The SWI/SNF Chromatin-Remodeling Factor Stimulates Repair by Human Excision Nuclease in the Mononucleosome Core Particle

REFERENCES

• Aalfs, J. D., and R. E. Kingston. 2000. What does ′chromatin remodeling' mean? Trends Biochem. Sci. 25: 548–555.
   PubMed Web of Science ®Google Scholar
• Bessho, T., A. Sancar, L. H. Thompson, and M. P. Thelen. 1997. Reconstitution of human excision nuclease with recombinant XPF-ERCC1 complex. J. Biol. Chem. 272: 3833–3837.
   PubMed Web of Science ®Google Scholar
• Branum, M. E., J. T. Reardon, and A. Sancar. 2001. DNA repair excision nuclease attacks undamaged DNA. A potential source of spontaneous mutations. J. Biol. Chem. 276: 25421–25426.
   PubMed Web of Science ®Google Scholar
• Evans, E., J. G. Moggs, J. R. Hwang, J. M. Egly, and R. D. Wood. 1997. Mechanism of open complex and dual incision formation by human nucleotide excision repair factors. EMBO J. 16: 6559–6573.
   PubMed Web of Science ®Google Scholar
• Fry, C. J., and C. L. Peterson. 2002. Unlocking the gates to gene expression. Science 295: 1847–1848.
   PubMedGoogle Scholar
• Gaillard, P.-H. L., E. M.-D. Martini, P. D. Kaufman, B. Stillman, E. Moustacchi, and G. Almouzni. 1996. Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I. Cell 86: 887–896.
   PubMed Web of Science ®Google Scholar
• Green, C. M., and G. Almouzni. 2002. When repair meets chromatin. EMBO Rep. 3:28–33.
   PubMed Web of Science ®Google Scholar
• Guzder, S. N., Y. Habraken, P. Sung, L. Prakash, and S. Prakash. 1995. Reconstitution of yeast nucleotide excision repair with purified Rad proteins, replication protein A, and transcription factor TFIIH. J. Biol. Chem. 270: 12973–12976.
   PubMedGoogle Scholar
• Hara, R., J. Mo, and A. Sancar. 2000. DNA damage in the nucleosome core is refractory to repair by human excision nuclease. Mol. Cell. Biol. 20: 9173–9181.
   PubMedGoogle Scholar
• Hara, R., C. P. Selby, M. Liu, D. H. Price, and A. Sancar. 1999. Human transcription release factor 2 dissociates RNA polymerase I and II stalled at a cyclobutane thymine dimer. J. Biol. Chem. 274: 24779–24786.
   PubMedGoogle Scholar
• Hayes, J. J., and A. P. Wolffe. 1992. Transcription factor interaction with nucleosomal DNA. Bioessays 14: 597–603.
   PubMedGoogle Scholar
• Huang, J. C., D. L. Svoboda, J. T. Reardon, and A. Sancar. 1992. Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5′ and the 6th phosphodiester bond 3′ to the photodimer. Proc. Natl. Acad. Sci. USA 89: 3664–3668.
   PubMed Web of Science ®Google Scholar
• Ito, T., M. Bulger, M. J. Pazin, R. Kobayashi, and J. T. Kadonaga. 1997. ACF, an ISWI-containing and ATP-utilizing chromatin remodeling factor. Cell 90: 145–155.
   PubMedGoogle Scholar
• Kazantsev, A., D. Mu, A. F. Nichols, X. Zhao, S. Linn, and A. Sancar. 1996. Functional complementation of xeroderma pigmentosum complementation group E by replication protein A in an in vitro system. Proc. Natl. Acad. Sci. USA 93: 5014–5018.
   PubMedGoogle Scholar
• Kingston, R. E., and G. L. Narlikar. 1999. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13: 2339–2352.
   PubMed Web of Science ®Google Scholar
• Kornberg, R. D., and Y. Lorch. 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98: 285–294.
   PubMed Web of Science ®Google Scholar
• Kosmoski, J. V., E. J. Ackerman, and M. J. Smerdon. 2001. DNA repair of a single UV photoproduct in a designed nucleosome. Proc. Natl. Acad. Sci. USA 98: 10113–10118.
   PubMedGoogle Scholar
• Kosmoski, J. V., and M. J. Smerdon. 1999. Synthesis and nucleosome structure of DNA containing a UV photoproduct at a specific site. Biochemistry 38: 9485–9494.
   PubMedGoogle Scholar
• Kwon, J., K. B. Morshead, J. R. Guyon, R. E. Kingston, and M. A. Oettinger. 2000. Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. Mol. Cell 6: 1037–1048.
   PubMedGoogle Scholar
• Lee, T. I., and R. A. Young. 2000. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34: 77–137.
   PubMed Web of Science ®Google Scholar
• LeRoy, G., G. Orphanides, W. S. Lane, and D. Reinberg. 1998. Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science 282: 1900–1904.
   PubMedGoogle Scholar
• Lindsley, J. E., and R. P. P. Fuchs. 1994. Use of single-turnover kinetics to study bulky adduct bypass by T7 DNA polymerase. Biochemistry 33: 764–772.
   PubMed Web of Science ®Google Scholar
• Liu, X., and M. J. Smerdon. 2000. Nucleotide excision repair of the 5S ribosomal RNA gene assembled into a nucleosome. J. Biol. Chem. 275: 23729–23735.
   PubMedGoogle Scholar
• Logie, C., and C. L. Peterson. 1997. Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays. EMBO J. 16: 6772–6782.
   PubMed Web of Science ®Google Scholar
• Logie, C., and C. L. Peterson. 1999. Purification and biochemical properties of yeast SWI/SNF complex. Methods Enzymol. 304: 726–741.
   PubMedGoogle Scholar
• Mann, D. B., D. L. Springer, and M. J. Smerdon. 1997. DNA damage can alter the stability of nucleosome: effects are dependent on damage type. Proc. Natl. Acad. Sci. USA 94: 2215–2220.
   PubMedGoogle Scholar
• Matsunaga, T., C. H. Park, T. Bessho, D. Mu, and A. Sancar. 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.
   PubMed Web of Science ®Google Scholar
• Mu, D., E. Bertrand-Burggraf, J.-C. Huang, R. P. P. Fuchs, and A. Sancar. 1994. Human and E. coli excinucleases are affected differently by the sequence context of acetylaminofluorene-guanine adduct. Nucleic Acids Res. 22: 4869–4871.
   PubMedGoogle Scholar
• Mu, D., D. S. Hsu, and A. Sancar. 1996. Reaction mechanism of human DNA repair excision nuclease. J. Biol. Chem. 271: 8285–8294.
   PubMed Web of Science ®Google Scholar
• Mu, D., C. H. Park, T. Matsunaga, D. S. Hsu, J. T. Reardon, and A. Sancar. 1995. Reconstitution of human DNA repair excision nuclease in a highly defined system. J. Biol. Chem. 270: 2415–2418.
   PubMed Web of Science ®Google Scholar
• Mu, D., M. Wakasugi, D. S. Hsu, and A. Sancar. 1997. Characterization of reaction intermediates of human excision repair nuclease. 1997. J. Biol. Chem. 272: 28971–28979.
   PubMed Web of Science ®Google Scholar
• Reardon, J. T., D. Mu, and A. Sancar. 1996. Overproduction, purification, and characterization of the XPC subunit of the human DNA repair excision nuclease. J. Biol. Chem. 271: 19451–19456.
   PubMedGoogle Scholar
• Sancar, A. 1996. DNA excision repair. Annu. Rev. Biochem. 65: 43–81.
   PubMed Web of Science ®Google Scholar
• Shrader, T. E., and D. M. Crothers. 1989. Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA 86: 7418–7422.
   PubMed Web of Science ®Google Scholar
• Smerdon, M. J., and F. Thoma. 1990. Site-specific DNA repair at the nucleosome level in a yeast minichromosome. Cell 61: 675–684.
   PubMedGoogle Scholar
• Steger, D. J., A. Eberharter, S. John, P. A. Grant, and J. L. Workman. 1998. Purified histone acetyltransferase complex stimulate HIV-1 transcription from preassembled nucleosomal arrays. Proc. Natl. Acad. Sci. USA 95: 12924–12929.
   PubMed Web of Science ®Google Scholar
• Strahl, B. D., and D. Allis. 2000. The language of covalent histone modifications. Nature 403: 41–45.
   PubMed Web of Science ®Google Scholar
• Sugasawa, K., C. Masutani, and F. Hanaoka. 1993. Cell-free repair of UV-damaged simian virus 40 chromosome in human cell extracts. I. Development of a cell-free system detecting excision repair of UV-irradiated SV40 chromosomes. J. Biol. Chem. 268: 9098–9104.
   PubMedGoogle Scholar
• Svoboda, D. L., J-. S. Taylor, J. E. Hearst, and A. Sancar. 1993. DNA repair by eukaryotic nucleotide excision nuclease. Removal of thymine dimer and psoralen monoadduct by HeLa cell-free extract and of thymine dimer by Xenopus laevis oocytes. J. Biol. Chem. 268: 1931–1936.
   PubMedGoogle Scholar
• Tanaka, S., M. Livingston-Zatchej, and F. Thoma. 1996. Chromatin structure of the yeast URA3 gene at high resolution provides insight into structure and positioning of nucleosome in the chromosomal context. J. Biol. Chem. 257: 919–934.
   Google Scholar
• Tang, J. Y., B. J. Hwang, J. M. Ford, P. C. Hanawalt, and G. Chu. 2000. Xeroderma pigmentosum p48 gene enhances global genomic repair and suppresses UV-induced mutagenesis. Mol. Cell 5: 737–744.
   PubMedGoogle Scholar
• Thoma, F. 1999. Light and dark in chromatin repair: repair of UV-induced DNA lesions by photolyase and nucleotide excision repair. EMBO J. 18: 6585–6598.
   PubMed Web of Science ®Google Scholar
• Tjisterman, M., R. De Pril, J. G. Tasseron-DeJong, and J. Brouwer. 1999. RNA polymerase II transcription suppresses nucleosomal modification of UV-induced (6-4) photoproducts and cyclobutane pyrimidine dimer repair in yeast. Mol. Cell. Biol. 19: 934–940.
   PubMedGoogle Scholar
• Tsukiyama, T., C. Daniel, J. Tamkun, and C. Wu. 1995. ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell 83: 1021–1026.
   PubMedGoogle Scholar
• Tyler, J. K., and J. T. Kadonaga. 1999. The “dark side”of chromatin remodeling: repressive effects on transcription. Cell 99: 443–446.
   PubMed Web of Science ®Google Scholar
• Ura, K., M. Araki, H. Saeki, C. Masutani, T. Ito, S. Iwai, T. Mizukoshi, Y. Kaneda, and F. Hanaoka. 2001. ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes. EMBO J. 20: 2004–2014.
   PubMedGoogle Scholar
• Vignali, M., A. H. Hassan, K. E. Neely, and J. L. Workman. 2000. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol. 20: 1899–1910.
   PubMed Web of Science ®Google Scholar
• Wakasugi, M., A. Kawashima, H. Morioka, S. Linn, A. Sancar, T. Mori, O. Nikaido, and T. Matsunaga. 2002. DDB accumulates at DNA damage sites immediately after UV irradiation and directly stimulates nucleotide excision repair. J. Biol. Chem. 277: 1637–1640.
   PubMed Web of Science ®Google Scholar
• Wakasugi, M., and A. Sancar. 1999. Order of assembly of human DNA excision repair nuclease. J. Biol. Chem. 274: 18759–18768.
   PubMed Web of Science ®Google Scholar
• Wakasugi, M., and A. Sancar. 1998. Assembly, subunit composition, and footprint of human DNA repair excision nuclease. Proc. Natl. Acad. Sci. USA 95: 6669–6674.
   PubMedGoogle Scholar
• Wang, Z., X. Wu, and E. C. Friedberg. 1991. Nucleotide excision repair by human cell extract is suppressed in reconstituted nucleosomes. J. Biol. Chem. 266: 22472–22478.
   PubMed Web of Science ®Google Scholar
• Wolffe, A. P. 1997. Chromatin: structure and function. Academic Press, Inc., New York, N.Y.
   Google Scholar
• Wolffe, A. P., and J. J. Hayes. 1993. Transcription factor interactions with model nucleosomal templates. Methods Mol. Genet. 2: 314–329.
   Google Scholar
• Wood, R. D. 1996. DNA repair in eukaryotes. Annu. Rev. Biochem. 65: 135–167.
   PubMed Web of Science ®Google Scholar
• Workman, J. L., I. C. A. Taylor, and R. E. Kingston, R. G. Roeder. 1991. Control of class II gene transcription during in vitro nucleosome assembly. Methods Cell Biol. 35: 419–447.
   PubMedGoogle Scholar
• Yudkovsky, N., C. Logie, S. Hahn, and C. L. Peterson. 1999. Recruitment of the SWI/SNF chromatin remodeling complex by transcriptional activators. Genes Dev. 13: 2369–2374.
   PubMedGoogle Scholar
• Zamble, D. B., D. Mu, J. T. Reardon, A. Sancar, and S. J. Lippard. 1996. Repair of cisplatin-DNA adducts by the mammalian excision nuclease. Biochemistry 35: 10004–10013.
   PubMed Web of Science ®Google Scholar