yoon, Kyonggeun ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

^b STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; EXCISION REPAIR CROSS COMPLEMENTING PROTEIN 1; OLIGODEOXYNUCLEOTIDE; PLASMID DNA; PROTEIN XPF; PROTEIN XPG; RNA POLYMERASE; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; DNA MODIFICATION; DNA REPAIR; DNA STRAND; EPISOME; EXCISION REPAIR; GENE ACTIVITY; GENE INDUCTION; GENE TARGETING; GENETIC COMPLEMENTATION; GENETIC TRANSCRIPTION; MISMATCH REPAIR; MODEL; MOUSE; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

ANIMALS; BASE PAIR MISMATCH; CELL LINE; DNA REPAIR; DNA-BINDING PROTEINS; ENDONUCLEASES; GENE TARGETING; HUMANS; NUCLEAR PROTEINS; OLIGONUCLEOTIDES; PLASMIDS; TRANSCRIPTION FACTORS;

ANIMALIA;

EID: 33645800191     PISSN: 15454576     EISSN: None     Source Type: Journal    
DOI: 10.1089/oli.2006.16.94     Document Type: Article

References (38)

1. ANDERSEN, M.S., SORENSEN, C.B., BOLUND, L., and JENSEN, T.G. (2002). Mechanisms underlying targeted gene correction using chimeric RNA/DNA and single-stranded DNA oligonucleotides. J. Mol. Med. 80, 770-781.
2. BROOKMAN, K.W., LAMERDIN, I.E., THELEN, M.P., HWANG, M., REARDON, J.T., SANCAR, A., ZHOU, Z.Q., WALTER, C.A., PARRIS, C.N., and THOMPSON, L.H. (1996). ERCC4 (XPF) encodes a human nucleotide excision repair protein with eukaryotic recombination homologs. Mol. Cell. Biol. 16, 6553-6562.
3. CHIU, S.K., LOW, K.B., YUAN, A., and RADDING, C.M. (1997). Resolution of an early RecA-recombination intermediate by a junction-specific endonuclease. Proc. Natl. Acad. Sci. USA 94, 6079-6083.
4. COLE-STRAUSS, A., GAMPER, H., HOLLOMAN, W.K., MUNOZ, M., CHENG, N., and KMIEC, E.B. (1999). Targeted gene repair directed by the chimeric RNA/DNA oligonucleotide in a mammalian cell-free extract. Nucleic Acids Res. 27, 1323-1330.
5. DEKKER, M., BROUWERS, C., and TE RIELE, H. (2003). Targeted gene modification in mismatch-repair-deficient embryonic stem cells by single-stranded DNA oligonucleotides. Nucleic Acids Res. 31, e27.
6. DUNAND-SAUTHIER, I., HOHL, M., THOREL, F., JAQUIER-GUBLER, P., CLARKSON, S.G., and SCHARER, O.D. (2005). The spacer region of XPG mediates recruitment to nucleotide excision repair complexes and determines substrate specificity. J. Biol. Chem. 280, 7030-7037.
7. ENZLIN, J.H., and SCHARER, O.D. (2002). The active site of the DNA repair endonuclease XPF-ERCC1 forms a highly conserved nuclease motif. EMBO J. 21, 2045-2053.
8. EVANS, E., and ALANI, E. (2000). Roles for mismatch repair factors in regulating genetic recombination. Mol. Cell. Biol. 20 ,7839-7844.
9. GAMPER, H.B., Jr., COLE-STRAUSS, A., METZ, R., PAREKH, H., KUMAR, R., and KMIEC, E.B. (2000). A plausible mechanism for gene correction by chimeric oligonucleotides. Biochemistry 39, 5808-5816.
10. HANAWALT, P.C., FORD, J.M., and LLOYD, D.R. (2003). Functional characterization of global genomic DNA repair and its implications for cancer. Mutat. Res. 544, 107-114.
11. HOHL, M., THOREL, F., CLARKSON, S.G., and SCHARER, O.D. (2003). Structural determinants for substrate binding and catalysis by the structure-specific endonuclease XPG. J. Biol. Chem. 278, 19500-19508.
12. IGOUCHEVA, O., ALEXEEV, V., PRYCE, M., and YOON, K. (2003). Transcription affects formation and processing of intermediates in oligonucleotide-mediated gene alteration. Nucleic Acids Res. 31, 2659-2670.
13. IGOUCHEVA, O., ALEXEEV, V., and YOON, K. (2001). Targeted gene correction by small single-stranded oligonucleotides in mammalian cells. Gene Ther. 8, 391-399.
14. IGOUCHEVA, O., ALEXEEV, V., and YOON, K. (2004a). Mechanism of gene repair open for discussion. Oligonucleotides 14, 311-321.
15. IGOUCHEVA, O., ALEXEEV, V., and YOON, K. (2004b). Oligonucleotide- directed mutagenesis and targeted gene correction: A mechanistic point of view. Curr. Mol. Med. 4, 445-463.
16. IGOUCHEVA, O., ALEXEEV, V., and YOON, K. (2006). Differential cellular responses to exogenous DNA in mammalian cells and its effect on oligonucleotide-directed gene modification. Gene Ther. 13, 266-275.
17. IGOUCHEVA, O., PERITZ, A.E., LEVY, D., and YOON, K. (1999). A sequence-specific gene correction by an RNA-DNA oligonucleotide in mammalian cells characterized by transfection and nuclear extract using a lacZ shuttle system. Gene Ther. 6, 1960-1971.
18. IGOUCHEVA, O., and YOON, K. (2005). Gene targeting by oligonucleotides in keratinocytes. Methods Mol. Biol. 289, 287-302.
19. KREN, B.T., and STEER, C.J. (2002). The application of DNA repair vectors to gene therapy. Curr. Opin. Biotechnol. 13, 473-481.
20. LI, X.T., COSTANTINO, N., LU, L.Y., LIU, D.P., WATT, R.M., CHEAH, K.S., COURT, D.L., and HUANG, J.D. (2003). Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res 31, 6674-6687.
21. LIU, L., PAREKH-OLMEDO, H., and KMIEC, E.B. (2003a). The development and regulation of gene repair. Nat. Rev. Genet. 4, 679-689.
22. LIU, L., USHER, M., HU, Y., and KMIEC, E.B. (2003b). Nuclease activity of Saccharomyces cerevisiae Mrel 1 functions in targeted nucleotide alteration. Appl. Environ. Microbiol. 69, 6216-6224.
23. MATSUNAGA, T., PARK, C.H., BESSHO, T., MU, D., and SANCAR, A. (1996). Replication protein A confers structure-specific endonuclease activities to the XPF-ERCC1 and XPG subunits of human DNA repair excision nuclease. J. Biol. Chem. 271, 11047-11050.
24. MODRICH, P., and LAHUE, R. (1996). Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu. Rev. Biochem. 65, 101-133.
25. NIEDERNHOFER, L.J., ESSERS, J., WEEDA, G., BEVERLOO, B., DE WIT, J., MUIJTIENS, M., ODIJK, H., HOEIJMAKERS, J.H., and KANAAR, R. (2001). The structure-specific endonuclease Ercc1-Xpf is required for targeted gene replacement in embryonic stem cells. EMBO J. 20, 6540-6549.
26. NIEDERNHOFER, L.J., ODIJK, H., BUDZOWSKA, M., VAN DRUNEN, E., MAAS, A., THEIL, A.F., DE WIT, J., JASPERS, N.G., BEVERLOO, H.B., HOEIJMAKERS, J.H., and KANAAR, R. (2004). The structure-specific endonuclease Ercc1-Xpf is required to resolve DNA interstrand cross-link-induced double-strand breaks. Mol. Cell. Biol. 24, 5776-5787.
27. O'DONOVAN, A., DAVIES, A.A., MOGGS, J.G., WEST, S.C., and WOOD, R.D. (1994). XPG endonuclease makes the 3′ incision in human DNA nucleotide excision repair. Nature 371, 432-435.
28. PAREKH-OLMEDO, H., FERRARA, L., BRACHMAN, E., and KMIEC, E.B. (2004). Gene therapy progress and prospects: Targeted gene repair. Gene Ther. 12, 639-646.
29. PARK, C.H., BESSHO, T., MATSUNAGA, T., and SANCAR, A. (1995). Purification and characterization of the XPF-ERCC1 complex of human DNA repair excision nuclease. J. Biol. Chem. 270, 22657-22660.
30. PICHIERRI, P., FRANCHITTO, A., PIERGENTILI, R., COLUSSI, C., and PALITTI, F. (2001). Hypersensitivity to camptothecin in MSH2-deficient cells is correlated with a role for MSH2 protein in recombinational repair. Carcinogenesis 22, 1781-1787.
31. RICE, M.C., BRUNER, M., CZYMMEK, K., and KMIEC, E.B. (2001). In vitro and in vivo nucleotide exchange directed by chimeric RNA/DNA oligonucleotides in Saccharomyces cerevisae. Mol. Microbiol. 40, 857-868.
32. SARKER, A.H., TSUTAKAWA, S.E., KOSTEK, S., NG, C., SHIN, D.S., PERIS, M., CAMPEAU, E., TAINER, J.A., NOGALES, E., and COOPER, P.K. (2005). Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: Insights for transcription-coupled repair and Cockayne syndrome. Mol. Cell. 20, 187-198.
33. THOMPSON, L.H. (1998). Chinese hamster cells meet DNA repair: An entirely acceptable affair. Bioessays 20, 589-597.
34. THOMPSON, L.H., CARRANO, A.V., SATO, K., SALAZAR, E.P., WHITE, B.F., STEWART, S.A., MINKLER, J.L., and SICILIANO, M.J. (1987). Identification of nucleotide-excision-repair genes on human chromosomes 2 and 13 by functional complementation in hamster-human hybrids. Somat. Cell. Mol. Genet. 13, 539-551.
35. TIAN, M., and ALT, F.W. (2000). Transcription-induced cleavage of immunoglobulin switch regions by nucleotide excision repair nucleases in vitro. J. Biol. Chem. 275, 24163-24172.
36. TIAN, M., JONES, D.A., SMITH, M., SHINKURA, R., and ALT, F.W. (2004a). Deficiency in the nuclease activity of xeroderma pigmentosum G in mice leads to hypersensitivity to UV irradiation. Mol. Cell. Biol. 24, 2237-2242.
37. TIAN, M., SHINKURA, R., SHINKURA, N., and ALT, F.W. (2004b). Growth retardation, early death, and DNA repair defects in mice deficient for the nucleotide excision repair enzyme XPF. Mol. Cell. Biol. 24, 1200-1205.
38. WAKASUGI, M., REARDON, J.T., and SANCAR, A. (1997). The non-catalytic function of XPG protein during dual incision in human nucleotide excision repair. J. Biol. Chem. 272, 16030-16034.