**Abstract**

Base excision repair (BER) is the major pathway for the repair of oxidized bases and apurinic/apyrimidinic (abasic; AP) sites produced by reaction with reactive oxygen/nitrogen species (ROS/RNS). These metabolites are generated spontaneously by endogenous cellular processes and also by environmental agents. Because most of these lesions are promutagenic, linked to diverse disease-associated somatic mutations, as well as heritable single nucleotide polymorphisms (SNPs) in the normal human population, their prompt repair is warranted. Impairment of repair leading to mutation, a hallmark of cancer, underscores the essentiality of BER for maintaining genome integrity in humans and other mammals. In mammals, repair of oxidized bases and other BER substrates is initiated by DNA glycosylases (DGs), which excise the damaged bases and cleave the DNA strands at the resulting AP sites, followed by sequential end processing, gap-filling DNA synthesis, and ligation. *In vitro* BER performed with naked DNA substrates has been extensively studied, which delineates its basic mechanistic steps and subpathways. However, recent interest is directed to unraveling BER in cell chromatin, including its regulation via posttranslational modifications (PTMs), which occurs possibly in concert with nucleosome remodeling. Emerging reports on various PTMs of BER enzymes indicate that the PTMs, while dispensable for the enzymatic activity, regulate overall repair by modulating interactions with other repair proteins and chromatin factors, assembly of BER complexes, as well as turnover of the proteins, and may ultimately dictate the cellular phenotype. Here, we discuss recent advances in the BER field by reviewing the PTMs and how they regulate BER in chromatin.

**Keywords:** oxidative stress, base oxidation, base excision repair, posttranslational modifications, acetylation, phosphorylation, SUMOylation, methylation, chromatin

#### **1. Introduction**

DNA, the genetic repository of all cellular functions, is packaged with histones into chromatin consisting of nucleosome units. One hundred forty-seven base pair (bp) segments in DNA wrap ~1.65 times in a left-handed superhelical turn around a histone octamer consisting of two histone H2A-H2B dimers and a H3-H4 tetramer, which form the nucleosome core; the adjacent nucleosomes are separated by some

50 bp unfolded, linker DNA bound to histone H1 or H5. Organization of DNA into chromatin enables the compaction required to accommodate large eukaryotic genomes inside the cell nucleus. This compaction renders DNA inaccessible to any DNA transaction machinery. Replication and transcription are tightly coordinated with specific interactions of their complexes with DNA [1, 2].

The integrity of DNA is under constant threat, naturally from endogenous sources, as well as by environmental factors in the form of a chemical addition, an alteration in the nitrogen base structure, thereby creating an abnormal nucleotide, or a break in one or both strands of DNA [3–8]. Cellular metabolic processes including mitochondrial respiration and hydrolytic reactions generate reactive molecules, such as reactive oxygen species (ROS), reactive nitrogen species (RNS), and alkylating agents. Some chemical bonds in DNA are susceptible to spontaneous hydrolysis. About 70,000 lesions are generated per cell, per day in humans. Single-strand breaks (SSBs), as well as a plethora of oxidized bases, are formed during oxidative genome damage. In addition, deamination, depurination, depyrimidination, double-strand breaks (DSBs), propano-, etheno-, and malondialdehyde-derived DNA adducts, base propenals, and alkylated bases are also formed endogenously. Environmental factors such as UV rays, ionizing radiation (IR), heat, and chemicals from tobacco smoke and industrial sources pose additional risks to DNA.

#### **2. Oxidative genome damage and oxidized bases**

 For aerobic organisms, oxygen acts like a double-edged sword; while it is absolutely essential for life, it is also a threat to the life, recognized as the "Oxygen Paradox" [9–11]. ROS, which include the superoxide anion (O2 •<sup>−</sup>), hydrogen peroxide (H2O2), singlet oxygen (1 O2), and the hydroxyl radical (• OH), along with RNS, for example, peroxynitrite (ONOO<sup>−</sup>) react with all biological molecules including DNA. The hydroxyl radical having the highest reduction potential is mainly generated from Fenton reaction between reduced redox active metal ions (Fe2+, Cu+ ) and H2O2 [12], as well as by the IR-induced radiolysis of water [13]. A wide variety of cellular antioxidant defense mechanisms including both redox-buffering enzymatic and nonenzymatic systems have evolved, for example, superoxide dismutases, catalases, glutathione peroxidases, peroxiredoxins, and glutaredoxins; these counteract the detrimental effect of oxidative stress to the biological molecules, and an imbalance in their homeostasis leads to increased damage to the biomolecules [14].

A plethora of oxidized base lesions are generated mostly from guanine (G) in DNA, which has the lowest redox potential among the natural bases. Other lesions including 2-deoxyribose modifications, SSBs, DSBs, and protein-DNA cross-links are also ROS reaction products in DNA [10, 14–17]. Nearly 100 such lesions have been identified; however, because of the lack of sensitivity of the techniques used to identify the lesions and inherent instability of some of them, the total number formed in the genome under a pro-oxidant environment is likely to be much higher [18].

 The most commonly formed oxidized base lesion is 7,8-dihydro-8-oxoguanine (8-oxoguanine, 8-oxoG), which was discovered by Kasai and Nishimura in 1983 and coined as 8-hydroxyguanine [19–21]. All the nucleobases are also ionized by IR and by high intensity 266-ns laser photolysis. The DNA bases undergo one-electron oxidation (one electron ionization potential of G<A<C~T). 8-oxoG is generated at a much higher level (>5-fold) than the combined level of other one-electron base oxidation products. Singlet oxygen (1 O2), the major ROS in UVA-mediated oxidation of DNA, specifically targets G and 2-deoxyribose moiety [22–24]. Other major oxidized base lesions are 5-hydroxy-6-hydrothymine, thymine glycol (TG), cytosine glycol (CG), 5-hydroxycytosine (5-OHC), uracil glycol (UG), 5-hydroxyuracil

*Regulation of Oxidized Base Repair in Human Chromatin by Posttranslational Modification DOI: http://dx.doi.org/10.5772/intechopen.81979* 

#### **Table 1.**

*Common oxidized bases detected in DNA.* 

 (5-OHU), 8-hydroxyadenine, and 2-hydroxyadenine [14, 17]. Hypochlorous acid (HOCl), generated by myeloperoxidase in neutrophils during inflammation, chlorinates both DNA and RNA bases [25, 26], and the main products are 5-chlorocytosine, 8-chloroadenine, and 8-chloroguanine. A summary of commonly formed oxidized bases detected in cellular DNA is shown in **Table 1** [16]. Apart from ROS-induced generation of oxidized bases, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) are formed enzymatically during transcriptional reprogramming involving oxidative demethylation of 5-methyl C (5mC), mostly localized in promoter CpG islands, induced by TET dioxygenases [27, 28]. However, enzymatically generated 5-methyl C oxidation products are produced >2-fold higher than that from direct oxidative damage to DNA [29, 30]. Additionally, tandem base lesions are produced by radicals generated from • OH or one-electron oxidation reactions. Examples include the addition of either 5-(uracilyl)methyl radicals or 6-hydroxy-5,6-dihydrocytosin-5-yl radicals to 5′-adjacent guanine moieties in the DNA of cells exposed to H2O2 [31, 32] and formation of a guanine-thymine cross-link upon initial formation of guanine radical cation [33, 34]. One-electron oxidation also leads to DNA-protein cross-links. UVA irradiation of 6-thioguanine-containing DNA forms DNA-protein cross-links in human cells [33, 35].

#### **3. Fate of oxidized bases and accumulation of mutations**

ROS-induced oxidized base lesions and AP sites if left unrepaired are replicated by replicative or DNA translesion synthesis (TLS) polymerases [36]. Their misreplication generates mutations, a hallmark of cancer genomes, which account for two-thirds of single base pair substitutions [37–40]. Furthermore, single nucleotide polymorphisms (SNPs), observed in normal human genomes, also likely result from such spontaneous single base pair substitutions. U and 5-OHU, the spontaneous and ROS-induced oxidative deamination product of C, respectively, preferably pair with A during replication, resulting in GC → AT transition mutation; 8-oxoG,

the predominant oxidized base lesion mispairs with A, leading to GC → TA transversion mutation [41, 42]. In response to continuous assault by both endogenous and environmental factors, cellular defense mechanisms including diverse DNA repair pathways have evolved in all organisms to correct these base modifications and maintain genomic integrity.
