REFERENCES
- Anderson, J., A. Thastrom, and J. Widom. 2002. Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Mol. Cell. Biol. 22:7147–7157.
- Anderson, J., and J. Widom. 2000. Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 296:979–987.
- Beard, B. C., S. H. Wilson, and M. J. Smerdon. 2003. Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes. Proc. Natl. Acad. Sci. USA 100:7465–7470.
- Blaisdell, J. O., and S. S. Wallace. 2007. Rapid determination of the active fraction of DNA repair glycosylases: a novel fluorescence assay for trapped intermediates. Nucleic Acids Res. 35:1601–1611.
- Cappelli, E., R. Taylor, M. Cevasco, A. Abbondandolo, K. Caldecott, and G. Frosina. 1997. Involvement of XRCC1 and DNA ligase III gene products in DNA base excision repair. J. Biol. Chem. 272:23970–23975.
- Chafin, D. R., J. M. Vitolo, L. A. Henricksen, R. A. Bambara, and J. J. Hayes. 2000. Human DNA ligase I efficiently seals nicks in nucleosomes. EMBO J. 19:5492–5501.
- David, S. S., and S. D. Williams. 1998. Chemistry of glycosylases and endonucleases involved in base-excision repair. Chem. Rev. 98:1221–1262.
- Dianova, I. I., K. M. Sleeth, S. L. Allinson, J. L. Parsons, C. Breslin, K. W. Caldecott, and G. L. Dianov. 2004. XRCC1-DNA polymerase beta interaction is required for efficient base excision repair. Nucleic Acids Res. 32:2550–2555.
- Dong, F., J. Hansen, and K. van Holde. 1990. DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro. Proc. Natl. Acad. Sci. USA 87:5724–5728.
- Enright, H. U., W. J. Miller, and R. P. Hebbel. 1992. Nucleosomal histone protein protects DNA from iron-mediated damage. Nucleic Acids Res. 20:3341–3346.
- Felsenfeld, G., and M. Groudine. 2003. Controlling the double helix. Nature 421:448–453.
- Geraghty, D. S., H. B. Sucic, J. Chen, and D. S. Pederson. 1998. Evidence that partial unwrapping of DNA from nucleosomes facilitates the binding of heat shock factor following DNA replication in yeast. J. Biol. Chem. 273:20463–20472.
- Godde, J. S., and A. P. Wolffe. 1995. Disruption of reconstituted nucleosomes. The effect of particle concentration, MgCl2 and KCl concentration, the histone tails, and temperature. J. Biol. Chem. 270:27399–27402.
- Groth, A., W. Rocha, A. Verreault, and G. Almouzni. 2007. Chromatin challenges during DNA replication and repair. Cell 128:721–733.
- Hanawalt, P., and G. Sivak. 1999. Transcription-coupled DNA repair, p. 169–179. In D. A. Karakaya (ed.), Advances in DNA damage and repair. Plenum Publishers, New York, NY.
- Howe, L., and J. Ausio. 1998. Nucleosome translational position, not histone acetylation, determines TFIIIA binding to nucleosomal Xenopus laevis 5S rRNA genes. Mol. Cell. Biol. 18:1156–1162.
- Huggins, C. F., D. R. Chafin, S. Aoyagi, L. A. Henricksen, R. A. Bambara, and J. J. Hayes. 2002. Flap endonuclease 1 efficiently cleaves base excision repair and DNA replication intermediates assembled into nucleosomes. Mol. Cell 10:1201–1211.
- Katafuchi, A., T. Nakano, A. Masaoka, H. Terato, S. Iwai, F. Hanaoka, and H. Ide. 2004. Differential specificity of human and Escherichia coli endonuclease III and VIII homologues for oxidative base lesions. J. Biol. Chem. 279:14464–14471.
- Kleczkowska, H. E., G. Marra, T. Lettieri, and J. Jiricny. 2001. hMSH3 and hMSH6 interact with PCNA and colocalize with it to replication foci. Genes Dev. 15:724–736.
- Kornberg, R. D., and Y. Lorch. 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294.
- Lett, J. T. 1990. Damage to DNA and chromatin structure from ionizing radiations, and the radiation sensitivities of mammalian cells. Prog. Nucleic Acid Res. Mol. Biol. 39:305–352.
- Li, B., M. Carey, and J. L. Workman. 2007. The role of chromatin during transcription. Cell 128:707–719.
- Li, G., M. Levitus, C. Bustamante, and J. Widom. 2005. Rapid spontaneous accessibility of nucleosomal DNA. Nat. Struct. Mol. Biol. 12:46–53.
- Li, G., and J. Widom. 2004. Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11:763–769.
- Li, Q., and O. Wrange. 1995. Accessibility of a glucocorticoid response element in a nucleosome depends on its rotational positioning. Mol. Cell. Biol. 15:4375–4384.
- Liang, Q., and P. C. Dedon. 2001. Cu(II)/H2O2-induced DNA damage is enhanced by packaging of DNA as a nucleosome. Chem. Res. Toxicol. 14:416–422.
- Liu, X., S. Choudhury, and R. Roy. 2003. In vitro and in vivo dimerization of human endonuclease III stimulates its activity. J. Biol. Chem. 278:50061–50069.
- Lucchini, R., R. E. Wellinger, and J. M. Sogo. 2001. Nucleosome positioning at the replication fork. EMBO J. 20:7294–7302.
- Marenstein, D. R., M. K. Chan, A. Altamirano, A. K. Basu, R. J. Boorstein, R. P. Cunningham, and G. W. Teebor. 2003. Substrate specificity of human endonuclease III (hNTH1). Effect of human APE1 on hNTH1 activity. J. Biol. Chem. 278:9005–9012.
- Marenstein, D. R., M. T. Ocampo, M. K. Chan, A. Altamirano, A. K. Basu, R. J. Boorstein, R. P. Cunningham, and G. W. Teebor. 2001. Stimulation of human endonuclease III by Y box-binding protein 1 (DNA-binding protein B). Interaction between a base excision repair enzyme and a transcription factor. J. Biol. Chem. 276:21242–21249.
- Matsumoto, Y., and K. Kim. 1995. Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair. Science 269:699–702.
- Nilsen, H., T. Lindahl, and A. Verreault. 2002. DNA base excision repair of uracil residues in reconstituted nucleosome core particles. EMBO J. 21:5943–5952.
- Núñez, M. E., K. T. Noyes, and J. K. Barton. 2002. Oxidative charge transport through DNA in nucleosome core particles. Chem. Biol. 9:403–415.
- Ocampo-Hafalla, M. T., A. Altamirano, A. K. Basu, M. K. Chan, J. E. A. Ocampo, A. Cummings, Jr., R. J. Boorstein, R. P. Cunningham, and G. W. Teebor. 2006. Repair of thymine glycol by hNth1 and hNeil1 is modulated by base pairing and cis-trans epimerization. DNA Repair 5:444–454.
- Pascal, J. M., P. J. O'Brien, A. E. Tomkinson, and T. Ellenberger. 2004. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432:473–478.
- Pennings, S., G. Meersseman, and E. M. Bradbury. 1991. Mobility of positioned nucleosomes on 5S rDNA. J. Mol. Biol. 220:101–110.
- Peterson, C. L., and J. Cote. 2004. Cellular machineries for chromosomal DNA repair. Genes Dev. 18:602–616.
- Pfeifer, G. P. 1997. Formation and processing of UV photoproducts: effects of DNA sequence and chromatin environment. Photochem. Photobiol. 65:270–283.
- Polach, K. J., and J. Widom. 1995. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254:130–149.
- Protacio, R. U., K. J. Polach, and J. Widom. 1997. Coupled-enzymatic assays for the rate and mechanism of DNA site exposure in a nucleosome. J. Mol. Biol. 274:708–721.
- Rydberg, B. 2001. Radiation-induced DNA damage and chromatin structure. Acta Oncol. 40:682–685.
- Simon, R. H., and G. Felsenfeld. 1979. A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite. Nucleic Acids Res. 6:689–696.
- Simpson, R. T., and P. Kunzler. 1979. Chromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. Nucleic Acids Res. 6:1387–1415.
- Simpson, R. T., and D. W. Stafford. 1983. Structural features of a phased nucleosome core particle. Proc. Natl. Acad. Sci. USA 80:51–55.
- Studitsky, V. M., W. Walter, M. Kireeva, M. Kashlev, and G. Felsenfeld. 2004. Chromatin remodeling by RNA polymerases. Trends Biochem. Sci. 29:127–135.
- Tomschik, M., H. Zheng, K. van Holde, J. Zlatanova, and S. H. Leuba. 2005. Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 102:3278–3283.
- Ura, K., J. J. Hayes, and A. P. Wolffe. 1995. A positive role for nucleosome mobility in the transcriptional activity of chromatin templates: restriction by linker histones. EMBO J. 14:3752–3765.
- van Hoffen, A., A. S. Balajee, A. A. van Zeeland, and L. H. Mullenders. 2003. Nucleotide excision repair and its interplay with transcription. Toxicology 193:79–90.
- van Holde, K. E. 1989. Chromatin. Springer Verlag, New York, NY.
- Wallace, S. S. 2002. Biological consequences of free radical-damaged DNA bases. Free Radic. Biol. Med. 33:1–14.
- Wallace, S. S. 1998. Enzymatic processing of radiation-induced free radical damage in DNA. Radiat. Res. 150:S60–S79.
- Wolffe, A. 1998. Chromatin structure and function, p. 240–341. Academic Press, San Diego, CA.