**8. Perspective on the role of DNA repair in cognitive functions**

The evidence discussed above in Section 6 clearly indicated that neuronal activity causes DNA double-strand breaks, especially in early response genes after neuronal stimulation. NHEJ repair is required to repair these breaks, and NHEJ repair is required for long-term memory formation. As discussed in Section 7, long-term memory formation depends on large numbers of epigenetic alterations including methylations and demethylations of cytosine in DNA. Although it is known that repair of double-strand breaks by NHEJ repair can leave epigenetic alterations (scars) (including alterations in the pattern of cytosine methylation) after the repair occurs, it is not known whether the NHEJ repair "scars" are a major portion of these epigenetic alterations. About a thousand demethylations occur during long-term memory formation in rats and mice. Base excision repair is central to demethylation of 5mC to cytosine. A deficiency in the TET/base excision repair pathway causes diminished epigenetic demethylations of DNA as well as alterations in memory.

Overall, memory and learning depend on epigenetic alterations. Two forms of DNA repair, NHEJ repair and base excision repair, have essential roles in cognitive functions, and at least base excision repair has a direct role in regulating one major type of epigenetic alteration, the demethylation of 5mC to cytosine in DNA during memory formation.

#### **9. Conclusion**

In eukaryotic cell nuclei, DNA is associated with histone proteins in highly organized and compact structures to form chromatin. When the DNA is damaged, repair enzymes need to gain access to the damage, and this requires modification of the compact structure. These modifications, termed epigenetic alterations, include acetylation of histones, methylation of histones and methylation of CpG sequences in DNA. Such epigenetic alterations can allow access of repair enzymes to sites of DNA damage while not disturbing the DNA base-pair sequence.

DNA repair processes are characteristically initiated rapidly and completed in a short period of minutes to hours, but epigenetic alterations introduced by such repair may be retained after repair is completed. A type of epigenetic alteration that can last after repair of a double-strand break is the DNA methylation of CpG islands in gene promoters. Such epigenetic alterations can silence gene expression. Also, several types of oxidative DNA damage are removed by base excision repair. Base excision repair is accompanied by epigenetic alterations of histones that are associated with genes containing CpG islands in their promoters. These epigenetic alterations can cause decreased transcription of the genes.

The persistent behavioral changes that are a prominent feature of addictions appear to be the result of epigenetic alterations that affect gene expression in particular regions of the brain. Specific epigenetic alterations have been found to be associated with addiction to alcohol, nicotine and cocaine. The epigenetic alterations that occur in those particular regions of the brain are considered to be involved with each of the addictions. Nicotine and cocaine, and alcohol through its metabolic product acetaldehyde, cause DNA damage in the brain. Such DNA damage is subject to DNA repair processes that likely cause at least a portion of the long lasting epigenetic alterations found in the brains of addicted individuals.

In humans and other mammals inherited mutations in genes necessary for DNA repair can cause neurodegenerative diseases. Examples of such diseases are ataxia telangiectasia, Huntington's disease, Aicardi-Goutières syndrome and Cockayne syndrome. The deficiencies in DNA repair in these diseases cause disruptions in the pattern of epigenetic alterations required for normal neuronal function. These epigenetic alterations likely underlie key features of the neurodegenerative disease phenotypes.

 Learning and new memories occur when mice explore a new, strange environment. Exploration of a novel environment increases the number of neurons with double-strand breaks in neuronal DNA, particularly in the dentate gyrus, which is involved in spatial learning and memory. Another neuronal activity, visual stimulation, was found to cause DNA double-strand breaks. Direct stimulation of the striatum region of the brain also caused DNA double-strand breaks. Memory retention of context associated electric shock events in mice involved induction of double-strand breaks and their repair by the process of non-homologous end joining in the hippocampus, a region of the brain known to be important in forming memories. Inhibition of non-homologous end joining substantially diminished memory retention.

The anterior cingulate cortex is a brain region important for long-term memory formation. Long-term memory (4 weeks in mice) subsequent to a contextual conditioning experience was found to be associated with substantial retention of a differential DNA methylation and gene expression pattern in the anterior cingulate cortex. In addition, differential DNA methylation in the hippocampus appears to be associated with short-term memory formation. Together, long-term and short-term memory formations are associated with on the order of a thousand demethylations of cytosines in neuron genomes during memory consolidation. Demethylation of 5-methylcytosine to cytosine in DNA depends on base excision repair.

 In general, the evidence indicates that, in mammals, DNA repair processes can cause epigenetic alterations in chromatin, some of which are long lasting. These epigenetic alterations can have negative consequences on neurological function such as in certain addictions and neurodegenerative diseases. In addition, epigenetic alterations resulting from DNA repair processes, such as non-homologous end joining and base excision repair, appear to have a positive role in facilitating adaptive cognitive capabilities that include memory and learning.
