title: AP endonuclease 1 prevents the extension of a T/G mismatch by DNA polymerase β to prevent mutations in CpGs during base excision repair.
abstract: Dynamics of DNA methylation and demethylation at CpG clusters are involved in gene regulation. CpG clusters have been identified as hot spots of mutagenesis because of their susceptibility to oxidative DNA damage. Damaged Cs and Gs at CpGs can disrupt a normal DNA methylation pattern through modulation of DNA methylation and demethylation, leading to mutations and deregulation of gene expression. DNA base excision repair (BER) plays a dual role of repairing oxidative DNA damage and mediating an active DNA demethylation pathway on CpG clusters through removal of a T/G mismatch resulting from deamination of a 5mC adjacent to a guanine that can be simultaneously damaged by oxidative stress. However, it remains unknown how BER processes clustered lesions in CpGs and what are the consequences from the repair of these lesions. In this study, we examined BER of an abasic lesion next to a DNA demethylation intermediate, the T/G mismatch in a CpG dinucleotide, and its effect on the integrity of CpGs. Surprisingly, we found that the abasic lesion completely abolished the activity of thymine DNA glycosylase (TDG) for removing the mismatched T. However, we found that APE1 could still efficiently incise the abasic lesion leaving a 3-terminus mismatched T, which was subsequently extended by pol β. This in turn resulted in a C to T transition mutation. Interestingly, we also found that APE1 3'-5' exonuclease activity efficiently removed the mismatched T, thereby preventing pol β extension of the mismatched nucleotide and the resulting mutation. Our results demonstrate a crucial role of APE1 3'-5' exonuclease activity in combating mutations in CpG clusters caused by an intermediate of DNA demethylation during BER.
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States.
authors.forename: Yanhao
authors.initials: Y
authors.lastname: Lai
authors.affiliation: Biochemistry Ph.D. Program, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States.
authors.forename: Zhongliang
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Osemota
authors.affiliation: Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States; Biochemistry Ph.D. Program, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States; Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States. Electronic address: yualiu@fiu.edu.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Liu
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism; D020137:Base Pair Mismatch; D018899:CpG Islands; D004247:DNA / Q000235:genetics* / Q000378:metabolism; D004249:DNA Damage; D019175:DNA Methylation; D019951:DNA Polymerase beta / Q000235:genetics* / Q000378:metabolism; D004260:DNA Repair; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D009154:Mutation; D044502:Thymine DNA Glycosylase / Q000235:genetics* / Q000378:metabolism
chemical_list: D044503:5-Methylcytosine; D004247:DNA; D019951:DNA Polymerase beta; D044502:Thymine DNA Glycosylase; C085108:APEX1 protein, human; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase
keywords: AP endonuclease 1; Base excision repair; CpG islands; DNA damage; DNA demethylation; DNA polymerase β