of Work: We are examining the relationship between the structures of DNA polymerases and their functions, including fidelity. Among several accomplishments in FY01, two are particularly significant. 1) Development of a normal human immune system capable of reacting with a vast array of foreign antigens requires that immunoglobulin genes undergo somatic mutation at a rate that may be a billion-fold higher than the average genomic mutation rate. The enzymological basis for this hypermutation has been sought for over 25 years. This year we reported that two human DNA polymerases that are highly inaccurate, pol eta and pol kappa, generate errors during DNA synthesis whose type and location match those arising during somatic hypermutation. This suggests that one or both of these enzymes may contribute to the development of the normal human immune system. 2) DNA polymerase iota is the only human polymerase that regularly violates normal Watson-Crick base pairing rules. Unlike other polymerases, it prefers to match thymine with guanine rather than adenine and has thus been considered to be """"""""error-prone"""""""". We discovered that pol iota has 5'-dRPase activity, which removes damage from the 5' end of a broken DNA strand. This result and additional data suggest that pol iota could participate in specialized types of repair of DNA damage resulting from environmental stress. Among several possibilities that will be explored, one particularly intriguing hypothesis is that by pairing guanine with thymine, pol iota may prevent misrepair of deaminated 5-methylcytosines, thus actually stabilizing rather than mutating the human genome.
| Orebaugh, Clinton D; Lujan, Scott A; Burkholder, Adam B et al. (2018) Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing. Methods Mol Biol 1672:329-345 |
| Burkholder, Adam B; Lujan, Scott A; Lavender, Christopher A et al. (2018) Muver, a computational framework for accurately calling accumulated mutations. BMC Genomics 19:345 |
| Zhou, Zhi-Xiong; Williams, Jessica S; Kunkel, Thomas A (2018) Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis. J Vis Exp : |
| Williams, Jessica S; Kunkel, Thomas A (2018) Studying Topoisomerase 1-Mediated Damage at Genomic Ribonucleotides. Methods Mol Biol 1703:241-257 |
| Kaminski, Andrea M; Tumbale, Percy P; Schellenberg, Matthew J et al. (2018) Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis. Nat Commun 9:2642 |
| Huang, Shar-Yin N; Williams, Jessica S; Arana, Mercedes E et al. (2017) Topoisomerase I-mediated cleavage at unrepaired ribonucleotides generates DNA double-strand breaks. EMBO J 36:361-373 |
| Jamsen, Joonas A; Beard, William A; Pedersen, Lars C et al. (2017) Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Nat Commun 8:253 |
| Burgers, Peter M J; Kunkel, Thomas A (2017) Eukaryotic DNA Replication Fork. Annu Rev Biochem 86:417-438 |
| Lujan, Scott A; Williams, Jessica S; Kunkel, Thomas A (2016) DNA Polymerases Divide the Labor of Genome Replication. Trends Cell Biol 26:640-654 |
| Watt, Danielle L; Buckland, Robert J; Lujan, Scott A et al. (2016) Genome-wide analysis of the specificity and mechanisms of replication infidelity driven by imbalanced dNTP pools. Nucleic Acids Res 44:1669-80 |
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