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Neurospora Importin α Is Required for Normal Heterochromatic Formation and DNA Methylation


The epigenetic information contained in chromatin is essential for development of higher organisms, and if misregulated, can lead to the unregulated growth associated with human cancers. Chromatin is typically classified into two basic types: gene-rich 'euchromatin', and gene-poor heterochromatin, which is also rich in repeated DNA and 'repressive chromatin marks'. As in humans and eukaryotes generally, heterochromatin in Neurospora crassa is decorated with DNA methylation and histone H3 lysine 9 (H3K9) methylation, but unlike the case in mammals, loss of these epigenetic marks does not compromise viability. In Neurospora, the DCDC, a five-member Cul4-based protein complex, trimethylates H3K9. Little information is available on the regulation of DCDC or similar complexes in other organisms. Using forward genetics, we identified a novel role for Importin α (NUP-6) for the function of DCDC. Although NUP-6 typically functions in nucleocytoplasmic transport, the dim-3 strain, which contains an altered nup-6 gene that reduces DNA methylation and H3K9me3, shows normal nuclear transport of the heterochromatin machinery and a canonical transport substrate. Two DCDC members are mislocalized from heterochromatin in the dim-3 mutant, signifying that NUP-6 may be important for targeting key proteins to incipient heterochromatic DNA. The euchromatic complex SAGA has increased euchromatin localization in dim-3, suggesting that NUP-6 may localize multiple chromatin complexes to sub-nuclear genomic targets.


Vyšlo v časopise: Neurospora Importin α Is Required for Normal Heterochromatic Formation and DNA Methylation. PLoS Genet 11(3): e32767. doi:10.1371/journal.pgen.1005083
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005083

Souhrn

The epigenetic information contained in chromatin is essential for development of higher organisms, and if misregulated, can lead to the unregulated growth associated with human cancers. Chromatin is typically classified into two basic types: gene-rich 'euchromatin', and gene-poor heterochromatin, which is also rich in repeated DNA and 'repressive chromatin marks'. As in humans and eukaryotes generally, heterochromatin in Neurospora crassa is decorated with DNA methylation and histone H3 lysine 9 (H3K9) methylation, but unlike the case in mammals, loss of these epigenetic marks does not compromise viability. In Neurospora, the DCDC, a five-member Cul4-based protein complex, trimethylates H3K9. Little information is available on the regulation of DCDC or similar complexes in other organisms. Using forward genetics, we identified a novel role for Importin α (NUP-6) for the function of DCDC. Although NUP-6 typically functions in nucleocytoplasmic transport, the dim-3 strain, which contains an altered nup-6 gene that reduces DNA methylation and H3K9me3, shows normal nuclear transport of the heterochromatin machinery and a canonical transport substrate. Two DCDC members are mislocalized from heterochromatin in the dim-3 mutant, signifying that NUP-6 may be important for targeting key proteins to incipient heterochromatic DNA. The euchromatic complex SAGA has increased euchromatin localization in dim-3, suggesting that NUP-6 may localize multiple chromatin complexes to sub-nuclear genomic targets.


Zdroje

1. Henikoff S (2000) Heterochromatin function in complex genomes. Biochim Biophys Acta 1470: O1–8. 10656988

2. Grewal SI, Jia S (2007) Heterochromatin revisited. Nat Rev Genet 8: 35–46. 17173056

3. Buhler M, Gasser SM (2009) Silent chromatin at the middle and ends: lessons from yeasts. EMBO J 28: 2149–2161. doi: 10.1038/emboj.2009.185 19629038

4. Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, et al. (2009) Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res 19: 427–437. doi: 10.1101/gr.086231.108 19092133

5. Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: 247–257. 10555141

6. Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL (1996) Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273: 654–657. 8662558

7. Foss HM, Roberts CJ, Claeys KM, Selker EU (1993) Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation. Science 262: 1737–1741. 7505062

8. Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Selker EU (2010) Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin. Proc Natl Acad Sci U S A 107: 8310–8315. doi: 10.1073/pnas.1000328107 20404183

9. Kouzminova E, Selker EU (2001) Dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J 20: 4309–4323. 11483533

10. Honda S, Selker EU (2008) Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Mol Cell Biol 28: 6044–6055. doi: 10.1128/MCB.00823-08 18678653

11. Freitag M, Hickey PC, Khlafallah TK, Read ND, Selker EU (2004) HP1 is essential for DNA methylation in Neurospora. Mol Cell 13: 427–434. 14967149

12. Nielsen PR, Nietlispach D, Mott HR, Callaghan J, Bannister A, et al. (2002) Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 416: 103–107. 11882902

13. Tamaru H, Selker EU (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414: 277–283. 11713521

14. Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, et al. (2003) Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet 34: 75–79. 12679815

15. Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Knip M, et al. (2010) DNA methylation and normal chromosome behavior in Neurospora depend on five components of a histone methyltransferase complex, DCDC. PLoS Genet 6: e1001196. doi: 10.1371/journal.pgen.1001196 21079689

16. Adhvaryu KK, Gessaman JD, Honda S, Lewis ZA, Grisafi PL, et al. (2014) The Cullin-4 complex DCDC does not require E3 ubiquitin ligase elements to control heterochromatin in Neurospora. Eukaryot Cell.

17. Gorlich D, Mattaj IW (1996) Nucleocytoplasmic transport. Science 271: 1513–1518. 8599106

18. Chook YM, Blobel G (2001) Karyopherins and nuclear import. Curr Opin Struct Biol 11: 703–715. 11751052

19. Goldfarb DS, Corbett AH, Mason DA, Harreman MT, Adam SA (2004) Importin α: a multipurpose nuclear-transport receptor. Trends Cell Biol 14: 505–514. 15350979

20. Selker EU, Tountas NA, Cross SH, Margolin BS, Murphy JG, et al. (2003) The methylated component of the Neurospora crassa genome. Nature 422: 893–897. 12712205

21. Takeda AA, Freitas FZ, Magro AJ, Bernardes NE, Fernandes CA, et al. (2013) Biophysical characterization of the recombinant Importin α from Neurospora crassa. Protein Pept Lett 20: 8–16. 22789101

22. Conti E, Uy M, Leighton L, Blobel G, Kuriyan J (1998) Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin α. Cell 94: 193–204. 9695948

23. Matsuura Y, Stewart M (2004) Structural basis for the assembly of a nuclear export complex. Nature 432: 872–877. 15602554

24. Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, et al. (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 103: 10352–10357. 16801547

25. Carsiotis M, Jones RF, Wesseling AC (1974) Cross-pathway regulation: histidine-mediated control of histidine, tryptophan, and arginine biosynthetic enzymes in Neurospora crassa. J Bacteriol 119: 893–898. 4368540

26. Lee HC, Chang SS, Choudhary S, Aalto AP, Maiti M, et al. (2009) qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459: 274–277. doi: 10.1038/nature08041 19444217

27. Honda S, Lewis ZA, Shimada K, Fischle W, Sack R, et al. (2012) Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation. Nat Struct Mol Biol 19: 471–477, S471. doi: 10.1038/nsmb.2274 22504884

28. Smith KM, Kothe GO, Matsen CB, Khlafallah TK, Adhvaryu KK, et al. (2008) The fungus Neurospora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9. Epigenetics Chromatin 1: 5. doi: 10.1186/1756-8935-1-5 19014414

29. Leung SW, Harreman MT, Hodel MR, Hodel AE, Corbett AH (2003) Dissection of the karyopherin α nuclear localization signal (NLS)-binding groove: functional requirements for NLS binding. J Biol Chem 278: 41947–41953. 12917403

30. Pulliam KF, Fasken MB, McLane LM, Pulliam JV, Corbett AH (2009) The Classical Nuclear Localization Signal Receptor, Importin α, Is Required for Efficient Transition Through the G1/S Stage of the Cell Cycle in Saccharomyces cerevisiae. Genetics 181: 105–118. doi: 10.1534/genetics.108.097303 18984568

31. Umeda M, Izaddoost S, Cushman I, Moore MS, Sazer S (2005) The fission yeast Schizosaccharomyces pombe has two Importin α proteins, Imp1p and Cut15p, which have common and unique functions in nucleocytoplasmic transport and cell cycle progression. Genetics 171: 7–21. 15937127

32. Gruss OJ, Carazo-Salas RE, Schatz CA, Guarguaglini G, Kast J, et al. (2001) Ran induces spindle assembly by reversing the inhibitory effect of Importin α on TPX2 activity. Cell 104: 83–93. 11163242

33. Yano R, Oakes M, Yamaghishi M, Dodd JA, Nomura M (1992) Cloning and characterization of SRP1, a suppressor of temperature-sensitive RNA polymerase I mutations, in Saccharomyces cerevisiae. Mol Cell Biol 12: 5640–5651. 1448093

34. Solsbacher J, Maurer P, Bischoff FR, Schlenstedt G (1998) Cse1p is involved in export of yeast Importin α from the nucleus. Mol Cell Biol 18: 6805–6815. 9774694

35. Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, et al. (1996) A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell 84: 265–275. 8565072

36. Siniossoglou S, Lutzmann M, Santos-Rosa H, Leonard K, Mueller S, et al. (2000) Structure and assembly of the Nup84p complex. J Cell Biol 149: 41–54. 10747086

37. Larschan E, Winston F (2001) The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev 15: 1946–1956. 11485989

38. Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L (2011) SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell 44: 410–423. doi: 10.1016/j.molcel.2011.08.037 22055187

39. Gorlich D, Prehn S, Laskey RA, Hartmann E (1994) Isolation of a protein that is essential for the first step of nuclear protein import. Cell 79: 767–778. 8001116

40. Yusufzai TM, Tagami H, Nakatani Y, Felsenfeld G (2004) CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol Cell 13: 291–298. 14759373

41. Tabb MM, Tongaonkar P, Vu L, Nomura M (2000) Evidence for separable functions of Srp1p, the yeast homolog of importin α (Karyopherin α): role for Srp1p and Sts1p in protein degradation. Mol Cell Biol 20: 6062–6073. 10913188

42. Yano R, Oakes ML, Tabb MM, Nomura M (1994) Yeast Srp1p has homology to armadillo/plakoglobin/β-catenin and participates in apparently multiple nuclear functions including the maintenance of the nucleolar structure. Proc Natl Acad Sci U S A 91: 6880–6884. 8041713

43. Loeb JD, Schlenstedt G, Pellman D, Kornitzer D, Silver PA, et al. (1995) The yeast nuclear import receptor is required for mitosis. Proc Natl Acad Sci U S A 92: 7647–7651. 7644471

44. Shulga N, Roberts P, Gu Z, Spitz L, Tabb MM, et al. (1996) In vivo nuclear transport kinetics in Saccharomyces cerevisiae: a role for heat shock protein 70 during targeting and translocation. J Cell Biol 135: 329–339. 8896592

45. Hachet V, Kocher T, Wilm M, Mattaj IW (2004) Importin α associates with membranes and participates in nuclear envelope assembly in vitro. EMBO J 23: 1526–1535. 15014441

46. Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, et al. (2013) A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell 152: 969–983. doi: 10.1016/j.cell.2013.01.049 23452847

47. Weinmann L, Höck J, Ivacevic T, Ohrt T, Mütze J, et al. (2009) Importin-8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell 136: 496–507. doi: 10.1016/j.cell.2008.12.023 19167051

48. Capelson M, Liang Y, Schulte R, Mair W, Wagner U, et al. (2010) Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell 140: 372–383. doi: 10.1016/j.cell.2009.12.054 20144761

49. Kalverda B, Pickersgill H, Shloma VV, Fornerod M (2010) Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 140: 360–371. doi: 10.1016/j.cell.2010.01.011 20144760

50. Light WH, Freaney J, Sood V, Thompson A, D'Urso A, et al. (2013) A conserved role for human Nup98 in altering chromatin structure and promoting epigenetic transcriptional memory. PLoS Biol 11: e1001524. doi: 10.1371/journal.pbio.1001524 23555195

51. Davis RH (2000) Neurospora: Contributions of a Model Organism. Oxford: Oxford University Press. 333 p.

52. Honda S, Selker EU (2009) Tools for fungal proteomics: multifunctional Neurospora vectors for gene replacement, protein expression and protein purification. Genetics 182: 11–23. doi: 10.1534/genetics.108.098707 19171944

53. Oakley CE, Weil CF, Kretz PL, Oakley BR (1987) Cloning of the riboB locus of Aspergillus nidulans. Gene 53: 293–298. 3038695

54. Miao VP, Freitag M, Selker EU (2000) Short TpA-rich segments of the ζ-η region induce DNA methylation in Neurospora crassa. J Mol Biol 300: 249–273. 10873464

55. Pomraning KR, Smith KM, Bredeweg EL, Connolly LR, Phatale PA, et al. (2012) Library preparation and data analysis packages for rapid genome sequencing. Methods Mol Biol 944: 1–22. doi: 10.1007/978-1-62703-122-6_1 23065605

56. Jamieson K, Rountree MR, Lewis ZA, Stajich JE, Selker EU (2013) Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci U S A 110: 6027–6032. doi: 10.1073/pnas.1303750110 23530226

57. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359. doi: 10.1038/nmeth.1923 22388286

58. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29: 24–26. doi: 10.1038/nbt.1754 21221095

59. Harris EY, Ponts N, Le Roch KG, Lonardi S (2012) BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinformatics 28: 1795–1796. doi: 10.1093/bioinformatics/bts264 22563065

60. Rountree MR, Selker EU (1997) DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev 11: 2383–2395. 9308966

61. Adhvaryu KK, Berge E, Tamaru H, Freitag M, Selker EU (2011) Substitutions in the amino-terminal tail of Neurospora histone H3 have varied effects on DNA methylation. PLoS Genet 7: e1002423. doi: 10.1371/journal.pgen.1002423 22242002

62. Bistis GN, Perkins DD, Read ND (2003) Different cell types in Neurospora crassa. Fungal Genet Newsl 50: 17–19.

63. Roberts CJ, Selker EU (1995) Mutations affecting the biosynthesis of S-adenosylmethionine cause reduction of DNA methylation in Neurospora crassa. Nucleic Acids Res 23: 4818–4826. 8532524

64. Adhvaryu KK, Selker EU (2008) Protein phosphatase PP1 is required for normal DNA methylation in Neurospora. Genes Dev 22: 3391–3396. doi: 10.1101/gad.1738008 19141471

65. Bowman BJ, Draskovic M, Freitag M, Bowman EJ (2009) Structure and distribution of organelles and cellular location of calcium transporters in Neurospora crassa. Eukaryot Cell 8: 1845–1855. doi: 10.1128/EC.00174-09 19801418

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