DNA Topoisomerase III Localizes to Centromeres and Affects Centromeric CENP-A Levels in Fission Yeast
Centromeres are specialized chromatin regions marked by the presence of nucleosomes containing the centromere-specific histone H3 variant CENP-A, which is essential for chromosome segregation. Assembly and disassembly of nucleosomes is intimately linked to DNA topology, and DNA topoisomerases have previously been implicated in the dynamics of canonical H3 nucleosomes. Here we show that Schizosaccharomyces pombe Top3 and its partner Rqh1 are involved in controlling the levels of CENP-ACnp1 at centromeres. Both top3 and rqh1 mutants display defects in chromosome segregation. Using chromatin immunoprecipitation and tiling microarrays, we show that Top3, unlike Top1 and Top2, is highly enriched at centromeric central domains, demonstrating that Top3 is the major topoisomerase in this region. Moreover, centromeric Top3 occupancy positively correlates with CENP-ACnp1 occupancy. Intriguingly, both top3 and rqh1 mutants display increased relative enrichment of CENP-ACnp1 at centromeric central domains. Thus, Top3 and Rqh1 normally limit the levels of CENP-ACnp1 in this region. This new role is independent of the established function of Top3 and Rqh1 in homologous recombination downstream of Rad51. Therefore, we hypothesize that the Top3-Rqh1 complex has an important role in controlling centromere DNA topology, which in turn affects the dynamics of CENP-ACnp1 nucleosomes.
Vyšlo v časopise:
DNA Topoisomerase III Localizes to Centromeres and Affects Centromeric CENP-A Levels in Fission Yeast. PLoS Genet 9(3): e32767. doi:10.1371/journal.pgen.1003371
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003371
Souhrn
Centromeres are specialized chromatin regions marked by the presence of nucleosomes containing the centromere-specific histone H3 variant CENP-A, which is essential for chromosome segregation. Assembly and disassembly of nucleosomes is intimately linked to DNA topology, and DNA topoisomerases have previously been implicated in the dynamics of canonical H3 nucleosomes. Here we show that Schizosaccharomyces pombe Top3 and its partner Rqh1 are involved in controlling the levels of CENP-ACnp1 at centromeres. Both top3 and rqh1 mutants display defects in chromosome segregation. Using chromatin immunoprecipitation and tiling microarrays, we show that Top3, unlike Top1 and Top2, is highly enriched at centromeric central domains, demonstrating that Top3 is the major topoisomerase in this region. Moreover, centromeric Top3 occupancy positively correlates with CENP-ACnp1 occupancy. Intriguingly, both top3 and rqh1 mutants display increased relative enrichment of CENP-ACnp1 at centromeric central domains. Thus, Top3 and Rqh1 normally limit the levels of CENP-ACnp1 in this region. This new role is independent of the established function of Top3 and Rqh1 in homologous recombination downstream of Rad51. Therefore, we hypothesize that the Top3-Rqh1 complex has an important role in controlling centromere DNA topology, which in turn affects the dynamics of CENP-ACnp1 nucleosomes.
Zdroje
1. ShelbyRD, MonierK, SullivanKF (2000) Chromatin assembly at kinetochores is uncoupled from DNA replication. J Cell Biol 151: 1113–1118.
2. JansenLE, BlackBE, FoltzDR, ClevelandDW (2007) Propagation of centromeric chromatin requires exit from mitosis. J Cell Biol 176: 795–805.
3. MoreeB, MeyerCB, FullerCJ, StraightAF (2011) CENP-C recruits M18BP1 to centromeres to promote CENP-A chromatin assembly. J Cell Biol 194: 855–871.
4. HayashiT, FujitaY, IwasakiO, AdachiY, TakahashiK, et al. (2004) Mis16 and Mis18 are required for CENP-A loading and histone deacetylation at centromeres. Cell 118: 715–729.
5. FujitaY, HayashiT, KiyomitsuT, ToyodaY, KokubuA, et al. (2007) Priming of centromere for CENP-A recruitment by human hMis18alpha, hMis18beta, and M18BP1. Dev Cell 12: 17–30.
6. BarnhartMC, KuichPH, StellfoxME, WardJA, BassettEA, et al. (2011) HJURP is a CENP-A chromatin assembly factor sufficient to form a functional de novo kinetochore. J Cell Biol 194: 229–243.
7. MaddoxPS, HyndmanF, MonenJ, OegemaK, DesaiA (2007) Functional genomics identifies a Myb domain-containing protein family required for assembly of CENP-A chromatin. J Cell Biol 176: 757–763.
8. PidouxAL, ChoiES, AbbottJK, LiuX, KaganskyA, et al. (2009) Fission yeast Scm3: A CENP-A receptor required for integrity of subkinetochore chromatin. Mol Cell 33: 299–311.
9. WilliamsJS, HayashiT, YanagidaM, RussellP (2009) Fission yeast Scm3 mediates stable assembly of Cnp1/CENP-A into centromeric chromatin. Mol Cell 33: 287–298.
10. DunleavyEM, RocheD, TagamiH, LacosteN, Ray-GalletD, et al. (2009) HJURP is a cell-cycle-dependent maintenance and deposition factor of CENP-A at centromeres. Cell 137: 485–497.
11. FoltzDR, JansenLE, BaileyAO, YatesJR3rd, BassettEA, et al. (2009) Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell 137: 472–484.
12. ShuaibM, OuararhniK, DimitrovS, HamicheA (2010) HJURP binds CENP-A via a highly conserved N-terminal domain and mediates its deposition at centromeres. Proc Natl Acad Sci U S A 107: 1349–1354.
13. DechassaML, WynsK, LiM, HallMA, WangMD, et al. (2011) Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes. Nat Commun 2: 313.
14. ShivarajuM, CamahortR, MattinglyM, GertonJL (2011) Scm3 is a centromeric nucleosome assembly factor. J Biol Chem 286: 12016–12023.
15. FuruyamaT, DalalY, HenikoffS (2006) Chaperone-mediated assembly of centromeric chromatin in vitro. Proc Natl Acad Sci U S A 103: 6172–6177.
16. SekulicN, BassettEA, RogersDJ, BlackBE (2010) The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres. Nature 467: 347–351.
17. CamahortR, ShivarajuM, MattinglyM, LiB, NakanishiS, et al. (2009) Cse4 is part of an octameric nucleosome in budding yeast. Mol Cell 35: 794–805.
18. TachiwanaH, KagawaW, ShigaT, OsakabeA, MiyaY, et al. (2011) Crystal structure of the human centromeric nucleosome containing CENP-A. Nature 476: 232–235.
19. KingstonIJ, YungJS, SingletonMR (2011) Biophysical characterization of the centromere-specific nucleosome from budding yeast. J Biol Chem 286: 4021–4026.
20. FuruyamaT, HenikoffS (2009) Centromeric nucleosomes induce positive DNA supercoils. Cell 138: 104–113.
21. ZhangW, ColmenaresSU, KarpenGH (2012) Assembly of Drosophila centromeric nucleosomes requires CID dimerization. Mol Cell 45: 263–269.
22. DalalY, WangH, LindsayS, HenikoffS (2007) Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol 5: e218 doi:10.1371/journal.pbio.0050218
23. DimitriadisEK, WeberC, GillRK, DiekmannS, DalalY (2010) Tetrameric organization of vertebrate centromeric nucleosomes. Proc Natl Acad Sci U S A 107: 20317–20322.
24. KrassovskyK, HenikoffJG, HenikoffS (2011) Tripartite organization of centromeric chromatin in budding yeast. Proc Natl Acad Sci U S A
25. BuiM, DimitriadisEK, HoischenC, AnE, QuenetD, et al. (2012) Cell-cycle-dependent structural transitions in the human CENP-A nucleosome in vivo. Cell 150: 317–326.
26. ShivarajuM, UnruhJR, SlaughterBD, MattinglyM, BermanJ, et al. (2012) Cell-cycle-coupled structural oscillation of centromeric nucleosomes in yeast. Cell 150: 304–316.
27. PattertonHG, von HoltC (1993) Negative supercoiling and nucleosome cores. I. The effect of negative supercoiling on the efficiency of nucleosome core formation in vitro. J Mol Biol 229: 623–636.
28. AlmouzniG, MechaliM (1988) Assembly of spaced chromatin involvement of ATP and DNA topoisomerase activity. Embo J 7: 4355–4365.
29. GarintherWI, SchultzMC (1997) Topoisomerase function during replication-independent chromatin assembly in yeast. Mol Cell Biol 17: 3520–3526.
30. Durand-DubiefM, PerssonJ, NormanU, HartsuikerE, EkwallK (2010) Topoisomerase I regulates open chromatin and controls gene expression in vivo. Embo J 29: 2126–2134.
31. Durand-DubiefM, SvenssonJP, PerssonJ, EkwallK (2011) Topoisomerases, chromatin and transcription termination. Transcription 2: 66–70.
32. KimRA, WangJC (1992) Identification of the yeast TOP3 gene product as a single strand-specific DNA topoisomerase. J Biol Chem 267: 17178–17185.
33. GoulaouicH, RoulonT, FlamandO, GrondardL, LavelleF, et al. (1999) Purification and characterization of human DNA topoisomerase IIIalpha. Nucleic Acids Res 27: 2443–2450.
34. GangloffS, McDonaldJP, BendixenC, ArthurL, RothsteinR (1994) The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol Cell Biol 14: 8391–8398.
35. LaursenLV, AmpatzidouE, AndersenAH, MurrayJM (2003) Role for the fission yeast RecQ helicase in DNA repair in G2. Mol Cell Biol 23: 3692–3705.
36. WuL, DaviesSL, NorthPS, GoulaouicH, RiouJF, et al. (2000) The Bloom's syndrome gene product interacts with topoisomerase III. J Biol Chem 275: 9636–9644.
37. ChangM, BellaouiM, ZhangC, DesaiR, MorozovP, et al. (2005) RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex. Embo J 24: 2024–2033.
38. MullenJR, NallasethFS, LanYQ, SlagleCE, BrillSJ (2005) Yeast Rmi1/Nce4 controls genome stability as a subunit of the Sgs1-Top3 complex. Mol Cell Biol 25: 4476–4487.
39. YinJ, SobeckA, XuC, MeeteiAR, HoatlinM, et al. (2005) BLAP75, an essential component of Bloom's syndrome protein complexes that maintain genome integrity. Embo J 24: 1465–1476.
40. HarmonFG, DiGateRJ, KowalczykowskiSC (1999) RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: a conserved mechanism for control of DNA recombination. Mol Cell 3: 611–620.
41. WuL, HicksonID (2002) The Bloom's syndrome helicase stimulates the activity of human topoisomerase IIIalpha. Nucleic Acids Res 30: 4823–4829.
42. WuL, HicksonID (2003) The Bloom's syndrome helicase suppresses crossing over during homologous recombination. Nature 426: 870–874.
43. CejkaP, PlankJL, BachratiCZ, HicksonID, KowalczykowskiSC (2010) Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1-Top3. Nat Struct Mol Biol 17: 1377–1382.
44. OakleyTJ, GoodwinA, ChakravertyRK, HicksonID (2002) Inactivation of homologous recombination suppresses defects in topoisomerase III-deficient mutants. DNA Repair (Amst) 1: 463–482.
45. CromieGA, HyppaRW, SmithGR (2008) The fission yeast BLM homolog Rqh1 promotes meiotic recombination. Genetics 179: 1157–1167.
46. WinTZ, GoodwinA, HicksonID, NorburyCJ, WangSW (2004) Requirement for Schizosaccharomyces pombe Top3 in the maintenance of chromosome integrity. J Cell Sci 117: 4769–4778.
47. WinTZ, MankouriHW, HicksonID, WangSW (2005) A role for the fission yeast Rqh1 helicase in chromosome segregation. J Cell Sci 118: 5777–5784.
48. HopeJC, CruzataLD, DuvshaniA, MitsumotoJ, MaftahiM, et al. (2007) Mus81-Eme1-dependent and -independent crossovers form in mitotic cells during double-strand break repair in Schizosaccharomyces pombe. Mol Cell Biol 27: 3828–3838.
49. DaveyS, HanCS, RamerSA, KlassenJC, JacobsonA, et al. (1998) Fission yeast rad12+ regulates cell cycle checkpoint control and is homologous to the Bloom's syndrome disease gene. Mol Cell Biol 18: 2721–2728.
50. DoeCL, DixonJ, OsmanF, WhitbyMC (2000) Partial suppression of the fission yeast rqh1(−) phenotype by expression of a bacterial Holliday junction resolvase. Embo J 19: 2751–2762.
51. GoodwinA, WangSW, TodaT, NorburyC, HicksonID (1999) Topoisomerase III is essential for accurate nuclear division in Schizosaccharomyces pombe. Nucleic Acids Res 27: 4050–4058.
52. MaftahiM, HanCS, LangstonLD, HopeJC, ZigourasN, et al. (1999) The top3(+) gene is essential in Schizosaccharomyces pombe and the lethality associated with its loss is caused by Rad12 helicase activity. Nucleic Acids Res 27: 4715–4724.
53. OhM, ChoiIS, ParkSD (2002) Topoisomerase III is required for accurate DNA replication and chromosome segregation in Schizosaccharomyces pombe. Nucleic Acids Res 30: 4022–4031.
54. MurrayJM, LindsayHD, MundayCA, CarrAM (1997) Role of Schizosaccharomyces pombe RecQ homolog, recombination, and checkpoint genes in UV damage tolerance. Mol Cell Biol 17: 6868–6875.
55. StewartE, ChapmanCR, Al-KhodairyF, CarrAM, EnochT (1997) rqh1+, a fission yeast gene related to the Bloom's and Werner's syndrome genes, is required for reversible S phase arrest. Embo J 16: 2682–2692.
56. YuasaT, HayashiT, IkaiN, KatayamaT, AokiK, et al. (2004) An interactive gene network for securin-separase, condensin, cohesin, Dis1/Mtc1 and histones constructed by mass transformation. Genes Cells 9: 1069–1082.
57. ChangelaA, DiGateRJ, MondragonA (2001) Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature 411: 1077–1081.
58. JangYK, JinYH, ShimYS, KimMJ, YooEJ, et al. (1995) Evidences for possible involvement of Rhp51 protein in mitotic events including chromosome segregation. Biochem Mol Biol Int 37: 329–337.
59. MiyabeI, MorishitaT, HishidaT, YoneiS, ShinagawaH (2006) Rhp51-dependent recombination intermediates that do not generate checkpoint signal are accumulated in Schizosaccharomyces pombe rad60 and smc5/6 mutants after release from replication arrest. Mol Cell Biol 26: 343–353.
60. ChoiES, StralforsA, CastilloAG, Durand-DubiefM, EkwallK, et al. (2011) Identification of noncoding transcripts from within CENP-A chromatin at fission yeast centromeres. J Biol Chem 286: 23600–23607.
61. RogO, MillerKM, FerreiraMG, CooperJP (2009) Sumoylation of RecQ helicase controls the fate of dysfunctional telomeres. Mol Cell 33: 559–569.
62. NakamuraK, OkamotoA, KatouY, YadaniC, ShitandaT, et al. (2008) Rad51 suppresses gross chromosomal rearrangement at centromere in Schizosaccharomyces pombe. Embo J 27: 3036–3046.
63. McFarlaneRJ, HumphreyTC (2010) A role for recombination in centromere function. Trends Genet 26: 209–213.
64. CollinsKA, FuruyamaS, BigginsS (2004) Proteolysis contributes to the exclusive centromere localization of the yeast Cse4/CENP-A histone H3 variant. Curr Biol 14: 1968–1972.
65. CarlstenJO, SzilagyiZ, LiuB, LopezMD, SzasziE, et al. (2012) Mediator Promotes CENP-A Incorporation at Fission Yeast Centromeres. Mol Cell Biol 32: 4035–4043.
66. HarmonFG, BrockmanJP, KowalczykowskiSC (2003) RecQ helicase stimulates both DNA catenation and changes in DNA topology by topoisomerase III. J Biol Chem 278: 42668–42678.
67. LandoD, EndesfelderU, BergerH, SubramanianL, DunnePD, et al. (2012) Quantitative single-molecule microscopy reveals that CENP-A(Cnp1) deposition occurs during G2 in fission yeast. Open Biol 2: 120078.
68. ChanFL, WongLH (2012) Transcription in the maintenance of centromere chromatin identity. Nucleic Acids Res 40 (22) 11178–88 doi:10.1093/nar/gks921
69. ChenES, SaitohS, YanagidaM, TakahashiK (2003) A cell cycle-regulated GATA factor promotes centromeric localization of CENP-A in fission yeast. Mol Cell 11: 175–187.
70. WalfridssonJ, BjerlingP, ThalenM, YooEJ, ParkSD, et al. (2005) The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres. Nucleic Acids Res 33: 2868–2879.
71. MorenoS, KlarA, NurseP (1991) Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol 194: 795–823.
72. HaganIM, HyamsJS (1988) The use of cell division cycle mutants to investigate the control of microtubule distribution in the fission yeast Schizosaccharomyces pombe. J Cell Sci 89 (Pt 3) 343–357.
73. Durand-DubiefM, EkwallK (2009) Chromatin immunoprecipitation using microarrays. Methods Mol Biol 529: 279–295.
74. LantermannAB, StraubT, StralforsA, YuanGC, EkwallK, et al. (2010) Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat Struct Mol Biol 17: 251–257.
75. StralforsA, WalfridssonJ, BhuiyanH, EkwallK (2011) The FUN30 chromatin remodeler, Fft3, protects centromeric and subtelomeric domains from euchromatin formation. PLoS Genet 7: e1001334 doi:10.1371/journal.pgen.1001334
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Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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