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  • Review Article
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R-loops as Janus-faced modulators of DNA repair

Abstract

R-loops are non-B DNA structures with intriguing dual consequences for gene expression and genome stability. In addition to their recognized roles in triggering DNA double-strand breaks (DSBs), R-loops have recently been demonstrated to accumulate in cis to DSBs, especially those induced in transcriptionally active loci. In this Review, we discuss whether R-loops actively participate in DSB repair or are detrimental by-products that must be removed to avoid genome instability.

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Fig. 1: Current models for RNA–DNA hybrid accumulation in cis to DSBs.
Fig. 2: A function of R-loops in local transcriptional repression.
Fig. 3: Function of R-loops in the successive DSB repair steps.

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References

  1. Crossley, M. P., Bocek, M. & Cimprich, K. A. R-loops as cellular regulators and genomic threats. Mol. Cell 73, 398–411 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Vanoosthuyse, V. Strengths and weaknesses of the current strategies to map and characterize R-loops. Noncoding RNA 4, 9 (2018).

    Article  PubMed Central  Google Scholar 

  3. Ginno, P. A., Lott, P. L., Christensen, H. C., Korf, I. & Chédin, F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol. Cell 45, 814–825 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Sanz, L. A. et al. Prevalent, dynamic, and conserved R-loop structures associate with specific epigenomic signatures in mammals. Mol. Cell 63, 167–178 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Luna, R., Rondón, A. G., Pérez-Calero, C., Salas-Armenteros, I. & Aguilera, A. The THO complex as a paradigm for the prevention of cotranscriptional R-loops. Cold Spring Harb. Symp. Quant. Biol. 84, 105–114 (2019).

    Article  PubMed  Google Scholar 

  6. Marnef, A. & Legube, G. m6A RNA modification as a new player in R-loop regulation. Nat. Genet. 52, 27–28 (2020).

    Article  CAS  PubMed  Google Scholar 

  7. Chedin, F. & Benham, C. J. Emerging roles for R-loop structures in the management of topological stress. J. Biol. Chem. 295, 4684–4695 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Posse, V. et al. RNase H1 directs origin-specific initiation of DNA replication in human mitochondria. PLoS Genet. 15, e1007781 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. García-Muse, T. & Aguilera, A. R loops: from physiological to pathological roles. Cell 179, 604–618 (2019).

    Article  PubMed  CAS  Google Scholar 

  10. Zong, D., Oberdoerffer, P., Batista, P. J. & Nussenzweig, A. RNA: a double-edged sword in genome maintenance. Nat. Rev. Genet. 21, 651–670 (2020).

    Article  CAS  PubMed  Google Scholar 

  11. Brambati, A., Zardoni, L., Nardini, E., Pellicioli, A. & Liberi, G. The dark side of RNA:DNA hybrids. Mutat. Res. 784, 108300 (2020).

    Article  CAS  Google Scholar 

  12. Promonet, A. et al. Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites. Nat. Commun. 11, 3940 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Groh, M., Albulescu, L. O., Cristini, A. & Gromak, N. Senataxin: genome guardian at the interface of transcription and neurodegeneration. J. Mol. Biol. 429, 3181–3195 (2017).

    Article  CAS  PubMed  Google Scholar 

  14. Niehrs, C. & Luke, B. Regulatory R-loops as facilitators of gene expression and genome stability. Nat. Rev. Mol. Cell Biol. 21, 167–178 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Stolz, R. et al. Interplay between DNA sequence and negative superhelicity drives R-loop structures. Proc. Natl Acad. Sci. USA 116, 6260–6269 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Puget, N., Miller, K. M. & Legube, G. Non-canonical DNA/RNA structures during transcription-coupled double-strand break repair: roadblocks or bona fide repair intermediates? DNA Repair 81, 102661 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Paull, T. T. RNA–DNA hybrids and the convergence with DNA repair. Crit. Rev. Biochem. Mol. Biol. 54, 371–384 (2019).

    Article  CAS  PubMed  Google Scholar 

  18. Britton, S. et al. DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal. Nucleic Acids Res. 42, 9047–9062 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Teng, Y. et al. ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB. Nat. Commun. 9, 4115 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Yasuhara, T. et al. Human Rad52 promotes XPG-mediated R-loop processing to initiate transcription-associated homologous recombination repair. Cell 175, 558–570.e11 (2018).

    Article  CAS  PubMed  Google Scholar 

  21. Cohen, S. et al. Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations. Nat. Commun. 9, 533 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Lu, W.-T. et al. Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair. Nat. Commun. 9, 532 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. D’Alessandro, G. et al. BRCA2 controls DNA:RNA hybrid level at DSBs by mediating RNase H2 recruitment. Nat. Commun. 9, 5376 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Ohle, C. et al. Transient RNA–DNA hybrids are required for efficient double-strand break repair. Cell 167, 1001–1013.e7 (2016).

    Article  CAS  PubMed  Google Scholar 

  25. Jang, Y. et al. Intrinsically disordered protein RBM14 plays a role in generation of RNA:DNA hybrids at double-strand break sites. Proc. Natl Acad. Sci. USA 117, 5329–5338 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Yu, Z. et al. DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions. NAR Cancer 2, zcaa028 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  27. Tan, J. et al. An R-loop-initiated CSB–RAD52–POLD3 pathway suppresses ROS-induced telomeric DNA breaks. Nucleic Acids Res. 48, 1285–1300 (2020).

    Article  CAS  PubMed  Google Scholar 

  28. Matsui, M. et al. USP42 enhances homologous recombination repair by promoting R-loop resolution with a DNA–RNA helicase DHX9. Oncogenesis 9, 60 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Alfano, L. et al. Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation. Nucleic Acids Res. 47, 4068–4085 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhang, C. et al. METTL3 and N6-methyladenosine promote homologous recombination-mediated repair of DSBs by modulating DNA–RNA hybrid accumulation. Mol. Cell 79, 425–442.e7 (2020).

    Article  CAS  PubMed  Google Scholar 

  31. Rawal, C. C. et al. Senataxin ortholog Sen1 limits DNA:RNA hybrid accumulation at DNA double-strand breaks to control end resection and repair fidelity. Cell Rep. 31, 107603 (2020).

    Article  CAS  PubMed  Google Scholar 

  32. Domingo-Prim, J. et al. EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks. Nat. Commun. 10, 2135 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Li, L. et al. DEAD box 1 facilitates removal of RNA and homologous recombination at DNA double-strand breaks. Mol. Cell. Biol. 36, 2794–2810 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Brustel, J., Kozik, Z., Gromak, N., Savic, V. & Sweet, S. M. M. Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented by the RNA:DNA helicase senataxin. Sci. Rep. 8, 3850 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  35. Vítor, A. C., Huertas, P., Legube, G. & de Almeida, S. F. Studying DNA double-strand break repair: an ever-growing toolbox. Front. Mol. Biosci. 7, 24 (2020).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. D’Alessandro, G. & d Adda di Fagagna, F. Transcription and DNA damage: holding hands or crossing swords? J. Mol. Biol. 429, 3215–3229 (2017).

    Article  PubMed  CAS  Google Scholar 

  37. Pessina, F. et al. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat. Cell Biol. 21, 1286–1299 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Michelini, F. et al. Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks. Nat. Cell Biol. 19, 1400–1411 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Sharma, S. et al. MRE11–RAD50–NBS1 complex is sufficient to promote transcription by RNA polymerase II at double-strand breaks by melting DNA ends. Cell Rep. 34, 108565 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Vítor, A. C. et al. Single-molecule imaging of transcription at damaged chromatin. Sci. Adv. 5, eaau1249 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Burger, K., Schlackow, M. & Gullerova, M. Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks. Nucleic Acids Res. 47, 3467–3484 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Zicari, S. et al. DNA dependent protein kinase (DNA-PK) enhances HIV transcription by promoting RNA polymerase II activity and recruitment of transcription machinery at HIV LTR. Oncotarget 11, 699–726 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Jonkers, I. & Lis, J. T. Getting up to speed with transcription elongation by RNA polymerase II. Nat. Rev. Mol. Cell Biol. 16, 167–177 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Chen, L. et al. R-ChIP using inactive RNase H reveals dynamic coupling of R-loops with transcriptional pausing at gene promoters. Mol. Cell 68, 745–757.e5 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Zhang, X. et al. Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. Nat. Commun. 8, 15908 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  46. Edwards, D. S. et al. BRD4 prevents R-loop formation and transcription-replication conflicts by ensuring efficient transcription elongation. Cell Rep. 32, 108166 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Shivji, M. K. K., Renaudin, X., Williams, Ç. H. & Venkitaraman, A. R. BRCA2 regulates transcription elongation by RNA polymerase II to prevent R-loop accumulation. Cell Rep. 22, 1031–1039 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Caron, P., van der Linden, J. & van Attikum, H. Bon voyage: a transcriptional journey around DNA breaks. DNA Repair 82, 102686 (2019).

    Article  CAS  PubMed  Google Scholar 

  49. Awwad, S. W., Abu-Zhayia, E. R., Guttmann-Raviv, N. & Ayoub, N. NELF-E is recruited to DNA double-strand break sites to promote transcriptional repression and repair. EMBO Rep. 18, 745–764 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Shanbhag, N. M., Rafalska-Metcalf, I. U., Balane-Bolivar, C., Janicki, S. M. & Greenberg, R. A. ATM-dependent chromatin changes silence transcription in cis to DNA double-strand breaks. Cell 141, 970–981 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Iannelli, F. et al. A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks. Nat. Commun. 8, 15656 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Shah, N. et al. Tyrosine-1 of RNA polymerase II CTD controls global termination of gene transcription in mammals. Mol. Cell 69, 48–61.e6 (2018).

    Article  CAS  PubMed  Google Scholar 

  53. Collin, P., Jeronimo, C., Poitras, C. & Robert, F. RNA polymerase II CTD tyrosine 1 is required for efficient termination by the Nrd1–Nab3–Sen1 pathway. Mol. Cell 73, 655–669.e7 (2019).

    Article  CAS  PubMed  Google Scholar 

  54. Jonkers, I., Kwak, H. & Lis, J. T. Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. eLife 3, e02407 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  55. Pavri, R. et al. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 125, 703–717 (2006).

    Article  CAS  PubMed  Google Scholar 

  56. Veloso, A. et al. Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res. 24, 896–905 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Clouaire, T. et al. Comprehensive mapping of histone modifications at DNA double-strand breaks deciphers repair pathway chromatin signatures. Mol. Cell 72, 250–262.e6 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Morales, J. C. et al. XRN2 links transcription termination to DNA damage and replication stress. PLoS Genet. 12, e1006107 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  59. Richard, P., Feng, S. & Manley, J. L. A SUMO-dependent interaction between senataxin and the exosome, disrupted in the neurodegenerative disease AOA2, targets the exosome to sites of transcription-induced DNA damage. Genes Dev. 27, 2227–2232 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Marin-Vicente, C., Domingo-Prim, J., Eberle, A. B. & Visa, N. RRP6/EXOSC10 is required for the repair of DNA double-strand breaks by homologous recombination. J. Cell Sci. 128, 1097–1107 (2015).

    CAS  PubMed  Google Scholar 

  61. Blasius, M., Wagner, S. A., Choudhary, C., Bartek, J. & Jackson, S. P. A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response. Genes Dev. 28, 1977–1982 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Bader, A. S. & Bushell, M. DNA:RNA hybrids form at DNA double-strand breaks in transcriptionally active loci. Cell Death Dis. 11, 280 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Francia, S. et al. Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 488, 231–235 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Bonath, F., Domingo-Prim, J., Tarbier, M., Friedländer, M. R. & Visa, N. Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks. Nucleic Acids Res. 46, 11869–11882 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Tan-Wong, S. M., Dhir, S. & Proudfoot, N. J. R-loops promote antisense transcription across the mammalian genome. Mol. Cell 76, 600–616.e6 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Mazina, O. M., Keskin, H., Hanamshet, K., Storici, F. & Mazin, A. V. Rad52 inverse strand exchange drives RNA-templated DNA double-strand break repair. Mol. Cell 67, 19–29.e3 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Salas-Armenteros, I. et al. Human THO–Sin3A interaction reveals new mechanisms to prevent R-loops that cause genome instability. EMBO J. 36, 3532–3547 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Sheridan, R. M., Fong, N., D’Alessandro, A. & Bentley, D. L. Widespread backtracking by RNA pol II is a major effector of gene activation, 5′ pause release, termination, and transcription elongation rate. Mol. Cell 73, 107–118.e4 (2019).

    Article  CAS  PubMed  Google Scholar 

  69. Zatreanu, D. et al. Elongation factor TFIIS prevents transcription stress and R-loop accumulation to maintain genome stability. Mol. Cell 76, 57–69.e9 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Ribeiro de Almeida, C. et al. RNA helicase DDX1 converts RNA G-quadruplex structures into R-loops to promote IgH class switch recombination. Mol. Cell 70, 650–662.e8 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Feretzaki, M. et al. RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops. Nature 587, 303–308 (2020).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  73. Ariel, F. et al. R-loop mediated trans action of the APOLO long noncoding RNA. Mol. Cell 77, 1055–1065.e4 (2020).

    Article  CAS  PubMed  Google Scholar 

  74. Zaitsev, E. N. & Kowalczykowski, S. C. A novel pairing process promoted by Escherichia coli RecA protein: inverse DNA and RNA strand exchange. Genes Dev. 14, 740–749 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Wahba, L., Gore, S. K. & Koshland, D. The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability. eLife 2, e00505 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  76. Kasahara, M., Clikeman, J. A., Bates, D. B. & Kogoma, T. RecA protein-dependent R-loop formation in vitro. Genes Dev. 14, 360–365 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Lafuente-Barquero, J., García-Rubio, M. L., Martin-Alonso, M. S., Gómez-González, B. & Aguilera, A. Harmful DNA:RNA hybrids are formed in cis and in a Rad51-independent manner. eLife 9, e56674 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Mazina, O. M. et al. Replication protein A binds RNA and promotes R-loop formation. J. Biol. Chem. 295, 14203–14213 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Sanz, L. A. & Chédin, F. High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing. Nat. Protoc. 14, 1734–1755 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Crossley, M. P., Bocek, M. J., Hamperl, S., Swigut, T. & Cimprich, K. A. qDRIP: a method to quantitatively assess RNA–DNA hybrid formation genome-wide. Nucleic Acids Res. 48, e84 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Abakir, A. et al. N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nat. Genet. 52, 48–55 (2020).

    Article  CAS  PubMed  Google Scholar 

  82. Yang, X. et al. m6A promotes R-loop formation to facilitate transcription termination. Cell Res. 29, 1035–1038 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Li, M. & Klungland, A. Modifications and interactions at the R-loop. DNA Repair 96, 102958 (2020).

    Article  CAS  PubMed  Google Scholar 

  84. Zhang, L.-H. et al. The SUMOylated METTL8 induces R-loop and tumorigenesis via m3C. iScience 23, 100968 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Kang, H. J. et al. TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution. Nucleic Acids Res. 49, 269–284 (2021).

    Article  PubMed  CAS  Google Scholar 

  86. Peer, E., Rechavi, G. & Dominissini, D. Epitranscriptomics: regulation of mRNA metabolism through modifications. Curr. Opin. Chem. Biol. 41, 93–98 (2017).

    Article  CAS  PubMed  Google Scholar 

  87. Xiang, Y. et al. RNA m6A methylation regulates the ultraviolet-induced DNA damage response. Nature 543, 573–576 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Chen, H. et al. m5C modification of mRNA serves a DNA damage code to promote homologous recombination. Nat. Commun. 11, 2834 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Gómez-González, B. & Aguilera, A. Looping the (R) loop in DSB repair via RNA methylation. Mol. Cell 79, 361–362 (2020).

    Article  PubMed  CAS  Google Scholar 

  90. Rondón, A. G. & Aguilera, A. What causes an RNA–DNA hybrid to compromise genome integrity? DNA Repair 81, 102660 (2019).

    Article  PubMed  CAS  Google Scholar 

  91. Infantino, V. & Stutz, F. The functional complexity of the RNA-binding protein Yra1: mRNA biogenesis, genome stability and DSB repair. Curr. Genet. 66, 63–71 (2020).

    Article  CAS  PubMed  Google Scholar 

  92. Skourti-Stathaki, K. et al. R-loops enhance polycomb repression at a subset of developmental regulator genes. Mol. Cell 73, 930–945.e4 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Ui, A., Nagaura, Y. & Yasui, A. Transcriptional elongation factor ENL phosphorylated by ATM recruits polycomb and switches off transcription for DSB repair. Mol. Cell 58, 468–482 (2015).

    Article  CAS  PubMed  Google Scholar 

  94. Kakarougkas, A. et al. Requirement for PBAF in transcriptional repression and repair at DNA breaks in actively transcribed regions of chromatin. Mol. Cell 55, 723–732 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Sanchez, A. et al. BMI1–UBR5 axis regulates transcriptional repression at damaged chromatin. Proc. Natl Acad. Sci. USA 113, 11243–11248 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Ayrapetov, M. K., Gursoy-Yuzugullu, O., Xu, C., Xu, Y. & Price, B. D. DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin. Proc. Natl Acad. Sci. USA 111, 9169–9174 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Lemaître, C. & Soutoglou, E. Double strand break (DSB) repair in heterochromatin and heterochromatin proteins in DSB repair. DNA Repair 19, 163–168 (2014).

    Article  PubMed  CAS  Google Scholar 

  98. Yang, Q. et al. G9a coordinates with the RPA complex to promote DNA damage repair and cell survival. Proc. Natl Acad. Sci. USA 114, E6054–E6063 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Wu, W. et al. Interaction of BARD1 and HP1 is required for BRCA1 retention at sites of DNA damage. Cancer Res. 75, 1311–1321 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Skourti-Stathaki, K., Proudfoot, N. J. & Gromak, N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol. Cell 42, 794–805 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Skourti-Stathaki, K., Kamieniarz-Gdula, K. & Proudfoot, N. J. R-loops induce repressive chromatin marks over mammalian gene terminators. Nature 516, 436–439 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Rivosecchi, J. et al. Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription. EMBO J. 38, e101955 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  103. Mersaoui, S. Y. et al. Arginine methylation of the DDX5 helicase RGG/RG motif by PRMT5 regulates resolution of RNA:DNA hybrids. EMBO J. 38, e100986 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  104. Cristini, A., Groh, M., Kristiansen, M. S. & Gromak, N. RNA/DNA hybrid interactome identifies DXH9 as a molecular player in transcriptional termination and R-loop-associated DNA damage. Cell Rep. 23, 1891–1905 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Sharma, M. & Wente, S. R. Nucleocytoplasmic shuttling of Gle1 impacts DDX1 at transcription termination sites. Mol. Biol. Cell 31, 2398–2408 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Nguyen, H. D. et al. Functions of replication protein A as a sensor of R loops and a regulator of RNaseH1. Mol. Cell 65, 832–847.e4 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Hatchi, E. et al. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol. Cell 57, 636–647 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Welty, S. et al. RAD52 is required for RNA-templated recombination repair in post-mitotic neurons. J. Biol. Chem. 293, 1353–1362 (2018).

    Article  CAS  PubMed  Google Scholar 

  109. Bhatia, V. et al. BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature 511, 362–365 (2014).

    Article  CAS  PubMed  Google Scholar 

  110. Symington, L. S. Mechanism and regulation of DNA end resection in eukaryotes. Crit. Rev. Biochem. Mol. Biol. 51, 195–212 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Marini, F., Rawal, C. C., Liberi, G. & Pellicioli, A. Regulation of DNA double strand breaks processing: focus on barriers. Front. Mol. Biosci. 6, 55 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Daley, J. M. et al. Specificity of end resection pathways for double-strand break regions containing ribonucleotides and base lesions. Nat. Commun. 11, 3088 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Makharashvili, N. et al. Sae2/CtIP prevents R-loop accumulation in eukaryotic cells. eLife 7, e42733 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  114. Dang, T. T. & Morales, J. C. XRN2 links RNA:DNA hybrid resolution to double strand break repair pathway choice. Cancers 12, 1821 (2020).

    Article  CAS  PubMed Central  Google Scholar 

  115. Sollier, J. et al. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability. Mol. Cell 56, 777–785 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Stork, C. T. et al. Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage. eLife 5, e17548 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  117. Marnef, A. et al. A cohesin/HUSH- and LINC-dependent pathway controls ribosomal DNA double-strand break repair. Genes Dev. 33, 1175–1190 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Keskin, H. et al. Transcript-RNA-templated DNA recombination and repair. Nature 515, 436–439 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Meers, C., Keskin, H. & Storici, F. DNA repair by RNA: templated, or not templated, that is the question. DNA Repair 44, 17–21 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Meers, C. et al. Genetic characterization of three distinct mechanisms supporting RNA-driven DNA repair and modification reveals major role of DNA polymerase ζ. Mol. Cell 79, 1037–1050.e5 (2020).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  121. Wei, L. et al. DNA damage during the G0/G1 phase triggers RNA-templated, Cockayne syndrome B-dependent homologous recombination. Proc. Natl Acad. Sci. USA 112, E3495–E3504 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Mirman, Z. et al. 53BP1–RIF1–shieldin counteracts DSB resection through CST- and Polα-dependent fill-in. Nature 560, 112–116 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Itoh, T. & Tomizawa, J. Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H. Proc. Natl Acad. Sci. USA 77, 2450–2454 (1980).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Stuckey, R., García-Rodríguez, N., Aguilera, A. & Wellinger, R. E. Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system. Proc. Natl Acad. Sci. USA 112, 5779–5784 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Amon, J. D. & Koshland, D. RNase H enables efficient repair of R-loop induced DNA damage. eLife 5, e20533 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  126. Costantino, L. & Koshland, D. Genome-wide map of R-loop-induced damage reveals how a subset of R-loops contributes to genomic instability. Mol. Cell 71, 487–497.e3 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Dilley, R. L. et al. Break-induced telomere synthesis underlies alternative telomere maintenance. Nature 539, 54–58 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Roumelioti, F.-M. et al. Alternative lengthening of human telomeres is a conservative DNA replication process with features of break-induced replication. EMBO Rep. 17, 1731–1737 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Silva, B. et al. FANCM limits ALT activity by restricting telomeric replication stress induced by deregulated BLM and R-loops. Nat. Commun. 10, 2253 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  130. Pan, X. et al. FANCM suppresses DNA replication stress at ALT telomeres by disrupting TERRA R-loops. Sci. Rep. 9, 19110 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Pan, X. et al. FANCM, BRCA1, and BLM cooperatively resolve the replication stress at the ALT telomeres. Proc. Natl Acad. Sci. USA 114, E5940–E5949 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Lu, R. et al. The FANCM–BLM–TOP3A–RMI complex suppresses alternative lengthening of telomeres (ALT). Nat. Commun. 10, 2252 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  133. Cohen, S. et al. BLM-dependent Break-Induced Replication handles DSBs in transcribed chromatin upon impaired RNA:DNA hybrids dissolution. Preprint at BioRxiv https://doi.org/10.1101/2020.05.13.093112 (2020).

  134. Hatchi, E. et al. BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2–RAD52. Nature https://doi.org/10.1038/s41586-020-03150-2 (2021).

  135. Whalen, J. M. & Freudenreich, C. H. Location, location, location: the role of nuclear positioning in the repair of collapsed forks and protection of genome stability. Genes 11, 635 (2020).

    Article  CAS  PubMed Central  Google Scholar 

  136. Caridi, P. C., Delabaere, L., Zapotoczny, G. & Chiolo, I. And yet, it moves: nuclear and chromatin dynamics of a heterochromatic double-strand break. Philos. Trans. R. Soc. Lond. B Biol. Sci. 372, 20160291 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  137. Marnef, A. & Legube, G. Organizing DNA repair in the nucleus: DSBs hit the road. Curr. Opin. Cell Biol. 46, 1–8 (2017).

    Article  CAS  PubMed  Google Scholar 

  138. García-Benítez, F., Gaillard, H. & Aguilera, A. Physical proximity of chromatin to nuclear pores prevents harmful R loop accumulation contributing to maintain genome stability. Proc. Natl Acad. Sci. USA 114, 10942–10947 (2017).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  139. Gaillard, H., García-Benítez, F. & Aguilera, A. Gene gating at nuclear pores prevents the formation of R loops. Mol. Cell. Oncol. 5, e1405140 (2018).

    Article  PubMed  CAS  Google Scholar 

  140. Aten, J. A. et al. Dynamics of DNA double-strand breaks revealed by clustering of damaged chromosome domains. Science 303, 92–95 (2004).

    Article  CAS  PubMed  Google Scholar 

  141. Aymard, F. et al. Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes. Nat. Struct. Mol. Biol. 24, 353–361 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Roukos, V. et al. Spatial dynamics of chromosome translocations in living cells. Science 341, 660–664 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Altmeyer, M. et al. Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose). Nat. Commun. 6, 8088 (2015).

    Article  CAS  PubMed  Google Scholar 

  144. Kilic, S. et al. Phase separation of 53BP1 determines liquid-like behavior of DNA repair compartments. EMBO J. 38, e101379 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  145. Singatulina, A. S. et al. PARP-1 activation directs FUS to DNA damage sites to form PARG-reversible compartments enriched in damaged DNA. Cell Rep. 27, 1809–1821.e5 (2019).

    Article  CAS  PubMed  Google Scholar 

  146. Fay, M. M. & Anderson, P. J. The role of RNA in biological phase separations. J. Mol. Biol. 430, 4685–4701 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Garcia-Jove Navarro, M. et al. RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates. Nat. Commun. 10, 3230 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. Ries, R. J. et al. m6A enhances the phase separation potential of mRNA. Nature 571, 424–428 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Harami, G. M. et al. Phase separation by ssDNA binding protein controlled via protein–protein and protein–DNA interactions. Proc. Natl Acad. Sci. USA 117, 26206–26217 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Pessina, F. et al. DNA damage triggers a new phase in neurodegeneration. Trends Genet. 37, 337–354 (2021).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Funding in G.L.’s laboratory was provided by grants from the European Research Council (ERC-2014-CoG 647344), the Agence Nationale pour la Recherche (ANR-14-CE10-0002-01), the Institut National Contre le Cancer (INCA) and the Ligue Nationale Contre le Cancer (LNCC). We thank S. Egloff (CBI, Toulouse) and D. Lane (CBI, Toulouse) for their critical reading of the manuscript and apologize to colleagues whose work was not cited due to space constraints.

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Marnef, A., Legube, G. R-loops as Janus-faced modulators of DNA repair. Nat Cell Biol 23, 305–313 (2021). https://doi.org/10.1038/s41556-021-00663-4

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