Normal cellular functions and organism survival depend on a high degree of genetic stability. Recent evidence, however, is increasingly revealing that the genome is subject to complex sequence alterations. Prominent examples include meiotic DNA recombination, movement within chromosomes of special DNA sequences called transposable elements, and the recently defined DNA rearrangements critically influencing brain development and function. Accumulating evidence suggests that genomic alterations, mediated by DNA double-strand break (DSB) formation and repair, play an important role in brain physiology, ageing, cancer, psychiatric and neurodegenerative disorders.

Genome Maintenance

The fundamental characteristic of living cells is their ability to create and maintain order in a chaotic universe. This ability depends on the accurate duplication of vast quantities of genetic information carried in form of DNA, a process called DNA replication. Continued surveillance and repair are also critical for maintaining order, as DNA is constantly damaged by chemicals and radiation from the environment, as well as by thermal accidents and reactive molecules generated inside the cell. The protein machines that replicate and repair the cell’s DNA catalyse some of the most rapid and accurate processes known to biology. Although occasional genetic changes drive evolution and enhance the long-term survival of a species, the survival of the individual depends on a high degree of genetic stability (32-34).

Tens of thousands of random changes are created every day in the DNA of a human cell by heat, metabolic accidents, radiation and chemicals from the environment. For example, about 18000 purine bases (adenine and guanine) are lost from the DNA of a human cell every day because their N-glycosyl linkages to deoxyribose hydrolyse, a spontaneous reaction called depurination. Similarly, about 100 cytosine bases are lost per cell per day due to spontaneous deamination of cytosine to uracil in DNA. Thanks to the remarkable efficiency of DNA repair, less than 0,02% of these random changes accumulate as permanent mutations in the DNA sequence (32-34).

Normal cellular functions depend on overall genome stability, but it is becoming increasingly apparent that the genome is subject to sequence alterations in the context of various cellular processes, such as meiotic DNA recombination, movement within chromosomes of special DNA sequences called transposable elements, and the recently defined DNA rearrangements critically influencing brain development and function.

Genomic Alterations During Development

Genomic alterations have been implicated in different forms of cancer, in ageing, and in neurodevelopmental and neurodegenerative disorders (1). Various forms of DNA damage can cause genomic alterations, and an especially dangerous kind is represented by DNA double-strand breaks (DSBs), which arise when both DNA strands are broken at a given genomic location. When the free DNA ends created by a double-strand break are not joined together in the same configuration, and instead fuse with the DNA ends created by breaks at other genomic locations, they create DNA rearrangements. Such rearrangements can occur within chromosomes but also between different chromosomes fusing them together and giving rise to inter-chromosomal translocations.

Apart from their potential to damage the genome, double-strand breaks (DSBs) are purposefully employed by cells to functionally modify genomic information. During meiosis, for example, the homologous recombination (HR) machinery uses DSBs to mediate the exchange of genomic sequences between homologous chromosomes (2). Homologous recombination is a key step in gamete (sperm and egg) production, catalysing the exchange of bits of genetic information between corresponding maternal and paternal chromosomes and creating new DNA sequence combinations in the chromosomes passed on to the offspring.

Development and function of the adaptive immune system also depend on DSB-mediated genomic alterations. Lymphocyte progenitors increase the diversity of their antigen receptors via V(D)J recombination (3). As part of this process, RAG endonuclease mediates DSB formation at the ends of antigen receptor gene segments known as V, D and J segments. Through subsequent processing and joining, V(D)J variable region exons are created. Similarly, mature B lymphocytes use DSBs in a process called immunoglobulin heavy (IgH) chain class switch recombination to alter the effector functions of a given antibody (4).

An increasing body of evidence now suggests that somatic cells, including neural cells, employ genomic alterations much more extensively than previously thought. As described in a following section, brain function variability and susceptibility to brain disorders are intimately linked to variations in the coding and non-coding regions of the genome. Indeed, frequent genomic alterations in dividing neural progenitor cells have been proposed to promote neuronal diversity and give rise to somatic brain mosaicism (5-7). Such genomic alterations may not only underlie neuronal diversity and physiology but also play a role in the etiology of neurodevelopmental and psychiatric disorders (6).

Repair of DNA Damage

The double-helical structure of DNA is especially well suited for storage of information and repair, as each strand carries a complete copy of the genetic information. Thus, if one strand is damaged, the complementary strand is generally used to restore the correct nucleotide sequences to the damaged strand. Due to the remarkable efficiency of DNA as an information storage material, all cells employ this mechanism to store their genetic information; only a few small viruses use single-strand DNA or RNA as their genetic material. The two most common pathways cells use to repair single-strand DNA damage are: base excision repair and nucleotide excision repair. In both, the damage is excised, after which a DNA polymerase uses the undamaged strand as a template to restore the original sequence to the damaged strand, and finally the remaining gap is closed by a DNA ligase so that the newly added nucleotide(s) are now part of a continuous strand.

Base Excision Repair

The two major repair pathways differ in the way the damage is removed from DNA. In base excision repair, a group of enzymes called DNA glycosylases recognise different types of altered bases in DNA and catalyse their hydrolytic removal. Each DNA glycosylase recognises and removes a specific kind of DNA base alteration, including the most common deaminated Cs, deaminated As, different types of alkylated or oxidised bases, bases with open rings, and bases in which a carbon-carbon double bond has been accidentally converted to a carbon-carbon single bond. The gap created by DNA glycosylase action is recognised by an enzyme called AP endonuclease (AP for apurinic or apyrimidinic, endo to indicate that the nuclease cleaves within the polynucleotide chain), which cuts the phosphodiester backbone of the damaged strand, after which DNA polymerase adds a new nucleotide and DNA ligase seals the nick (35-37).

Nucleotide Excision Repair

The second major repair pathway is called nucleotide excision repair. This mechanism can repair the damage created by larger changes in DNA structure. Such “heavier” lesions include those caused by the covalent reaction of DNA bases with large hydrocarbons (such as the carcinogen benzopyrene found in tobacco smoke and diesel exhaust), as well as the various pyrimidine dimers (T-T, T-C and C-C) caused by sunlight. In this pathway, a large multienzyme complex scans the DNA double-helix for distortions, rather than for specific base changes. Upon finding a lesion, it cleaves the phosphodiester backbone of the abnormal strand on both sides of the distortion, and a DNA helicase removes the single-strand oligonucleotide containing the lesion. The resulting single-strand gap in the DNA double-helix is then repaired by DNA polymerase and DNA ligase (35-37).

Nonhomologous End Joining

DNA double-strand breaks (DSBs) are especially dangerous, as no intact template strand is left to enable accurate repair. Ionising radiation, replication errors, oxidizing agents and other reactive metabolites produced in the cell can cause DSBs and lead to breakdown of chromosomes into smaller fragments and to loss of genes when cells divide. As with single-strand DNA damage, two distinct mechanisms have evolved to deal with DSBs. The first mechanism is called nonhomologous end joining (NHEJ) and is widely used in mammalian somatic cells. In this end-joining mechanism, the broken ends are simply brought together and rejoined by DNA ligation, generally with the loss of nucleotides at the site of joining. Although each repair event of this type introduces a mutation in the DNA double-helix, it is still widely employed as a “quick and dirty” solution to join broken chromosomes, as very little of the mammalian genome is strictly essential for life. By the time a human reaches the age of 70, the typical somatic cell houses about 2000 such scars distributed throughout the genome, due to inaccurate NHEJ repair events. NHEJ can prove especially problematic when broken ends of different chromosomes are fused to each other. This type of rearrangements result in chromosomes with two centromeres and chromosomes lacking centromeres altogether; both types being missegregated during cell division (37-40).

NHEJ is also critical for lymphocyte development and for neuronal development (14, 15), being critically involved in the genomic alterations occurring during neuronal development (see next section) and in the rearrangements responsible for antigen receptor diversification (V(D)J recombination) in lymphocyte progenitors (15, 16). NHEJ inactivation in mice prevents progenitor B and T lymphocytes from developing into mature B and T cells by blocking the assembly of functional antibody and T-cell receptor genes (4).

Homologous Recombination

A more accurate pathway acting to repair DSBs employs homologous recombination (HR). HR normally occurs in newly replicated DNA and uses the sister chromatid as a template for the repair process. NHEJ predominates in human cells, whereas HR is used during and shortly after DNA replication (S and G2 phases), when sister chromatids are available to serve as templates. HR takes place only between DNA duplexes with a high degree of sequence similarity (homology). The two DNA duplexes that are undergoing HR “read” each other’s sequences by engaging in extensive base-pairing between a single strand from one DNA duplex and the complementary single strand from the other. In contrast to NHEJ, HR can repair DSBs accurately without any loss or alteration of nucleotides at the site of repair. In essence, one of the damaged strands of the broken DNA duplex can use the complementary strand of the intact DNA duplex as a template for repair. First, the ends of the broken DNA are chewed back by a nuclease to generate overhanging, single-strand 3’ ends. The next step is strand exchange (or strand invasion), during which one of the single-strand 3’ ends from the damaged DNA duplex inserts itself into the template duplex and searches it for homologous sequences through base pairing. Once base-pairing is established, a DNA polymerase extends the invading strand by using the complementary sequence provided by the template strand, thus restoring the damaged DNA. In the next step, strand displacement, the invading DNA strand is released and the broken double-helix is re-formed. Further DNA synthesis fills in the gaps using the strands from the damaged DNA as template and DNA ligase seals in the remaining nicks in the phosphodiester backbone. Thus, instead of using the partner complementary strand as a repair template, as in most DNA repair pathways, HR exploits a complementary strand from a separate DNA duplex (37-40).

In addition to repairing DNA damage, HR is used during gamete (sperm and egg) production through meiosis, where it catalyses the exchange of sequences between maternal and paternal homologous chromosomes. This provides an evolutionary advantage by creating new sequence combinations in the chromosomes passed to the offspring. HR during meiosis produces chromosome crossing-over and gene conversion, resulting in hybrid chromosomes that contain genetic information from both the maternal and paternal homologues. In meiotic HR, a specialised protein (called Spo11 in yeast) breaks both strands of the DNA double-helix in one of the recombining chromosomes. A nuclease then degrades the ends leaving protruding 3’ single-strand ends, and the following recombination reactions resemble those described above for repair of double-strand breaks.

Genomic Alterations and Brain Function

Increasing evidence reveals that neural cells undergo extensive genomic rearrangements, as stem or progenitor cells during brain development and later as mature neuronal cells in the adult brain. These rearrangements involve recurring double-strand break (DSB) clusters (RDCs) and seem to be purposefully employed by neural progenitor cells to promote neuronal diversity (5-7) and by mature neurons to support lasting network adaptations (learning and memory) in response to increased neuronal activity/stimulation (8-13). When the DNA repair mechanisms discussed above are not functioning properly, the various DSBs initiated in neuronal genes cannot be accurately repaired and the result are neurodegenerative or psychiatric disorders and even cancer, as described in the following section.

Genomic Alterations In Neural Progenitors

The study of DSB formation and repair and their possible biological functions was facilitated by the development of approaches such as HTGTS (high-throughput genome-wide translocation sequencing) which identifies endogenous DSBs based on their translocation to bait DSBs introduced in defined genomic locations via CRISPR-Cas9 (17, 18). This approach revealed over 30 recurring DSB clusters (RDCs) throughout the genome of mouse neural stem/progenitor cells (NSPC) (19). Genomic alterations in most RDC-genes have been associated with psychiatric disorders such as autism or schizophrenia, and with brain cancers such as medulloblastoma and glioblastoma (20, 21). In the latter case, RDCs are believed to contribute to gene amplifications, deletions and translocations (19).

DSBs in NSPC RDC-genes may result from transcription-replication collisions and contribute to the formation of genomic copy number variations (CNVs) detected in normal neurons of the frontal cortex in humans (5). Most neuronal RDC-genes contain short exons and long introns, and it is believed that intronic DSBs are frequently joined to each other in different combinations (intronic recombination) and thereby leading via exon shuffling to gene diversification in NSPCs (22, 23). Thus, increased replication stress during neurodevelopment may result in DSB-mediated gene diversification in neural progenitors.

Genomic Alterations In Mature Neurons

Recent evidence highlights the importance of DSB-mediated recombination events in the function of non-replicating, mature neurons (8-10). Mature neurons are thought to incur frequent DNA lesions as a result of oxidative stress, transcription, and even neuronal stimulation, such as optogenetic activation or physiological neurobehavioral tasks (8-10). Neuronal activity-induced DSBs have been proposed to be induced by topoisomerase 2b (Top2b) in the promoters of early response genes, thereby increasing the expression of these genes (8). Similarly to Top2b, Spo11 (the endonuclease that generates DSBs during meiosis) has been suspected to contribute to the formation of activity-induced DSBs in neurons of the hippocampus (9). Neuronal activity-induced DSBs are likely repaired via nonhomologous end joining (NHEJ), as described above (8).

Most early response genes encode transcription regulators with roles in learning and memory (12, 13). The higher DSB burden of neuronal early response genes in comparison to other genes will translate over the lifespan into higher rates of genomic alterations in these genes due to an expected rate of imperfect DSB repair over time. Given the important role of early response genes in cognitive function, these alterations may play a critical part in ageing-associated cognitive decline. Taken together, these recent findings highlight the importance of DSB repair in cognition and neurodegenerative disorders such as Alzheimer’s disease (24), and provide a foundation for future studies of DSB formation and repair in neurons.

For more information on neuronal stem cells, mitochondria, and interventions aimed at improving cognitive function, please refer to my article on Mitochondria and Cognition.

Genomic Alterations in Cancer

Genome instability takes different forms in different cancers. In ovarian and breast cancers, for example, chromosome breaks, translocations and deletions are very common and they are frequently correlated with mutations and epigenetic silencing in genes essential for homologous recombination repair of DNA double-strand breaks, especially Brca1 and Brca2. Colorectal cancers, on the other hand, acquire their genomic instability in two main ways. The majority of cancers display visibly altered chromosomes due to a form of chromosomal instability, whereas others display point mutations scattered all over the genome reflecting a defect in DNA mismatch repair. Thus, genetic instability can be acquired by cancers in multiple ways, and it is not an accidental by-product of malignant behaviour, but a contributory cause.

Mice deficient for factors involved in homologous recombination repair (HR) or non-homologous end-joining (NHEJ) develop brain tumors which frequently exhibit complex genomic rearrangements. Chromothripsis and chromoanasynthesis are two forms of genetic instability that lead to such complex rearrangements and play a role in numerous cancers and congenital diseases (25-28). In the first of these two types of catastrophic events, chromothripsis, tens to hundreds of clustered DNA double-strand breaks (DSB) occur simultaneously and generate DNA fragments which are re-ligated by error-prone repair processes. The faulty repair process, with frequent loss of DNA fragments, produces a highly rearranged derivative chromosome, with oscillations between two or three copy number states (29). Conversely, the local rearrangements and altered copy number arising from chromoanasynthesis are due to serial microhomology-mediated template switching during DNA replication (26). Ongoing studies are using murine tumour models to recapitulate these phenomena and elucidate the mechanistic aspects underlying complex genomic rearrangements. A better understanding of the biochemical and signalling contexts in which these catastrophic events occur will be very beneficial for future biomedical applications.

As described above, homologous recombination (HR) and non-homologous end-joining (NHEJ) are two major repair pathways for DNA double-strand breaks (DSB) in mammalian cells. Conditional inactivation of key factors of these two repair pathways in the neural progenitors of mice brains leads to cancer formation, such as medulloblastoma and glioma (30, 31). The brain tumors that develop upon inactivation of factors such as Brca2 (HR), Xrcc4, or Lig4 (NHEJ) in neural progenitor cells frequently display complex genome rearrangements. Better understanding the development of these tumors will help elucidate the role of repair processes in catastrophic genomic events.

Discussion

The recently found implications of complex genomic rearrangements in neuronal function, brain mosaicism, neurodegeneration and cancer open a new level of understanding brain development and function, and bring forward previously unrecognised therapeutic strategies against neurodegenerative disorders and cancer (such as medulloblastomas or gliomas). It is very interesting that, depending on the cellular context, such genomic alterations have been implicated in ageing and neurodegenerative disorders, but they also provide the opportunity to functionally modify genomic information. Important examples would include DSB-mediated genomic alterations during meiotic recombination, or adaptive immune system maturation. In the latter case, V(D)J recombination in lymphocyte progenitors and IgH class switch recombination in mature B lymphocytes are critical for adaptive immunity.

Extensive genomic alterations may underlie neuronal diversity and functional differences amongst individuals, and even contribute to the etiology of neurodegenerative disorders. But how are these rearrangements generated? Fortunately, recent findings identified key repair factors, such as BRCA2 (HR), XRCC4 or Lig4 (NHEJ) which, upon inactivation, lead to complex genome rearrangements in neural progenitor cells. Intriguingly, these factors are key players in the two major pathways repairing DNA double-strand breaks (homologous recombination repair HR and non-homologous end-joining NHEJ), but have also been associated with the formation of brain tumors (medulloblastomas or high-grade gliomas).

How are neural RDCs (recurrent double-strand break clusters) distributed along the genome, and which may be their functional implications for brain development and function? Approaches, such as HTGTS, that allow identification of DSBs (double-strand breaks) genome-wide now provide fundamental insights into how DSBs are formed and repaired. For example, we now know that several classes of DSBs join preferentially to DSBs within the same topological domain (17-19). One of the most striking realisations is that genomic alterations in RDC-genes in neural stem/progenitor cells (NSPCs) have been associated with cancers and psychiatric disorders. On the other hand, DSBs in RDC-genes may contribute to gene diversity in NSPCs. It is possible that replication stress during neurodevelopment leads to an increased DSB frequency, which in turn promotes (via exon shuffling or alternative splicing) transcript diversification in neural cells.

Equally fascinating are the recent implications of DSB formation and repair in the function of mature neurons. Activity-induced DSBs in mature neurons may promote early response gene expression, which in turn impacts cognitive functions such as learning and memory. In this context, future studies will investigate how these DSBs form, with possible involvement of Top2b and Spo11, how these DSBs promote gene activation, and what are the connotations for our understanding of learning and memory.

While such pseudo-controlled genomic alterations can be beneficial for brain cell diversification and later for lasting network adaptations upon cognitive stimulation, they can also support cancerous transformation or psychiatric disorders if the key DSB repair pathways (HR and NHEJ) are not properly functioning. Both aspects are highly impactful and fascinating and warrant further investigation. Among other approaches, higher-resolution single-cell sequencing and murine tumor models will aid identification of signalling and repair factors involved in these genome rearrangements. Such insights will prove highly relevant for future biomedical applications in the context of brain physiology and disorders, cancer, and ageing-associated functional decline.

Author: Sebastian Florescu, PhD

HOMEPAGE

Published online in February 2020

References

1. Wang J, Lindahl T, Maintenance of Genome Stability, Genomics Proteomics Bioinformatics, 14 (2016) 119–121.
2. Neale MJ, Keeney S, Clarifying the mechanics of DNA strand exchange in meiotic recombination, Nature, 442 (2006) 153–158.
3. Schatz DG, Ji Y, Recombination centres and the orchestration of V(D)J recombination, Nat Rev Immunol, 11 (2011) 251–263.
4. Alt FW, Zhang Y, Meng FL, Guo C, Schwer B, Mechanisms of programmed DNA lesions and genomic instability in the immune system, Cell, 152 (2013) 417–429.
5. McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH, Mosaic copy number variation in human neurons, Science, 342 (2013) 632–637.
6. McConnell MJ, Moran JV et al. Brain Somatic Mosaicism N, Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network, Science, 356 (2017).
7. Poduri A, Evrony GD, Cai X, Walsh CA, Somatic mutation, genomic variation, and neurological disease, Science, 341 (2013) 1237758.
8. Madabhushi R, Gao F et al. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes, Cell, 161 (2015) 1592–1605.
9. Suberbielle E, Sanchez PE et al. Physiologic brain activity causes DNA double-strand breaks in neurons, with exacerbation by amyloid-beta, Nat Neurosci, 16 (2013) 613.
10. Crowe SL, Movsesyan VA, Jorgensen TJ, Kondratyev A, Rapid phosphorylation of histone H2A.X following ionotropic glutamate receptor activation, Eur J Neurosci, 23 (2006) 2351–2361.
11. Sekiguchi JM, Gao Y et al. Nonhomologous end-joining proteins are required for V(D)J recombination, normal growth, and neurogenesis, Cold Spring Harb Symp Quant Biol, 64 (1999) 169–181.
12. West AE, Greenberg ME, Neuronal activity-regulated gene transcription in synapse development and cognitive function, Cold Spring Harb Perspect Biol, 3 (2011).
13. Cholewa-Waclaw J, Bird A et al. The Role of Epigenetic Mechanisms in the Regulation of Gene Expression in the Nervous System, J Neurosci, 36 (2016) 11427–11434.
14. Frank KM, Sekiguchi JM et al. Late embryonic lethality and impaired V(D)J recombination in mice lacking DNA ligase IV, Nature, 396 (1998) 173–177.
15. Gao Y, Sun Y et al. A critical role for DNA end-joining proteins in both lymphogenesis and neurogenesis, Cell, 95 (1998) 891–902.
16. Chun J, Schatz DG, Rearranging views on neurogenesis: neuronal death in the absence of DNA end-joining proteins, Neuron, 22 (1999) 7–10.
17. Chiarle R, Zhang Y et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells, Cell, 147 (2011) 107–119.
18. Frock RL, Hu J et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases, Nat Biotechnol, 33 (2015) 179–186.
19. Wei PC, Chang AN, Kao J, Du Z, Meyers RM, Alt FW, Schwer B, Long neural genes harbor recurrent DNA break clusters in neural stem/progenitor cells, Cell, 164 (2016).
20. Northcott PA, Shih DJ, Peacock J et al. Subgroup-specific structural variation across 1,000 medulloblastoma genomes, Nature, 488 (2012) 49–56.
21. Frattini V, Trifonov V et al. The integrated landscape of driver genomic alterations in glioblastoma, Nat Genet, 45 (2013) 1141–1149.
22. Alt FW, Wei PC, Schwer B, Recurrently Breaking Genes in Neural Progenitors: Potential Roles of DNA Breaks in Neuronal Function, Degeneration and Cancer, in: Genome Editing in Neurosciences, 2017, pp. 63–72.
23. Gilbert W, The exon theory of genes, Cold Spring Harb Symp Quant Biol, 52 (1987).
24. Suberbielle E, Djukic B et al. DNA repair factor BRCA1 depletion occurs in Alzheimer brains and impairs cognitive function in mice, Nature communications, 6 (2015) 8897.
25. Stephens, P. J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27–40 (2011).
26. Holland, A. J. & Cleveland, D. W. Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements. Nat. Med. 18, 1630–1638 (2012).
27. Zhang, C. Z., Leibowitz, M. L. & Pellman, D. Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements. Genes Dev. 27 (2013).
28. Rode, A., Maass, K. K., Willmund, K. V., Lichter, P. & Ernst, A. Chromothripsis in cancer cells: an update. Int. J. Cancer 138, 2322–2333 (2016).
29. Korbel, J. O. & Campbell, P. J. Criteria for inference of chromothripsis in cancer genomes. Cell 152, 1226–1236 (2013).
30. Yan, C. T. et al. XRCC4 suppresses medulloblastomas with recurrent translocations in p53-deficient mice. Proc. Natl Acad. Sci. USA 103, 7378–7383 (2006).
31. Frappart, P. O. et al. Recurrent genomic alterations characterize medulloblastoma arising from DNA double-strand break repair deficiency. Proc. Natl Acad. Sci. USA 106, 1880–1885 (2009).
32. Cooper GM, Brudno M, Stone ES et al. (2004) Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res. 14, 539–548.
33. Hedges SB (2002) The origin and evolution of model organisms. Nat. Rev. Genet. 3.
34. Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Morgan, David; Raff, Martin; Roberts, Keith; Walter, Peter. Molecular Biology of the Cell. W. W. Norton & Company.
35. Hanawalt PC & Spivak G (2008) Transcription-coupled DNA repair: two decades of progress and surprises. Nat. Rev. Mol. Cell Biol. 9, 958–970.
36. Reardon JT & Sancar A (2005) Nucleotide excision repair. Prog. Nucleic Acid Res. Mol. Biol. 79, 183–235.
37. Malkova A & Haber JE (2012) Mutations arising during repair of chromosome breaks. Annu. Rev. Genet. 46, 455–473.
38. Chen Z, Yang H & Pavletich NP (2008) Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature 453, 489–494.
39. Moynahan ME & Jasin M (2010) Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat. Rev. Mol. Cell Biol. 11, 196–207.
40. Heyer WD, Ehmsen KT & Liu J (2010) Regulation of homologous recombination in eukaryotes. Annu. Rev. Genet. 44, 113–139.