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.
KeywordsR-loop Trinucleotide repeat instability Chromosome fragility Cytosine deamination Base excision repair (BER) MutLγ (Mlh1–Mlh3)
Thanks to Xiaofeng Allen Su for help with the figure. The author’s research is supported by the National Science Foundation (MCB1330743) and the National Institute of Health (GM122880 and GM105473).
- Lee JM, Chao WV, Vonsattel MJ, Pinto JP, Lucente RM, Abu-Elneel D, Ramos K, Mysore EM, Gillis JS, MacDonald T, Gusella ME, Harold JF, Stone D, Escott-Price TC, Han V, Vedernikov J, Holmans A, Jones P, Kwak L, Mahmoudi S, Orth M, Landwehrmeyer M, Paulsen GB, Dorsey JS, Shoulson ER, Myers IRH (2015) Identification of genetic factors that modify clinical onset of Huntington’s disease. Cell 162:516–526CrossRefGoogle Scholar
- McGinty RJ, Puleo F, Aksenova AY, Hisey JA, Shishkin AA, Pearson EL, Wang ET, Housman DE, Moore C, Mirkin SM (2017a) A defective mRNA cleavage and polyadenylation complex facilitates expansions of transcribed (GAA)n repeats associated with Friedreich’s ataxia. Cell Rep 20:2490–2500CrossRefPubMedPubMedCentralGoogle Scholar
- Mollersen L, Rowe AD, Illuzzi JL, Hildrestrand GA, Gerhold KJ, Tveteras L, Bjolgerud A, Wilson DM, 3rd, Bjoras M, Klungland A (2012) Neil1 is a genetic modifier of somatic and germline CAG trinucleotide repeat instability in R6/1 mice. Hum Mol Genet 21, 4939–4947CrossRefPubMedPubMedCentralGoogle Scholar
- Morales F, Vasquez M, Santamaria C, Cuenca P, Corrales E, Monckton DG (2016) A polymorphism in the MSH3 mismatch repair gene is associated with the levels of somatic instability of the expanded CTG repeat in the blood DNA of myotonic dystrophy type 1 patients. DNA Repair 40:57–66CrossRefPubMedGoogle Scholar
- Pinto RM, Dragileva E, Kirby A, Lloret A, Lopez E, St Claire J, Panigrahi GB, Hou C, Holloway K, Gillis T et al (2013) Mismatch repair genes Mlh1 and Mlh3 modify CAG instability in Huntington’s disease mice: genome-wide and candidate approaches. PLoS Genet 9:e1003930CrossRefPubMedPubMedCentralGoogle Scholar
- Polyzos A, Holt A, Brown C, Cosme C, Wipf P, Gomez-Marin A, Castro MR, Ayala-Pena S, McMurray CT (2016) Mitochondrial targeting of XJB-5–131 attenuates or improves pathophysiology in HdhQ150 animals with well-developed disease phenotypes. Hum Mol Genet 25:1792–1802CrossRefPubMedPubMedCentralGoogle Scholar