Recombinogenic Conditions Influence Partner Choice in Spontaneous Mitotic Recombination

English version České info

Mammalian common fragile sites are loci of frequent chromosome breakage and putative recombination hotspots. Here, we utilized Replication Slow Zones (RSZs), a budding yeast homolog of the mammalian common fragile sites, to examine recombination activities at these loci. We found that rates of URA3 inactivation of a hisG-URA3-hisG reporter at RSZ and non-RSZ loci were comparable under all conditions tested, including those that specifically promote chromosome breakage at RSZs (hydroxyurea [HU], mec1Δ sml1Δ, and high temperature), and those that suppress it (sml1Δ and rrm3Δ). These observations indicate that RSZs are not recombination hotspots and that chromosome fragility and recombination activity can be uncoupled. Results confirmed recombinogenic effects of HU, mec1Δ sml1Δ, and rrm3Δ and identified temperature as a regulator of mitotic recombination. We also found that these conditions altered the nature of recombination outcomes, leading to a significant increase in the frequency of URA3 inactivation via loss of heterozygosity (LOH), the type of genetic alteration involved in cancer development. Further analyses revealed that the increase was likely due to down regulation of intrachromatid and intersister (IC/IS) bias in mitotic recombination, and that RSZs exhibited greater sensitivity to HU dependent loss of IC/IS bias than non RSZ loci. These observations suggest that recombinogenic conditions contribute to genome rearrangements not only by increasing the overall recombination activity, but also by altering the nature of recombination outcomes by their effects on recombination partner choice. Similarly, fragile sites may contribute to cancer more frequently than non-fragile loci due their enhanced sensitivity to certain conditions that down-regulate the IC/IS bias rather than intrinsically higher rates of recombination.

Vyšlo v časopise: Recombinogenic Conditions Influence Partner Choice in Spontaneous Mitotic Recombination. PLoS Genet 9(11): e32767. doi:10.1371/journal.pgen.1003931
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003931

Souhrn

Zdroje

1. Hill T (1996) Features of the Chromosome Terminus Region. In: Neidhardt F, editor. Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington DC: ASM Press. pp. 1602–1615.

2. DalgaardJ, KlarA (2000) swi1 and swi3 perform Imprinting, pausing, and termination of DNA replication in S. pombe. Cell 102: 745–751.

3. ChaRS, KlecknerN (2002) ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones. Science 297: 602–606.

4. Sutherland G, Hecht F (1985) Fragile sites on human chromosomes. New York: Oxford University Press.

5. RothsteinR, MichelB, GangloffS (2000) Replication fork pausing and recombination or “gimme a break”. Genes Dev 14: 1–10.

6. MirkinEV, MirkinSM (2007) Replication fork stalling at natural impediments. Micro Mol Biol Rev 71: 13–35.

7. LambertS, CarrAM (2013) Impediments to replication fork movement: stabilisation, reactivation and genome instability. Chromosoma 122: 33–45.

8. BrouwerJ, WillemsenR, OostraB (2009) Microsatellite repeat instability and neurological disease. Bioessays 31: 71–83.

9. DurkinS, GloverT (2007) Chromosome fragile sites. Ann Rev Gen 41: 169–192.

10. GloverT, SteinC (1988) Chromosome breakage and recombination at fragile sites. Am J Hum Genet 43: 265–273.

11. RassoolF, McKeithanT, NeillyM, Van MelleE, EspinaR, et al. (1991) Preferential integration of marker DNA into the chromosomal fragile site at 3p14: An approach to cloning fragile sites. Proc Nat Acad Sci 88: 6657–6661.

12. PopescuN (2003) Genetic alterations in cancer as a result of breakage at fragile sites. Cancer Lett 192: 1–17.

13. FengW, Di RienziS, RaghuramanM, BrewerB (2011) Replication stress-induced chromosome breakage is correlated with replication fork progression and is preceded by single-stranded DNA formation. G3 1: 327–335.

14. LairdC, JaffeE, KarpenG, LambM, NelsonR (1987) Fragile sites in human chromosomes as regions of late-replicating DNA. Trends in Genetics 3: 274–281.

15. CasperA, NghiemP, ArltM, GloverT (2002) ATR Regulates Fragile Site Stability. Cell 111: 779–789.

16. Ozer-GalaiE, SchwartzM, RahatA, KeremB (2008) Interplay between ATM and ATR in the regulation of common fragile site stability. Oncogene 27: 2109–2117.

17. HarperJ, ElledgeS (2007) The DNA Damage Response: Ten Years After. Mol Cell 28: 739–745.

18. CarballoJA, ChaRS (2007) Meiotic roles of Mec1, a budding yeast homolog of mammalian ATR/ATM. Chromosome Res 15: 539–550.

19. SomyajitK, BasavarajuS, ScullyR, NagarajuG (2013) ATM- and ATR-mediated phosphorylation of XRCC3 regulates DNA double-strand break-induced checkpoint activation and repair. Mol Cell Biol 33: 1830–1844.

20. HashashN, JohnsonA, ChaR (2012) Topoisomerase II- and condensin-dependent breakage of MEC1ATR-sensitive fragile sites occurs independently of spindle tension, anaphase, or cytokinesis. PLoS Genet 8: e1002978.

21. HashashN, JohnsonAL, ChaRS (2011) Regulation of fragile sites expression in budding yeast by MEC1, RRM3 and hydroxyurea. J Cell Sci 124: 181–185.

22. ZhaoX, MullerEGD, RothsteinR (1998) A suppressor of two essential checkpoint genes identifies novel protein that negatively affects dNTP pools. Mol Cell 2: 329–340.

23. AlaniE, CaoL, KlecknerN (1987) A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics 116: 541–545.

24. LeaDE, CoulsonCA (1948) The distribution of the numbers of mutants in bacterial populations. J Genet 49: 264–284.

25. BierneH, MichelB (1994) When replication forks stop. Mol Microbiol 13: 17–23.

26. CarrA, PaekA, WeinertT (2011) DNA replication: failures and inverted fusions. Semin Cell Dev Biol 22: 866–874.

27. KadykLC, HartwellLH (1992) Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae. Genetics 132: 387–402.

28. IvessaA, LenzmeierB, BesslerJ, GoudsouzianL, SchnakenbergS, et al. (2003) The Saccharomyces cerevisiae Helicase Rrm3p Facilitates Replication Past Nonhistone Protein-DNA Complexes. Mol Cell 12: 1525–1536.

29. TorresJ, SchnakenbergS, ZakianV (2004) Sacchromyces cerevisiae Rrm3p DNA helicase promotes genome integrity by preventing replication fork stalling: viability of rrm3 cells require the intra-S-phase checkpoint and fork restart activities. Mol Cell Biol 24: 3198–3212.

30. ChengX, QinY, IvessaA (2009) Loss of mitochondrial DNA under genotoxic stress conditions in the absence of the yeast DNA helicase Pif1p occurs independently of the DNA helicase Rrm3p. Mol Genet Genomics 281: 631–645.

31. BarberaMA, PetesTD (2006) Selection and analysis of spontaneous reciprocal mitotic cross-overs in Saccharomyces cerevisiae. Proc Natl Acad Sci 103: 12819–12824.

32. MieczkowskiP, LemoineF, PetesT (2006) Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae. DNA Repair 5: 1010–1020.

33. SchwachaA, KlecknerN (1994) Identification of joint molecules that form frequently between homologs but rarely between sister chromatids during yeast meiosis. Cell 76: 51–63.

34. LichtenM, HaberJE (1989) Position effects in ectopic and allelic mitotic recombination in Saccharomyces cerevisiae. Genetics 123: 261–268.

35. ManceraE, BourgonR, BrozziA, HuberW, SteinmetzLM (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454: 479–485.

36. SzostakJW, Orr-WeaverTL, RothsteinRJ, StahlFW (1983) The double-strand-break repair model for recombination. Cell 33: 25–35.

37. KugouK, FukudaT, YamadaS, ItoM, SasanumaH, et al. (2009) Rec8 guides canonical Spo11 distribution along yeast metioic chromosomes. Mol Biol Cell 20: 3064–3076.

38. LambertS, MizunoK, BlaisonneauJ, MartineauS, ChanetR, et al. (2010) Homologous recombination restarts blocked replication forks at the expense of genome rearrangements by template exchange. Mol Cell 346–359.

39. MyungK, ChenC, KolodnerR (2001) Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae. Nature 411: 1073–1076.

40. AdmireA, ShanksL, DanzlN, WangM, WeierU, et al. (2006) Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint contols in yeast. Genes Dev 20.

41. TimsonJ (1975) Hydroxyurea. Mut Res 32: 115–132.

42. FriedelA, PikeB, GasserS (2009) ATR/Mec1: coordinating fork stability and repair. Curr Opin Cell Biol 21: 237–244.

43. BornerGV, KlecknerN, HunterN (2004) Crossover/noncrossover differentiation, synaptonemal complex formation, and regulatory surveillance at the leptotene/zygotene transition of meiosis. Cell 117: 29–45.

44. SchwachaA, KlecknerN (1997) Interhomolog bias during meiotic recombination: meiotic functions promote a highly differentiated interhomolog-only pathway. Cell 90: 1123–1135.

45. NiuH, WanL, BaumgartnerB, SchaeferD, LoidlJ, et al. (2005) Partner choice during meiosis is regulated by Hop1-promoted dimerization of Mek1. Mol Biol Cell 16: 5804–5818.

46. CarballoJA, JohnsonAL, SedgwickSG, ChaRS (2008) Phosphorylation of the axial element protein Hop1 by Mec1/Tel1 ensures meiotic interhomolog recombination. Cell 132: 758–770.

47. WierdlM, GreeneC, DattaA, Jinks-RobertsonS, PetesT (1996) Destablization of simple repetitive DNA sequences by transcription in yeast. Genetics 143: 713–721.

48. BordeV, WuT-C, LichtenM (1999) Use of a recombination-reporter insert to define meiotic recombination domains on chromosome III of Saccharomyces cerevisiae. Mol Cell Biol 19: 4832–4842.

49. HiraokaM, WatanabeK, UmezuK, MakiH (2000) Spontaneous Loss of Heterozygosity in Diploid Saccharomyces serecvisiae Cells. Genetics 156: 1531–1548.