Neurospora crassa, a model system for epigenetics research

Cold Spring Harbor Perspectives in Biology

Volumn 5, Issue 10, 2013, Pages

  Aramayo, Rodolfo ^a   Selker, Eric U ^b  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; SMALL UNTRANSLATED RNA;

BIOLOGICAL MODEL; DNA METHYLATION; EPIGENETICS; GENE DUPLICATION; GENE SILENCING; GENETICS; MEIOSIS; METABOLISM; METHYLATION; NEUROSPORA CRASSA; PHYSIOLOGY; POINT MUTATION; REVIEW;

DNA METHYLATION; EPIGENOMICS; GENE DUPLICATION; GENE SILENCING; HISTONES; MEIOSIS; METHYLATION; MODELS, GENETIC; NEUROSPORA CRASSA; POINT MUTATION; RNA, SMALL UNTRANSLATED;

EID: 84885023707     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a017921     Document Type: Article

References (71)

1. 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.
2. Alexander WG, Raju NB, Xiao H, Hammond TM, Perdue TD, Metzenberg RL, Pukkila PJ, Shiu PK. 2008. DCL-1 colocalizes with other components of the MSUD machinery and is required for silencing. Fungal Genet Biol 45: 719-727.
3. Allshire R, Ekwall K. 2014. Epigenetics in Saccharomyces pombe. Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a018770.
4. Aramayo R, Metzenberg RL. 1996. Meiotic transvection in fungi. Cell 86: 103-113.
5. +, a Neuros-pora crassa gene related to transcriptional regulators of fungal development. Genetics 144: 991-1003.
6. Bhat A, Kasbekar DP. 2001. Escape from repeat-induced point mutation of a gene-sized duplication in Neurospora crassa crosses that are heterozygous foralargerchromosome segment duplication. Genetics 157: 1581-1590.
7. Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, et al. 2004. Lessons from the genome sequence of Neurospora crassa: Tracing the path from genomic blueprint to multi cellular organism. Microbiol Mol Biol Rev 68: 1-108.
8. Chicas A, Cogoni C, Macino G. 2004. RNAI-dependent and RNAI-independent mechanisms contribute to the silencing of Ripped sequences in Neurospora crassa. Nucleic Acids Res 32: 4237-4243.
9. Chicas A, Forrest EC, Sepich S, Cogoni C, Macino G. 2005. Small interfering RNAs that trigger posttranscriptional gene silencing are not required for the histone H3 Lys9 methylation necessary for transgenic tandem repeat stabilization in Neurospora crassa. Mol Cell Biol 25: 3793-3801.
10. Cogoni C, Irelan JT, Schumacher M, Schmidhauser TJ, Selker EU, Mac-ino G. 1996. Transgene silencing of the al-1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA-DNA interactions or DNA methylation. EMBO J 15: 3153-3163.
11. Davis RH, de Serres FJ. 1970. Genetic and microbiological research techniques for Neurospora crassa. In Metabolism of amino acids amines (ed. Colowick SP, Kaplan NO), pp. 79-143. Academic, New York.
12. Elgin SCR, Reuter G. 2013. Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb Perspect Biol 5: a017780.
13. Freitag M, Williams RL, Kothe GO, Selker EU. 2002. A cytosine methyl-transferase homologue is essential for repeat-induced point mutation in Neurospora crassa. Proc Natl Acad Sci 99: 8802-8807.
14. Freitag M, Hickey PC, Khlafallah TK, Read ND, Selker EU. 2004a. HP1 is essential for DNA methylation in Neurospora. Mol Cell 13: 427-434.
15. Freitag M, Hickey PC, Raju NB, Selker EU, Read ND. 2004b. GFPas atool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassa. Fungal Genet Biol 41: 897-910.
16. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, Fitz-Hugh W, Ma LJ, Smirnov S, Purcell S, et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
17. Galagan JE, Selker EU. 2004. RIP: The evolutionary cost of genome defense. Trends Genet 20: 417-423.
18. Grunstein M, Gasser SM. 2013. Epigenetics in Saccharomyces cerevisiae. Cold Spring Harb Perspect Biol 5: a017491.
19. Goll MG, Bestor TH. 2005. Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481-514.
20. Hammond TM, Xiao H, Boone EC, Perdue TD, Pukkila PJ, Shiu PK. 2011. SAD-3, a putative helicase required for meiotic silencing by unpaired DNA, interacts with other components of the silencing machinery. G3 1: 369-376.
21. Honda S, Selker EU. 2008. Direct interaction between DNA methyltrans-ferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Mol Cell Biol 28: 6044-6055.
22. Honda S, Lewis ZA, Huarte M, Cho LY, David LL, Shi Y, Selker EU. 2010. The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassa. Genes Dev 24: 443-454.
23. Honda S, Lewis ZA, Shimada K, Fischle W, Sack R, Selker EU. 2012. HP1 forms distinct complexes to direct histone deacetylation and DNA methylation. Nat Struct Mol Biol 19: 471-477.
24. 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 110: 6227-6232.
25. Jia S, Kobayashi R, Grewal SI. 2005. Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble hetero-chromatin. Nat Cell Biol 7: 1007-1013.
26. Kelly WG, Aramayo R. 2007. Meiotic silencing and the epigenetics of sex. Chromosome Res 15: 633-651.
27. Kouzminova E, Selker EU. 2001. Dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J 20: 4309-4323.
28. Kutil BL, Seong KY, Aramayo R.2003. Unpaired genes do not silence their paired neighbors. Curr Genet 43: 425-432.
29. Lee DW, Pratt RJ, McLaughlin M, Aramayo R. 2003. An argonaute-like protein is required for meiotic silencing. Genetics 164: 821-828.
30. Lee DW, Seong KY, Pratt RJ, Baker K, Aramayo R. 2004. Properties of unpaired DNA required for efficient silencing in Neurospora crassa. Genetics 167: 131-150.
31. Lee HC, Chang SS, Choudhary S, Aalto AP, Maiti M, Bamford DH, Liu Y. 2009. Qi RNA is a new type of small interfering RNA induced by DNA damage. Nature 459: 274-277.
32. Lee HC, Aalto AP, Yang Q, Chang SS, Huang G, Fisher D, Cha J, Poranen MM, Bamford DH, Liu Y. 2010a. The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrant RNA and ds RNA for RNAI in a process requiring replication protein A and a DNA helicase. PLoS Biol 8: e1000496.
33. Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, et al. 2010b. Diverse pathways generate micro RNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 38: 803-814.
34. Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, Mohn F, Schubeler D, Selker EU. 2009. Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res 19: 427-437.
35. Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Knip M, Sack R, Selker EU. 2010a. DNA methylation and normal chromosome behavior in Neu-rospora depend on five components of a histone methyltransferase complex, DCDC. PLoS Genet 6: e1001196.
36. Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Selker EU. 2010b. Identification of DIM-7, a protein required to target the DIM-5 H3 methyl transferase to chromatin. Proc Natl Acad Sci 107: 8310-8315.
37. Li E, Zhang Y. 2014. DNA methylation in mammals. Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a019133.
38. Li F, Goto DB, Zaratiegui M, Tang X, Martienssen R, Cande WZ. 2005. Two novel proteins, Dos1 and Dos2, interact with Rik1 to regulate heterochromatic RNA interference and histone modification. Curr Biol 15: 1448-1457.
39. Martienssen RA, Zaratiegui M, Goto DB. 2005. RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe. Trends Genet 21: 450-456.
40. Nolan T, Braccini L, Azzalin G, De Toni A, Macino G, Cogoni C. 2005. The post-transcriptional gene silencing machinery functions independently of DNA methylation to repress a LINE1-like retrotransposon in Neurospora crassa. Nucleic Acids Res 33: 1564-1573.
41. Perkins DD. 1966. Details for collection of asci as unordered groups of eight projected ascospores. Neurospora Newslett 9: 11.
42. Perkins DD. 1988. Comments on Metzenberg's procedure for isolating unordered Neurospora asci. Fungal Genet Newslett 35: 29.
43. Perkins DD, Metzenberg RL, Raju NB, Selker EU, Barry EG. 1986. Reversal of a Neurospora translocation by crossing over involving displaced rDNA, and methylation of the rDNA segments that result from recombination. Genetics 114: 791-817.
44. Perkins DD, Margolin BS, Selker EU, Haedo SD. 1997. Occurrence of repeat induced point mutation in long segmental duplications of Neurospora. Genetics 147: 125-136.
45. Perkins DD, Radford A, Sachs MS. 2001. The Neurospora compendium: Chromosomal loci. Academic, San Diego.
46. Pickford AS, Catalanotto C, Cogoni C, Macino G. 2002. Quelling in Neurospora crassa. Adv Genet 46: 277-303.
47. Pikaard C, Mittelsten Scheid O. 2014. Epigenetic regulation in plants. Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a019315.
48. Pratt RJ, Lee DW, Aramayo R. 2004. DNA methylation affects meiotic trans-sensing, not meiotic silencing, in Neurospora. Genetics 168: 1925-1935.
49. Raju NB. 1980. Meiosis and ascospore genesis in Neurospora. Eur J Cell Biol 23: 208-223.
50. Raju NB. 1992. Genetic control of the sexual cycle in Neurospora. Mycol Res 96: 241-262.
51. Roberts CJ, Selker EU. 1995. Mutations affecting the biosynthesis of S-adenosylmethionine cause reduction of DNA methylation in Neu-rospora crassa. Nucleic Acids Res 23: 4818-4826.
52. Rossignol J-L, Faugeron G. 1994. Gene inactivation triggered by recognition between DNA repeats. Experientia 50: 307-317.
53. Selker EU. 1990a. DNA methylation and chromatin structure: A view from below. Trends Biochem Sci 15: 103-107.
54. Selker EU. 1990b. Premeiotic instability of repeated sequences in Neu-rospora crassa. Annu Rev Genet 24: 579-613.
55. Selker EU. 1998. Trichostatin A causes selective loss of DNA methylation in Neurospora. Proc Natl Acad Sci 95: 9430-9435.
56. Selker EU, Stevens JN. 1985. DNA methylation at asymmetric sites is associated with numerous transition mutations. Proc Natl Acad Sci 82: 8114-8118.
57. Selker EU, Cambareri EB, Jensen BC, Haack KR. 1987. Rearrangement of duplicated DNA in specialized cells of Neurospora. Cell 51: 741-752.
58. Selker EU, Freitag M, Kothe GO, Margolin BS, Rountree MR, Allis CD, Tamaru H. 2002. Induction and maintenance of nonsymmetrical DNA methylation in Neurospora. Proc Natl Acad Sci 99: 16485-16490.
59. Selker EU, Tountas NA, Cross SH, Margolin BS, Murphy JG, Bird AP, Freitag M. 2003. The methylated component of the Neurospora crassa genome. Nature 422: 893-897.
60. Shiu PK, Raju NB, Zickler D, Metzenberg RL. 2001. Meiotic silencing by unpaired DNA. Cell 107: 905-916.
61. Shiu PK, Zickler D, Raju NB, Ruprich-Robert G, Metzenberg RL. 2006. SAD-2 is required for meiotic silencing by unpaired DNA and peri-nuclear localization of SAD-1 RNA-directed RNA polymerase. Proc Natl Acad Sci 103: 2243-2248.
62. Singer MJ, Marcotte BA, Selker EU. 1995. DNA methylation associated with repeat-induced point mutation in Neurospora crassa. Mol Cell Biol 15: 5586-5597.
63. Smith KM, Kothe GO, Matsen CB, Khlafallah TK, Adhvaryu KK, Hemp-hill M, Freitag M, Motamedi MR, Selker EU. 2008. The fungus Neuros-pora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9. Epigenetics Chromatin 1: 5.
64. Smith KM, Dobosy JR, Reifsnyder JE, Rountree MR, Anderson DC, Green GR, Selker EU. 2010. H2B- and H3-specific histone deacetylases are required for DNA methylation in Neurospora crassa. Genetics 186: 1207-1216.
65. Smith KM, Phatale PA, Sullivan CM, Pomraning KR, Freitag M. 2011. Heterochromatin is required for normal distribution of Neurospora crassa CenH3. Mol Cell Biol 31: 2528-2542.
66. Tamaru H, Selker EU. 2001. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414: 277-283.
67. Tamaru H, Selker EU. 2003. Synthesis of signals for de novo DNA meth-ylation in Neurospora crassa. Mol Cell Biol 23: 2379-2394.
68. Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, Grewal SI, Allis CD, Cheng X, Selker EU. 2003. Trimethylated lysine 9of histone H3is a mark for DNA methylation in Neurospora crassa. Nat Genet 34: 75-79.
69. Thon G, Hansen KR, Altes SP, Sidhu D, Singh G, Verhein-Hansen J, Bonaduce MJ, Klar AJ. 2005. The Clr7 and Clr8 directionality factors and the Pcu4 cullin mediate heterochromatin formation in the fission yeast Schizosaccharomyces pombe. Genetics 171: 1583-1595.
70. Watters MK, Randall TA, Margolin BS, Selker EU, Stadler DR. 1999. Action of repeat-induced point mutation on both strands of a duplex and on tandem duplications of various sizes in Neurospora. Genetics 153: 705-714.
71. Wu CT, Morris JR. 1999. Transvection and other homology effects. Curr Opin Genet Dev 9: 237-246.