Out of Balance: R-loops in Human Disease

1. ThomasM, WhiteRL, DavisRW (1976) Hybridization of RNA to double-stranded DNA: formation of R-loops. Proc Natl Acad Sci U S A 73: 2294–2298.

2. WhiteRL, HognessDS (1977) R loop mapping of the 18S and 28S sequences in the long and short repeating units of Drosophila melanogaster rDNA. Cell 10: 177–192.

3. DroletM, BiX, LiuLF (1994) Hypernegative supercoiling of the DNA template during transcription elongation in vitro. J Biol Chem 269: 2068–2074.

4. AguileraA, Garcia-MuseT (2012) R loops: from transcription byproducts to threats to genome stability. Mol Cell 46: 115–124.

5. HamperlS, CimprichKA (2014) The contribution of co-transcriptional RNA∶DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst) 19: 84–94.

6. Skourti-StathakiK, ProudfootNJ (2014) A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes Dev 28: 1384–1396.

7. WahbaL, GoreSK, KoshlandD (2013) The homologous recombination machinery modulates the formation of RNA-DNA hybrids and associated chromosome instability. Elife 2: e00505.

8. BoguslawskiSJ, SmithDE, MichalakMA, MickelsonKE, YehleCO, et al. (1986) Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids. J Immunol Methods 89: 123–130.

9. PhillipsDD, GarbocziDN, SinghK, HuZ, LepplaSH, et al. (2013) The sub-nanomolar binding of DNA-RNA hybrids by the single-chain Fv fragment of antibody S9.6. J Mol Recognit 26: 376–381.

10. HuZ, ZhangA, StorzG, GottesmanS, LepplaSH (2006) An antibody-based microarray assay for small RNA detection. Nucleic Acids Res 34: e52.

11. El HageA, FrenchSL, BeyerAL, TollerveyD (2010) Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev 24: 1546–1558.

12. MischoHE, Gomez-GonzalezB, GrzechnikP, RondonAG, WeiW, et al. (2011) Yeast Sen1 helicase protects the genome from transcription-associated instability. Mol Cell 41: 21–32.

13. SunQ, CsorbaT, Skourti-StathakiK, ProudfootNJ, DeanC (2013) R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science 340: 619–621.

14. BecherelOJ, YeoAJ, StellatiA, HengEY, LuffJ, et al. (2013) Senataxin plays an essential role with DNA damage response proteins in meiotic recombination and gene silencing. PLoS Genet 9: e1003435.

15. YeoAJ, BecherelOJ, LuffJE, CullenJK, WongsurawatT, et al. (2014) R-Loops in Proliferating Cells but Not in the Brain: Implications for AOA2 and Other Autosomal Recessive Ataxias. PLoS ONE 9: e90219.

16. Skourti-StathakiK, ProudfootNJ, GromakN (2011) Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol Cell 42: 794–805.

17. GinnoPA, LimYW, LottPL, KorfI, ChedinF (2013) GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res 23: 1590–1600.

18. GinnoPA, LottPL, ChristensenHC, KorfI, ChedinF (2012) R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell 45: 814–825.

19. XuB, ClaytonDA (1996) RNA-DNA hybrid formation at the human mitochondrial heavy-strand origin ceases at replication start sites: an implication for RNA-DNA hybrids serving as primers. EMBO J 15: 3135–3143.

20. ItohT, TomizawaJ (1980) Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H. Proc Natl Acad Sci U S A 77: 2450–2454.

21. YuK, ChedinF, HsiehCL, WilsonTE, LieberMR (2003) R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat Immunol 4: 442–451.

22. ChanYA, AristizabalMJ, LuPY, LuoZ, HamzaA, et al. (2014) Genome-Wide Profiling of Yeast DNA∶RNA Hybrid Prone Sites with DRIP-Chip. PLoS Genet 10: e1004288.

23. TousC, AguileraA (2007) Impairment of transcription elongation by R-loops in vitro. Biochem Biophys Res Commun 360: 428–432.

24. HuertasP, AguileraA (2003) Cotranscriptionally formed DNA∶RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol Cell 12: 711–721.

25. NakamaM, KawakamiK, KajitaniT, UranoT, MurakamiY (2012) DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation. Genes Cells 17: 218–233.

26. Castellano-PozoM, Santos-PereiraJM, RondonAG, BarrosoS, AndujarE, et al. (2013) R loops are linked to histone H3 S10 phosphorylation and chromatin condensation. Mol Cell 52: 583–590.

27. YangY, McBrideKM, HensleyS, LuY, ChedinF, et al. (2014) Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell 53: 484–497.

28. Santos-PereiraJM, HerreroAB, Garcia-RubioML, MarinA, MorenoS, et al. (2013) The Npl3 hnRNP prevents R-loop-mediated transcription-replication conflicts and genome instability. Genes Dev 27: 2445–2458.

29. SordetO, RedonCE, Guirouilh-BarbatJ, SmithS, SolierS, et al. (2009) Ataxia telangiectasia mutated activation by transcription- and topoisomerase I-induced DNA double-strand breaks. EMBO Rep 10: 887–893.

30. LiX, ManleyJL (2005) Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122: 365–378.

31. StirlingPC, ChanYA, MinakerSW, AristizabalMJ, BarrettI, et al. (2012) R-loop-mediated genome instability in mRNA cleavage and polyadenylation mutants. Genes Dev 26: 163–175.

32. HelmrichA, BallarinoM, ToraL (2011) Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol Cell 44: 966–977.

33. TuduriS, CrabbeL, ContiC, TourriereH, Holtgreve-GrezH, et al. (2009) Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription. Nat Cell Biol 11: 1315–1324.

34. WahbaL, AmonJD, KoshlandD, Vuica-RossM (2011) RNase H and multiple RNA biogenesis factors cooperate to prevent RNA∶DNA hybrids from generating genome instability. Mol Cell 44: 978–988.

35. Herrera-MoyanoE, MerguiX, Garcia-RubioML, BarrosoS, AguileraA (2014) The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts. Genes Dev 28: 735–748.

36. CerritelliSM, CrouchRJ (2009) Ribonuclease H: the enzymes in eukaryotes. FEBS J 276: 1494–1505.

37. BouleJB, ZakianVA (2007) The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates. Nucleic Acids Res 35: 5809–5818.

38. ShinJH, KelmanZ (2006) The replicative helicases of bacteria, archaea, and eukarya can unwind RNA-DNA hybrid substrates. J Biol Chem 281: 26914–26921.

39. MoreiraMC, KlurS, WatanabeM, NemethAH, Le BerI, et al. (2004) Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2. Nat Genet 36: 225–227.

40. AnheimM, MongaB, FleuryM, CharlesP, BarbotC, et al. (2009) Ataxia with oculomotor apraxia type 2: clinical, biological and genotype/phenotype correlation study of a cohort of 90 patients. Brain 132: 2688–2698.

41. ChenYZ, BennettCL, HuynhHM, BlairIP, PulsI, et al. (2004) DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). Am J Hum Genet 74: 1128–1135.

42. SuraweeraA, LimY, WoodsR, BirrellGW, NasimT, et al. (2009) Functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation. Hum Mol Genet 18: 3384–3396.

43. SteinmetzEJ, WarrenCL, KuehnerJN, PanbehiB, AnsariAZ, et al. (2006) Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell 24: 735–746.

44. WestS, GromakN, ProudfootNJ (2004) Human 5′→3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432: 522–525.

45. SuraweeraA, BecherelOJ, ChenP, RundleN, WoodsR, et al. (2007) Senataxin, defective in ataxia oculomotor apraxia type 2, is involved in the defense against oxidative DNA damage. J Cell Biol 177: 969–979.

46. YuceO, WestSC (2013) Senataxin, defective in the neurodegenerative disorder ataxia with oculomotor apraxia 2, lies at the interface of transcription and the DNA damage response. Mol Cell Biol 33: 406–417.

47. AlzuA, BermejoR, BegnisM, LuccaC, PicciniD, et al. (2012) Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes. Cell 151: 835–846.

48. RichardP, FengS, ManleyJL (2013) 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.

49. VantaggiatoC, BondioniS, AiroldiG, BozzatoA, BorsaniG, et al. (2011) Senataxin modulates neurite growth through fibroblast growth factor 8 signalling. Brain 134: 1808–1828.

50. PowellWT, CoulsonRL, GonzalesML, CraryFK, WongSS, et al. (2013) R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation. Proc Natl Acad Sci U S A 110: 13938–13943.

51. HelmrichA, BallarinoM, NudlerE, ToraL (2013) Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol 20: 412–418.

52. ChonH, SparksJL, RychlikM, NowotnyM, BurgersPM, et al. (2013) RNase H2 roles in genome integrity revealed by unlinking its activities. Nucleic Acids Res 41: 3130–3143.

53. CerritelliSM, FrolovaEG, FengC, GrinbergA, LovePE, et al. (2003) Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice. Mol Cell 11: 807–815.

54. RydbergB, GameJ (2002) Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts. Proc Natl Acad Sci U S A 99: 16654–16659.

55. Nick McElhinnySA, KumarD, ClarkAB, WattDL, WattsBE, et al. (2010) Genome instability due to ribonucleotide incorporation into DNA. Nat Chem Biol 6: 774–781.

56. ReijnsMA, RabeB, RigbyRE, MillP, AstellKR, et al. (2012) Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell 149: 1008–1022.

57. LazzaroF, NovarinaD, AmaraF, WattDL, StoneJE, et al. (2012) RNase H and postreplication repair protect cells from ribonucleotides incorporated in DNA. Mol Cell 45: 99–110.

58. AranaME, KernsRT, WhareyL, GerrishKE, BushelPR, et al. (2012) Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae. DNA Repair (Amst) 11: 933–941.

59. CrowYJ, LeitchA, HaywardBE, GarnerA, ParmarR, et al. (2006) Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutieres syndrome and mimic congenital viral brain infection. Nat Genet 38: 910–916.

60. CrowYJ, RehwinkelJ (2009) Aicardi-Goutieres syndrome and related phenotypes: linking nucleic acid metabolism with autoimmunity. Hum Mol Genet 18: R130–136.

61. CrowYJ, HaywardBE, ParmarR, RobinsP, LeitchA, et al. (2006) Mutations in the gene encoding the 3′-5′ DNA exonuclease TREX1 cause Aicardi-Goutieres syndrome at the AGS1 locus. Nat Genet 38: 917–920.

62. RiceGI, KasherPR, ForteGM, MannionNM, GreenwoodSM, et al. (2012) Mutations in ADAR1 cause Aicardi-Goutieres syndrome associated with a type I interferon signature. Nat Genet 44: 1243–1248.

63. RiceGI, BondJ, AsipuA, BrunetteRL, ManfieldIW, et al. (2009) Mutations involved in Aicardi-Goutieres syndrome implicate SAMHD1 as regulator of the innate immune response. Nat Genet 41: 829–832.

64. Lee-KirschMA, WolfC, GuntherC (2014) Aicardi-Goutieres syndrome: a model disease for systemic autoimmunity. Clin Exp Immunol 175: 17–24.

65. RabeB (2013) Aicardi-Goutieres syndrome: clues from the RNase H2 knock-out mouse. J Mol Med (Berl) 91: 1235–1240.

66. HillerB, AchleitnerM, GlageS, NaumannR, BehrendtR, et al. (2012) Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity. J Exp Med 209: 1419–1426.

67. BubeckD, ReijnsMA, GrahamSC, AstellKR, JonesEY, et al. (2011) PCNA directs type 2 RNase H activity on DNA replication and repair substrates. Nucleic Acids Res 39: 3652–3666.

68. RigbyRE, WebbLM, MackenzieKJ, LiY, LeitchA, et al. (2014) RNA∶DNA hybrids are a novel molecular pattern sensed by TLR9. EMBO J 33: 542–558.

69. Lopez CastelA, ClearyJD, PearsonCE (2010) Repeat instability as the basis for human diseases and as a potential target for therapy. Nat Rev Mol Cell Biol 11: 165–170.

70. GrabczykE, MancusoM, SammarcoMC (2007) A persistent RNA.DNA hybrid formed by transcription of the Friedreich ataxia triplet repeat in live bacteria, and by T7 RNAP in vitro. Nucleic Acids Res 35: 5351–5359.

71. LinY, DentSY, WilsonJH, WellsRD, NapieralaM (2010) R loops stimulate genetic instability of CTG.CAG repeats. Proc Natl Acad Sci U S A 107: 692–697.

72. McIvorEI, PolakU, NapieralaM (2010) New insights into repeat instability: role of RNA*DNA hybrids. RNA Biol 7: 551–558.

73. ReddyK, TamM, BowaterRP, BarberM, TomlinsonM, et al. (2011) Determinants of R-loop formation at convergent bidirectionally transcribed trinucleotide repeats. Nucleic Acids Res 39: 1749–1762.

74. BelotserkovskiiBP, MirkinSM, HanawaltPC (2013) DNA sequences that interfere with transcription: implications for genome function and stability. Chem Rev 113: 8620–8637.

75. GrohM, LufinoMM, Wade-MartinsR, GromakN (2014) R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome. PLoS Genet 10: e1004318.

76. LoomisEW, SanzLA, ChedinF, HagermanPJ (2014) Transcription-Associated R-Loop Formation across the Human FMR1 CGG-Repeat Region. PLoS Genet 10: e1004294.

77. ColakD, ZaninovicN, CohenMS, RosenwaksZ, YangWY, et al. (2014) Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome. Science 343: 1002–1005.

78. HaeuslerAR, DonnellyCJ, PerizG, SimkoEA, ShawPG, et al. (2014) C9orf72 nucleotide repeat structures initiate molecular cascades of disease. Nature 507: 195–200.

79. HanahanD, WeinbergRA (2011) Hallmarks of cancer: the next generation. Cell 144: 646–674.

80. NegriniS, GorgoulisVG, HalazonetisTD (2010) Genomic instability–an evolving hallmark of cancer. Nat Rev Mol Cell Biol 11: 220–228.

81. ChernikovaSB, RazorenovaOV, HigginsJP, SishcBJ, NicolauM, et al. (2012) Deficiency in mammalian histone H2B ubiquitin ligase Bre1 (Rnf20/Rnf40) leads to replication stress and chromosomal instability. Cancer Res 72: 2111–2119.

82. BhatiaV, BarrosoSI, Garcia-RubioML, TuminiE, Herrera-MoyanoE, et al. (2014) BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature 511: 362–365.

83. JacksonBR, NoerenbergM, WhitehouseA (2014) A novel mechanism inducing genome instability in Kaposi's sarcoma-associated herpesvirus infected cells. PLoS Pathog 10: e1004098.

84. SikdarN, BanerjeeS, ZhangH, SmithS, MyungK (2008) Spt2p defines a new transcription-dependent gross chromosomal rearrangement pathway. PLoS Genet 4: e1000290.

85. San FilippoJ, SungP, KleinH (2008) Mechanism of eukaryotic homologous recombination. Annu Rev Biochem 77: 229–257.

86. ChaudhuriJ, TianM, KhuongC, ChuaK, PinaudE, et al. (2003) Transcription-targeted DNA deamination by the AID antibody diversification enzyme. Nature 422: 726–730.

87. RobbianiDF, NussenzweigMC (2013) Chromosome translocation, B cell lymphoma, and activation-induced cytidine deaminase. Annu Rev Pathol 8: 79–103.

88. RuizJF, Gomez-GonzalezB, AguileraA (2011) AID induces double-strand breaks at immunoglobulin switch regions and c-MYC causing chromosomal translocations in yeast THO mutants. PLoS Genet 7: e1002009.

89. DuquetteML, PhamP, GoodmanMF, MaizelsN (2005) AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation. Oncogene 24: 5791–5798.

90. BurnsMB, LackeyL, CarpenterMA, RathoreA, LandAM, et al. (2013) APOBEC3B is an enzymatic source of mutation in breast cancer. Nature 494: 366–370.

91. KulisM, EstellerM (2010) DNA methylation and cancer. Adv Genet 70: 27–56.

92. WongsurawatT, JenjaroenpunP, KwohCK, KuznetsovV (2011) Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity. Nucleic Acids Res 40: e16.

93. HynesNE, StoelzleT (2009) Key signalling nodes in mammary gland development and cancer: Myc. Breast Cancer Res 11: 210.

94. BalkB, MaicherA, DeesM, KlermundJ, Luke-GlaserS, et al. (2013) Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence. Nat Struct Mol Biol 20: 1199–1205.

95. PfeifferV, CrittinJ, GrolimundL, LingnerJ (2013) The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening. EMBO J 32: 2861–2871.

96. De AmicisA, PianeM, FerrariF, FanciulliM, DeliaD, et al. (2011) Role of senataxin in DNA damage and telomeric stability. DNA Repair (Amst) 10: 199–209.

97. WheelhouseRT, ChairesJB (2010) Drug binding to DNA×RNA hybrid structures. Methods Mol Biol 613: 55–70.

98. ShawNN, AryaDP (2008) Recognition of the unique structure of DNA∶RNA hybrids. Biochimie 90: 1026–1039.

99. ShawNN, XiH, AryaDP (2008) Molecular recognition of a DNA∶RNA hybrid: sub-nanomolar binding by a neomycin-methidium conjugate. Bioorg Med Chem Lett 18: 4142–4145.

100. CassidySB, DykensE, WilliamsCA (2000) Prader-Willi and Angelman syndromes: sister imprinted disorders. Am J Med Genet 97: 136–146.

101. MengL, PersonRE, BeaudetAL (2012) Ube3a-ATS is an atypical RNA polymerase II transcript that represses the paternal expression of Ube3a. Hum Mol Genet 21: 3001–3012.

102. WhiteR, SaxtyB, LargeJ, KettleboroughCA, JacksonAP (2013) Identification of small-molecule inhibitors of the ribonuclease H2 enzyme. J Biomol Screen 18: 610–620.

103. SipovaH, ZhangS, DudleyAM, GalasD, WangK, et al. (2010) Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Anal Chem 82: 10110–10115.

104. QaviAJ, KindtJT, GleesonMA, BaileyRC (2011) Anti-DNA∶RNA antibodies and silicon photonic microring resonators: increased sensitivity for multiplexed microRNA detection. Anal Chem 83: 5949–5956.

105. Gomez-GonzalezB, Garcia-RubioM, BermejoR, GaillardH, ShirahigeK, et al. (2011) Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles. EMBO J 30: 3106–3119.