Browsing by Subject "RPA"
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Item The mechanism of DNA double-strand break (DSB) resection in human cells(2013-05) Yang, Soo-Hyun; Paull, Tanya T.Homologous recombination (HR) repair is critical for the maintenance of genomic stability, as it is involved in the precise repair of DNA double-strand breaks (DSBs) using an intact homologous template for repair. The initiation of 5' strand resection of DNA ends is a critical determinant in this process, which commits cells to HR repair and prevents repair by non-homologous end joining (NHEJ). The human single-stranded DNA (ssDNA) binding complexes, RPA and SOSS1, are involved in regulating DSB signaling and HR repair. In this study, I demonstrate a novel function of SOSS1 in HR repair, in which SOSS1 stimulates hExo1-dependent resection. Despite its poor activity in binding duplex DNA, SOSS1 facilitates hExo1 recruitment to duplex DNA ends and promotes its activity in resection independently of MRN in vitro. MRN(X) is a highly conserved complex that is involved in the early steps of HR repair by regulating DSB resection. MRN interacts with CtIP and constitutes resection machinery that can perform limiting processing on DNA ends. In this study, I also examine the biochemical activities of MRN and CtIP in DSB resection through reconstituted in vitro assays. I show that the ATP-dependent DNA unwinding activity of MRN is responsible for overcoming Ku inhibition of hExo1- and Dna2/BLM-dependent resection activity in vitro. I propose that this unwinding step displaces Ku away from the DNA ends and facilitates the recruitment of hExo1 to the DNA ends for efficient resection. In addition, I show that CtIP can promote overcoming the inhibitory effect of Ku in resection together with MRN. Further, I demonstrate that MRN nuclease activity is required for efficient processing of covalent adducts from DNA ends in vitro, suggesting that the nucleolytic removal of covalent adducts by MRN generates free ends for hExo1- and Dna2/BLM binding. Overall, this study provides mechanistic insight into the regulation of DSB resection in human cells.Item Replication-associated base excision repair Of oxidized bases in the mammalian genome(2009-10-31) Corey Allen Theriot; John Papaconstantinou, Ph.D.; Tapas Hazra, Ph.D.; Sankar Mitra, Ph.D.; Isvan Boldogh, Ph.D.; Cornelis Elferink, Ph.D.; Alan Tomkinson, Ph.D.Reactive oxygen species (ROS), the most pervasive endogenous and radiation-induced genotoxic agents induce strand breaks and a plethora of base lesions in DNA that (except double-strand breaks) are repaired via the DNA base excision repair (BER) pathway. Four mammalian DNA glycosylases, namely, OGG1 and NTH1 in the Nth family, and NEIL1 and NEIL2 in the Nei family, with overlapping substrate range initiate BER by excising oxidized base lesions and cleaving the DNA strand. NEIL1 prefers oxidized pyrimidines or ring-opened purines as substrates and is upregulated at the mRNA and protein level during S-phase. NEIL1 also demonstrates the unique able to excise base lesions from forked or single-stranded DNA substrates that mimic intermediates generated during DNA replication. This suggests a direct linkage of NEIL1’s repair activity to genome replication. In addition, inactivating mutations in the NEIL1 gene have been epidemiologically linked with gastric cancer, NEIL1-downregulation induces a mutator phenotype and NEIL1 KO mice display symptoms of the human metabolic syndrome such as obesity, dyslipidemia, and fatty liver disease. These observations lead us to develop the working hypothesis that NEIL1 is involved in a preferential repair pathway for oxidized base damage in the replicating genome where repair of both template strands is equally important because an unrepaired base lesion in either strand could induce mutations. Thus, specific involvement of NEIL1 with the DNA replication machinery may be required to effectively and efficiently accomplish this. In support of our hypothesis, we have identified several new NEIL1 interacting proteins that are components of the DNA replication machinery, including Replication Protein A (RPA), Proliferating Cell Nuclear Antigen (PCNA), Flap Endonuclease 1 (FEN1), DNA Polymerase ä, Replication Factor C (RFC), and DNA Ligase I as well as the stress responsive Rad9-Rad1-Hus1 (9-1-1) DNA sliding clamp. We mapped the overlapping binding sites for all of these interacting protein partners to a small disordered region near the unconserved C-terminus of NEIL1 that is dispensable for its enzymatic activity. In support of the biological significance of these interactions, we showed that the DNA polymerase processivity factor and sliding clamp, PCNA, stimulates NEIL1’s activity on various DNA substrates including forked and single-stranded DNA. We also investigated NEIL1’s association with the DNA damage activated alternative sliding clamp 9-1-1 and showed direct interaction as well as stimulation of NEIL1 activity in a similar fashion as PCNA. In contrast, the RPA complex inhibits NEIL1’s activity when the damage is in the single-stranded region of a DNA primer-template structure, inhibition that is relieved in the presence of PCNA. These results suggest that PCNA and RPA, along with other proteins, collaborate to regulate a replication-associated repair pathway in mammalian cells that not only maintains efficient and proper replication but also repair of oxidative DNA damage to prevent mutagenesis and maintain genomic integrity.