Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro

Butler, Thomas J, Estep, Katrina N, Sommers, Joshua A, Maul, Robert W, Moore, Ann Zenobia, Bandinelli, Stefania, Cucca, Francesco, Tuke, Marcus A, Wood, Andrew R, Bharti, Sanjay Kumar, Bogenhagen, Daniel F, Yakubovskaya, Elena, Garcia-Diaz, Miguel, Guilliam, Thomas A, Byrd, Alicia K, Raney, Kevin D, Doherty, Aidan J, Ferrucci, Luigi, Schlessinger, David, Ding, Jun and Brosh, Jr, Robert M (2020) Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro. Human Molecular Genetics, 29 (8). pp. 1292-1309. ISSN 0964-6906

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Abstract

As the powerhouses of the eukaryotic cell, mitochondria must maintain their genomes which encode proteins essential for energy production. Mitochondria are characterized by guanine-rich DNA sequences that spontaneously form unusual three-dimensional structures known as G-quadruplexes (G4). G4 structures can be problematic for the essential processes of DNA replication and transcription because they deter normal progression of the enzymatic-driven processes. In this study, we addressed the hypothesis that mitochondrial G4 is a source of mutagenesis leading to base-pair substitutions. Our computational analysis of 2757 individual genomes from two Italian population cohorts (SardiNIA and InCHIANTI) revealed a statistically significant enrichment of mitochondrial mutations within sequences corresponding to stable G4 DNA structures. Guided by the computational analysis results, we designed biochemical reconstitution experiments and demonstrated that DNA synthesis by two known mitochondrial DNA polymerases (Pol γ, PrimPol) in vitro was strongly blocked by representative stable G4 mitochondrial DNA structures, which could be overcome in a specific manner by the ATP-dependent G4-resolving helicase Pif1. However, error-prone DNA synthesis by PrimPol using the G4 template sequence persisted even in the presence of Pif1. Altogether, our results suggest that genetic variation is enriched in G-quadruplex regions that impede mitochondrial DNA replication.

Item Type: Article
Keywords: DNA Helicases, DNA Polymerase gamma, DNA Primase, DNA Replication, DNA, Mitochondrial, DNA-Directed DNA Polymerase, G-Quadruplexes, Genome, Mitochondrial, Guanine, Humans, Italy, Mitochondria, Multifunctional Enzymes, Mutagenesis, Mutation, Nucleic Acid Conformation, Whole Genome Sequencing
Schools and Departments: School of Life Sciences > Sussex Centre for Genome Damage and Stability
SWORD Depositor: Mx Elements Account
Depositing User: Mx Elements Account
Date Deposited: 25 Aug 2021 08:01
Last Modified: 26 Aug 2021 09:35
URI: http://sro.sussex.ac.uk/id/eprint/101287

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