Repeat instability during DNA repair: Insights from model systems

The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them.

R-loops: targets for nuclease cleavage and repeat instability

R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

S-phase checkpoint regulations that preserve replication and chromosome integrity upon dNTP depletion

DNA replication stress, an important source of genomic instability, arises upon different types of DNA replication perturbations, including those that stall replication fork progression. Inhibitors of the cellular pool of deoxynucleotide triphosphates (dNTPs) slow down DNA synthesis throughout the genome. Following depletion of dNTPs, the highly conserved replication checkpoint kinase pathway, also known as the S-phase checkpoint, preserves the functionality and structure of stalled DNA replication forks and prevents chromosome fragmentation. The underlying mechanisms involve pathways extrinsic to replication forks, such as those involving regulation of the ribonucleotide reductase activity, the temporal program of origin firing, and cell cycle transitions. In addition, the S-phase checkpoint modulates the function of replisome components to promote replication integrity. This review summarizes the various functions of the replication checkpoint in promoting replication fork stability and genome integrity in the face of replication stress caused by dNTP depletion.

Role of recombination and replication fork restart in repeat instability

Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease. One important DNA repair mechanism to maintain genomic integrity is recombination. Though early studies dismissed recombination as a mechanism driving repeat expansion and instability, recent results indicate that mitotic recombination is a key pathway operating within repetitive DNA. The action is two-fold: first, it is an important mechanism to repair nicks, gaps, breaks, or stalled forks to prevent chromosome fragility and protect cell health; second, recombination can cause repeat expansions or contractions, which can be deleterious. In this review, we summarize recent developments that illuminate the role of recombination in maintaining genome stability at DNA repeats.

Fragility Extraordinaire: Unsolved Mysteries of Chromosome Fragile Sites

Chromosome fragile sites are a fascinating cytogenetic phenomenon now widely implicated in a slew of human diseases ranging from neurological disorders to cancer. Yet, the paths leading to these revelations were far from direct, and the number of fragile sites that have been molecularly cloned with known disease-associated genes remains modest. Moreover, as more fragile sites were being discovered, research interests in some of the earliest discovered fragile sites ebbed away, leaving a number of unsolved mysteries in chromosome biology. In this review we attempt to recount some of the early discoveries of fragile sites and highlight those phenomena that have eluded intense scrutiny but remain extremely relevant in our understanding of the mechanisms of chromosome fragility. We then survey the literature for disease association for a comprehensive list of fragile sites. We also review recent studies addressing the underlying cause of chromosome fragility while highlighting some ongoing debates. We report an observed enrichment for R-loop forming sequences in fragile site-associated genes than genomic average. Finally, we will leave the reader with some lingering questions to provoke discussion and inspire further scientific inquiries.

Evidence for chromosome fragility at the frataxin locus in Friedreich ataxia

Friedreich ataxia (FRDA) is a member of the Repeat Expansion Diseases, a group of genetic conditions resulting from an increase/expansion in the size of a specific tandem array. FRDA results from expansion of a GAA/TTC-tract in the first intron of the frataxin gene (FXN). The disease-associated tandem repeats all form secondary structures that are thought to contribute to the propensity of the repeat to expand. The subset of these diseases that result from a CGG/CCG-repeat expansion, such as Fragile X syndrome, also express a folate-sensitive fragile site coincident with the repeat on the affected chromosome. This chromosome fragility involves the generation of chromosome/chromatid gaps or breaks, or the high frequency loss of one or both copies of the affected gene when cells are grown under folate stress or as we showed previously, in the presence of an inhibitor of the ATM checkpoint kinase. Whether Repeat Expansion Disease loci containing different repeats form similar fragile sites was not known. We show here that the region of chromosome 9 that contains the FXN locus is intrinsically prone to breakage in vivo even in control cells. However, like FXS alleles, FRDA alleles show significantly elevated levels of chromosome abnormalities in the presence of an ATM inhibitor, consistent with the formation of a fragile site.

Analysis of chromosome damage by sister chromatid exchange (SCE) and redox homeostasis characterization on sheep flocks from Sardinian pasturelands

Over the last decades, an increase of pollutants of diverse origin (industrial, military, mining, etc.) was recorded in several areas of Sardinia Island. We report the results of a multidisciplinary and complementary study based on cytogenetic and physiological analyses. The data obtained show the effects of the environmental impact on six sheep flocks (Sardinian breed) grazing on natural pasturelands next to possible polluted areas and compared to three herds grazing in different areas far from those potentially contaminated and used as control. Sister chromatid exchange (SCE) test was used as cytogenetic test to analyze chromosomal damages and it was performed on peripheral blood samples collected from 129 adult sheep (age > 4 years) randomly selected from polluted (92 animals) and control (37 animals) areas. Two types of cell cultures were performed: without (normal cultures) and with the addition of 5-BrdU. SCE-mean values estimated over 35 cells counted for each animal were 8.65 ± 3.40, 8.10 ± 3.50, 8.05 ± 3.08, 7.42 ± 3.34, 9.28 ± 3.56 and 8.38 ± 3.29 in the exposed areas, whereas the average values were 7.86 ± 3.31 in the control group. Significant increases (P < 0.01) of SCEs were found in three investigated areas of Southern Sardinia. Furthermore, sheep of the same flocks were characterized for blood redox homeostasis in order to define the potential targets of oxidative damage and to identify biomarkers of the extent of animal exposure to environmental contaminants. The plasma levels of Asc, Toc and Ret were found to be significantly lower (P < 0.001) in exposed sheep (I, II, IV and V) than in the control group. TAC as well as GPx and SOD activities were higher in control than in the exposed groups (P < 0.001). Finally, plasma levels of N-Tyr, PC, and LPO were significantly lower (P < 0.001) in the control group than in the exposed groups.

Therapeutic research in the crystal chromosome disease Fanconi anemia

In the last decades there has been a great progress in understanding the pathological and genetic mechanisms involved in Fanconi anemia (FA), a rare disease characterized by chromosome fragility, congenital malformations, bone marrow failure (BMF) and high cancer predisposition. However, these advances have not gone in parallel with the development of medical treatments, with the exception of improved protocols of hematopoietic stem cell transplant (HSCT). BMF and hematological malignancies are the most important and life threatening conditions the patient suffer during the first and second decade of life, respectively, being HSCT the only curative treatment available. Solid tumors are the third hallmark of the disease, usually with poor prognosis as tumor resection is the only therapeutic option given that patients do not tolerate chemotherapy or radiation. With improved HSCT protocols, FA patient survival has increased, leading to a progressively increased number of solid malignancies in adult patients. Therapeutic research is currently focused in targeted therapies for solid tumors as well as in preventive options in the context of drug repurposing. This review summarizes current therapies and drugs used so far in clinical trials to treat Fanconi anemia, as well as the ones used in FA research with potential for future therapeutic opportunities including drugs that suppress chromosome fragility or are expected to delay the onset of BMF and cancer in Fanconi anemia.

Diagnosis of Fanconi's Anemia by Diepoxybutane Analysis in Children from Serbia

The high sensitivity of Fanconi's anemia (FA) cells to drug induced DNA interstrand crosslinks (ICL) such as diepoxybutane (DEB) was used as a part of FA screening in the children with clinical suspicion of FA. The study considered a total of 66 children with the hematological and/or congenital phenotypic symptoms reminiscent of FA. Blood samples from patients with clinical suspicion of FA and controls were collected for chromosome fragility evaluation by the DEB test. According to the results of DEB test, the patients were divided into two subgroups: FA displaying typical DEB sensitive cellular response and non FA. In this study, 10 out of 66 patients were found to have a FA cellular phenotype. The percentage of DEB-induced aberrant cells was increased more than 26 times in FA patients (range 22.00-82.00% with a mean of 48.32%) when compared to non FA patients (range 0.00-12.00% with a mean of 1.84%). The number of DEB-induced breaks/cells was more than 68 times higher in FA patients (range 0.26-4.39 with a mean of 1.37 breaks/cell) when compared to non FA patients (range 0.00-0.20 with a mean of 0.02 breaks/cell). The spontaneous chromosome fragility values in FA patients were overlapping those in non FA patients. Our results indicate that the DEB sensitivity test is the most reliable in vitro method for verification of the FA cellular phenotype.

Intersection of the fragile X-related disorders and the DNA damage response

The Repeat Expansion Diseases (REDs) are a large group of human genetic disorders that result from an increase in the number of repeats in a disease-specific tandem repeat or microsatellite. Emerging evidence suggests that the repeats trigger an error-prone form of DNA repair that causes the expansion mutation by exploiting a limitation in normal mismatch repair. Furthermore, while much remains to be understood about how the mutation causes pathology in different diseases in this group, there is evidence to suggest that some of the downstream consequences of repeat expansion trigger the DNA damage response in ways that contribute to disease pathology. This review will discuss these subjects in the context of the Fragile X-related disorders (aka the FMR1 disorders) that provide a particularly interesting example of the intersection between the repeats and the DNA damage response that may also be relevant for many other diseases in this group.