In particular, genetic mutations in genes involved in NHEJ lead to potential lethal lesions that not only cause loss of chromosomal content, but give rise to gross rearrangements.150, 151 In addition, since NHEJ plays a programmed role in class switch recombination and antibody Rabbit polyclonal to AACS diversity, defects in the pathway components lead to immunological impairment. oxygen species GSK2606414 (ROS) or other intracellular damaging GSK2606414 agents that challenge the genome integrity of an aerobic organism. These processes include, most notably, mitochondrial respiration, which produces chemical energy in the form of ATP that fuels many cellular operations. When considering spontaneous hydrolytic decay, the different endogenous metabolic genotoxins, the many environmental chemical agents, and background radiation, it has been estimated that approximately 104C105 DNA lesions are generated in each mammalian genome per day. In light of the adverse consequences of unwanted DNA modifications, our genetic material is a pivotal macromolecule that needs to be maintained and preserved in a timely and efficient manner. In particular, DNA damage can stall the replication or transcription machinery, leading to mutagenic or stress responses. For example, cells might erroneously bypass a miscoding lesion or transiently deploy low-fidelity DNA polymerases to overcome persistent DNA damage, choosing mutagenesis over cell death. Such mutational events can lead to either inactivation of tumor suppressor genes or activation of oncogenes, seeding the carcinogenic process. Alternatively, lesion-induced replication or transcription arrest can perturb cellular homeostasis, often promoting the activation of cell death responses, such as p53 (MIM:?191170)-dependent apoptosis. Given the importance of removing DNA damage from the genome and sustaining genomic integrity, organisms have evolved intricate interdependent systems that involve cell cycle check point pathways, the DNA-damage response (DDR), and DNA repair mechanisms. Deficiency in many members of these processes is associated with a range of diseases, including cancer predisposition, neurodegeneration, and premature aging. Overview of the Formation and Consequences of DNA Damage Intrinsic Damaging Agents Sources of DNA damage can be intrinsic or extrinsic. Intrinsic sources of DNA damage include spontaneous hydrolysis, replication mistakes, replicative stress, and reactions with endogenous chemicals, such as the ROS noted earlier (Table 1). As a chemical itself within an aqueous environment, DNA is subject to reactions with water, resulting in, for example, the spontaneous formation of an apurinic/apyrimidinic (AP) site (via hydrolysis of the glycosidic bond) or uracil from cytosine (via deamination).1 AP sites, which lack the instructional information of the base, are non-coding GSK2606414 templates that can cause mutagenic end-points or serve as blocks to replicative DNA or RNA polymerases.2, 3 Moreover, abasic sites have the potential to chemically react with guanine residues in the strand opposite, forming a more severe form of DNA damage, i.e., a covalent interstrand crosslink (ICL).4 Uracil in DNA base-pairs with adenine when copied, thereby changing the coding properties of the original deaminated cytosine, a feature that seemingly underlies the common cancer-associated CT mutational signature.5, 6 Additionally, even with a highly evolved replication apparatus that includes proofreading activity, approximately 1 nucleotide misincorporation occurs in every 108 insertion events. 7 The accidental incorporation of a ribonucleotide is even more frequent, given that they are present at concentrations of 30- to 200-fold higher than their corresponding dNTPs.8 Inappropriate base-pairs can drive mutagenic outcomes, and ribonucleotides can alter the coding properties of the genome, as well as protein binding platforms (such as used by a transcription factor), epigenetic landscapes, etc. Strand-slippage errors can also occur during DNA replication, particularly in microsatellite sequences (stretches of 2C6 nucleotide repeats), since nearby duplicate bases can stabilize the incorrect pairing and permit chromosome duplication to proceed, creating an insertion/deletion (indel) precursor.9, 10 A subsequent round of replication would result in an expansion or retraction event, such as commonly seen in diseases of trinucleotide repeats, like Huntington disease (MIM: 143100). Lastly, replication through either microsatellite sequences, which are often found in fragile sites within the chromosome, or transcription-derived R-loops (i.e., RNA-DNA hybrids), can?cause replicative stress, leading to fork collapse, the formation of double-strand breaks (DSBs), and genomic instability.11, 12, 13, 14 Table 1 Intrinsic and Extrinsic DNA-Damaging Agents, and the Types and Consequences of Associated DNA Damage and MutS homologs (MSH), i.e., MutS (composed of MSH2 [MIM: 609309] and MSH6 [MIM: 600678]), which detects base mismatches and indels of 1C2 nucleotides, or MutS (composed of MSH2 and MSH3 [MIM: 600887]), which resolves larger indels. While the mechanism by which DNA repair proteins recognize DNA perturbations requires further elucidation, upon mismatch detection, MutS or MutS is converted into a sliding clamp through the exchange of ADPATP in its nucleotide binding site, facilitating damage verification.45 The clamp then diffuses along the DNA and interacts with MutL, which consists of MutL homolog 1 (MLH1 [MIM: 120436]) and post-meiotic segregation2 (PMS2 [MIM: 600259]).46 Proliferating cell nuclear antigen (PCNA [MIM: 176740]), a key replicative sliding clamp for long-range DNA polymerization, is.