The Fanconi Anemia Pathway Protects Genome Integrity from R-loops

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R loops are co-transcriptional RNA-DNA hybrids that can have a physiological role in transcription and replication, but also may be a major threat to genome stability. To avoid the deleterious effects of R loops, specific factors prevent their formation or facilitate their removal. The double-strand break repair factor BRCA2 is among those that prevent R-loop accumulation. As BRCA2 also protects stalled replication forks and is the FANCD1 member of the Fanconi Anemia (FA) pathway, we studied the role of this pathway in preventing R loop accumulation and R loop-dependent genome instability. Using human and murine cells defective in FANCD2 or FANCA and primary bone marrow cells derived from FANCD2 deficient mice, we show that the FA pathway removes R loops and that many DNA breaks accumulated in FA cells are R loop-dependent. Importantly, FANCD2 foci accumulation is largely R loop-dependent, suggesting that the FA functions at R loop-containing sites. The FA pathway is primarily known as a DNA interstrand crosslinks (ICLs) repair pathway. Our findings reveal a novel function of the FA pathway in preventing R loop-mediated DNA damage, providing new clues to understand the relevance of R-loops as a natural source of genome instability and the way they are processed.

Vyšlo v časopise: The Fanconi Anemia Pathway Protects Genome Integrity from R-loops. PLoS Genet 11(11): e32767. doi:10.1371/journal.pgen.1005674
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005674

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Zdroje

1. Bartkova J, Horejsi Z, Koed K, Kramer A, Tort F, Zieger K, et al. DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature. 2005; 434: 864–70 15829956

2. Gorgoulis VG, Vassiliou LV, Karakaidos P, Zacharatos P, Kotsinas A, Liloglou T, et al. Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature. 2005; 434: 907–13 15829965

3. Aguilera A, Garcia-Muse T. Causes of genome instability. Annu Rev Genet. 2013; 47: 1–32 doi: 10.1146/annurev-genet-111212-133232 23909437

4. Aguilera A, Garcia-Muse T. R loops: from transcription byproducts to threats to genome stability. Molecular cell. 2012; 46: 115–24 doi: 10.1016/j.molcel.2012.04.009 22541554

5. Skourti-Stathaki K, Kamieniarz-Gdula K, Proudfoot NJ. R-loops induce repressive chromatin marks over mammalian gene terminators. Nature. 2014; 516: 436–9 doi: 10.1038/nature13787 25296254

6. Skourti-Stathaki K, Proudfoot NJ. A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes & development. 2014; 28: 1384–96

7. Alzu A, Bermejo R, Begnis M, Lucca C, Piccini D, Carotenuto W, et al. Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes. Cell. 2012; 151: 835–46 doi: 10.1016/j.cell.2012.09.041 23141540

8. Huertas P, Aguilera A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Molecular cell. 2003; 12: 711–21 14527416

9. Li X, Manley JL. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell. 2005; 122: 365–78 16096057

10. Mischo HE, Gomez-Gonzalez B, Grzechnik P, Rondon AG, Wei W, Steinmetz L, et al. Yeast Sen1 helicase protects the genome from transcription-associated instability. Molecular cell. 2011; 41: 21–32 doi: 10.1016/j.molcel.2010.12.007 21211720

11. Paulsen RD, Soni DV, Wollman R, Hahn AT, Yee MC, Guan A, et al. A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. Molecular cell. 2009; 35: 228–39 doi: 10.1016/j.molcel.2009.06.021 19647519

12. Stirling PC, Chan YA, Minaker SW, Aristizabal MJ, Barrett I, Sipahimalani P, et al. R-loop-mediated genome instability in mRNA cleavage and polyadenylation mutants. Genes & development. 2012; 26: 163–75

13. Wahba L, Amon JD, Koshland D, Vuica-Ross M. RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability. Molecular cell. 2011; 44: 978–88 doi: 10.1016/j.molcel.2011.10.017 22195970

14. Ginno PA, Lim YW, Lott PL, Korf I, Chedin F. GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res. 2013; 23: 1590–600 doi: 10.1101/gr.158436.113 23868195

15. Ginno PA, Lott PL, Christensen HC, Korf I, Chedin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Molecular cell. 2012; 45: 814–25 doi: 10.1016/j.molcel.2012.01.017 22387027

16. Gan W, Guan Z, Liu J, Gui T, Shen K, Manley JL, et al. R-loop-mediated genomic instability is caused by impairment of replication fork progression. Genes & development. 2011; 25: 2041–56

17. Wellinger RE, Prado F, Aguilera A. Replication fork progression is impaired by transcription in hyperrecombinant yeast cells lacking a functional THO complex. Mol Cell Biol. 2006; 26: 3327–34 16581804

18. Castellano-Pozo M, Santos-Pereira JM, Rondon AG, Barroso S, Andujar E, Perez-Alegre M, et al. R loops are linked to histone H3 S10 phosphorylation and chromatin condensation. Molecular cell. 2013; 52: 583–90 doi: 10.1016/j.molcel.2013.10.006 24211264

19. Groh M, Lufino MM, Wade-Martins R, Gromak N. R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome. PLoS Genet. 2014; 10: e1004318 doi: 10.1371/journal.pgen.1004318 24787137

20. Santos-Pereira JM, Aguilera A. R loops: new modulators of genome dynamics and function. Nature reviews Genetics. 2015; 16: 583–97 doi: 10.1038/nrg3961 26370899

21. El Achkar E, Gerbault-Seureau M, Muleris M, Dutrillaux B, Debatisse M. Premature condensation induces breaks at the interface of early and late replicating chromosome bands bearing common fragile sites. Proc Natl Acad Sci U S A. 2005; 102: 18069–74 16330769

22. Herrera-Moyano E, Mergui X, Garcia-Rubio ML, Barroso S, Aguilera A. The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts. Genes & development. 2014; 28: 735–48

23. Bhatia V, Barroso SI, Garcia-Rubio ML, Tumini E, Herrera-Moyano E, Aguilera A. BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature. 2014; 511: 362–5 doi: 10.1038/nature13374 24896180

24. Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, et al. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Molecular cell. 2015; 57: 636–47 doi: 10.1016/j.molcel.2015.01.011 25699710

25. Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, et al. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Molecular cell. 2001; 7: 249–62 11239454

26. Howlett NG, Taniguchi T, Olson S, Cox B, Waisfisz Q, De Die-Smulders C, et al. Biallelic inactivation of BRCA2 in Fanconi anemia. Science. 2002; 297: 606–9 12065746

27. Pace P, Johnson M, Tan WM, Mosedale G, Sng C, Hoatlin M, et al. FANCE: the link between Fanconi anaemia complex assembly and activity. EMBO J. 2002; 21: 3414–23 12093742

28. Timmers C, Taniguchi T, Hejna J, Reifsteck C, Lucas L, Bruun D, et al. Positional cloning of a novel Fanconi anemia gene, FANCD2. Molecular cell. 2001; 7: 241–8 11239453

29. Cerritelli SM, Frolova EG, Feng C, Grinberg A, Love PE, Crouch RJ. Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice. Molecular cell. 2003; 11: 807–15 12667461

30. Gaillard H, Herrera-Moyano E, Aguilera A. Transcription-associated genome instability. Chem Rev. 2013; 113: 8638–61 doi: 10.1021/cr400017y 23597121

31. Moldovan GL, D'Andrea AD. FANCD2 hurdles the DNA interstrand crosslink. Cell. 2009; 139: 1222–4 doi: 10.1016/j.cell.2009.12.006 20064367

32. Hill SJ, Clark AP, Silver DP, Livingston DM. BRCA1 pathway function in basal-like breast cancer cells. Mol Cell Biol. 2014; 34: 3828–42 doi: 10.1128/MCB.01646-13 25092866

33. Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y, Thoma NH, et al. BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. Science. 2002; 297: 1837–48 12228710

34. Lomonosov M, Anand S, Sangrithi M, Davies R, Venkitaraman AR. Stabilization of stalled DNA replication forks by the BRCA2 breast cancer susceptibility protein. Genes & development. 2003; 17: 3017–22

35. Schlacher K, Christ N, Siaud N, Egashira A, Wu H, Jasin M. Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell. 2011; 145: 529–42 doi: 10.1016/j.cell.2011.03.041 21565612

36. Kottemann MC, Smogorzewska A. Fanconi anaemia and the repair of Watson and Crick DNA crosslinks. Nature. 2013; 493: 356–63 doi: 10.1038/nature11863 23325218

37. Rosado IV, Langevin F, Crossan GP, Takata M, Patel KJ. Formaldehyde catabolism is essential in cells deficient for the Fanconi anemia DNA-repair pathway. Nat Struct Mol Biol. 2011; 18: 1432–4 doi: 10.1038/nsmb.2173 22081012

38. Dominguez-Sanchez MS, Barroso S, Gomez-Gonzalez B, Luna R, Aguilera A. Genome instability and transcription elongation impairment in human cells depleted of THO/TREX. PLoS Genet. 2011; 7: e1002386 doi: 10.1371/journal.pgen.1002386 22144908

39. ten Asbroek AL, van Groenigen M, Nooij M, Baas F. The involvement of human ribonucleases H1 and H2 in the variation of response of cells to antisense phosphorothioate oligonucleotides. European journal of biochemistry / FEBS. 2002; 269: 583–92 11856317

40. Taniguchi T, Garcia-Higuera I, Andreassen PR, Gregory RC, Grompe M, D'Andrea AD. S-phase-specific interaction of the Fanconi anemia protein, FANCD2, with BRCA1 and RAD51. Blood. 2002; 100: 2414–20 12239151

41. Andreassen PR, D'Andrea AD, Taniguchi T. ATR couples FANCD2 monoubiquitination to the DNA-damage response. Genes & development. 2004; 18: 1958–63

42. Houghtaling S, Timmers C, Noll M, Finegold MJ, Jones SN, Meyn MS, et al. Epithelial cancer in Fanconi anemia complementation group D2 (Fancd2) knockout mice. Genes & development. 2003; 17: 2021–35

43. Liu L, Yan Y, Zeng M, Zhang J, Hanes MA, Ahearn G, et al. Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. Cell. 2004; 116: 617–28 14980227

44. Montes de Oca R, Andreassen PR, Margossian SP, Gregory RC, Taniguchi T, Wang X, et al. Regulated interaction of the Fanconi anemia protein, FANCD2, with chromatin. Blood. 2005; 105: 1003–9 15454491

45. Sollier J, Stork CT, Garcia-Rubio ML, Paulsen RD, Aguilera A, Cimprich KA. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability. Molecular cell. 2014; 56: 777–85 doi: 10.1016/j.molcel.2014.10.020 25435140