The genomics of oxidative DNA damage, repair, and resulting mutagenesis

Abstract

Reactive oxygen species are a constant threat to DNA as they modify bases with the risk of disrupting genome function, inducing genome instability and mutation. Such risks are due to primary oxidative DNA damage and also mediated by the repair process. This leads to a delicate decision process for the cell as to whether to repair a damaged base at a specific genomic location or better leave it unrepaired. Persistent DNA damage can disrupt genome function, but on the other hand it can also contribute to gene regulation by serving as an epigenetic mark. When such processes are out of balance, pathophysiological conditions could get accelerated, because oxidative DNA damage and resulting mutagenic processes are tightly linked to ageing, inflammation, and the development of multiple age-related diseases, such as cancer and neurodegenerative disorders. Recent technological advancements and novel data analysis strategies have revealed that oxidative DNA damage, its repair, and related mutations distribute heterogeneously over the genome at multiple levels of resolution. The involved mechanisms act in the context of genome sequence, in interaction with genome function and chromatin. This review addresses what we currently know about the genome distribution of oxidative DNA damage, repair intermediates, and mutations. It will specifically focus on the various methodologies to measure oxidative DNA damage distribution and discuss the mechanistic conclusions derived from the different approaches. It will also address the consequences of oxidative DNA damage, specifically how it gives rise to mutations, genome instability, and how it can act as an epigenetic mark.

Keywords: 8-oxo-7,8-dihydroguanine; 8-oxoG; AP site; BER; Cancer; DNA damage; Epigenetics; Genomics; Mutagenesis; Oxidative stress; ROS.

Graphical abstract

Fig. 1

8-oxo-7,8-Dihydroguanine (8-oxoG). Under conditions of oxidative stress, 8-oxoG is the result of reactive oxygen species (ROS) modifying a guanine.

Fig. 2

Base excision repair (BER) of 8-oxo-7,8-dihydroguanine (8-oxoG). Oxidative DNA damage is repaired via several repair intermediates by base excision repair (BER). Through removal of the oxidized base, a reactive apurinic site (AP site) is formed. Incision of the strand creates a single strand break, and the damaged site is then repaired through either short or long patch BER (for details, please see main text).

Fig. 3

Methods to measure oxidative DNA damage genome-wide. Several methods have been developed that utilize next generation sequencing to assess the genome wide distribution of 8-oxoG and the repair intermediate AP site. For details on the methods, please see the main text.

Fig. 4

Route to C-to-A mutation through 8-oxoG-adenine-mismatches. Oxidative DNA damage provides direct routes to mutations. While guanine usually pairs with cytosine, 8-oxo-7,8-dihydroguanine (8-oxoG), the most frequent type of oxidative base damage, may cause mispairing with adenine through a conformational change. This is one route to oxidative DNA damage induced mutations.

Fig. 5

Routes to oxidative DNA damage dependent mutagenesis. Oxidative DNA damage provides direct and indirect routes to mutagenesis, particular on single nucleotides, i.e. C-to-A and T-to-G and their reverse complements. Mispairing of 8-oxoG with adenine during replication leads to C-to-A mutation through erroneous repair or in the next round of replication. The same mutation can however also be the result of replication encountering an AP site. Following the A-rule, an adenine may be incorporated opposite the AP site, which also leads to C-to-A mutation. Incorporation of 8-oxoG from an oxidized nucleotide pool may also lead to mispairing with adenine. Through erroneous repair or in the next round of replication, the mismatch may lead to T-to-G mutation.

Fig. 6

Oxidative DNA damage dependent mutational signatures. Oxidative DNA damage has been associated with several mutational signatures, fingerprints of mutagenic processes in the genome that can be extracted using non-negative matrix factorization. First, Signature 18 is associated with ROS and dominated by C-to-A mutations with preceding and following adenine or thymine. Signature 36 gives a similar profile and has been linked to somatic MUTYH mutations. Signatures 17a and b have been connected both to oxidative DNA damage from an oxidized nucleotide pool and treatment with 5-fluoro-uracil. Mutations occur in a very specific trinucleotide context, most distinctly T-to-G in the context of TTG.

Fig. 7

Mutation rates from oxidative DNA damage show specificity at different levels of resolution from eu- and heterochromatin to the immediate sequence context. Mutation rates derived from oxidative DNA damage show distinct distributions at multiple levels of resolution. On the scale of chromatin domains, heterochromatin accumulates the major mutation load. Coding sequence of genes as well as GC rich regulatory sequences are depleted, while nucleosome positions in general are also enriched in mutations. At the level of DNA secondary structure, mutations are enriched at positions, where the minor groove of the helix faces the nucleosome. At the immediate sequence context, C-to-A mutations are enriched for preceding and following adenine or thymine. T-to-G mutations occur most frequently in a context of CTT.