Identification and Functional Demonstration of miRNAs in the Fungus Cryptococcus neoformans

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Jiang, Nan ^a,b   Yang, Yaping ^a   Janbon, Guilhem ^c   Pan, Jiao ^a   Zhu, Xudong ^a  

^a NANKAI UNIVERSITY   (China)

^b Chinese Academy of Sciences   (China)

^c INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 1; MICRORNA 2; SHORT HAIRPIN RNA; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; CRYPTOCOCCUS NEOFORMANS; GENE EXPRESSION; GENE SILENCING; GENETIC VARIABILITY; MAMMAL; MOLECULAR EVOLUTION; MOLECULAR SIZE; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; PSEUDOGENE; REGULATORY MECHANISM; RNA ANALYSIS; RNA SEQUENCE; TRANSGENE; TRANSPOSON;

BASE SEQUENCE; CHROMOSOME MAPPING; CRYPTOCOCCUS NEOFORMANS; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENES, REPORTER; MICRORNAS; MOLECULAR SEQUENCE DATA; RNA INTERFERENCE; RNA, FUNGAL; SEQUENCE ANALYSIS, DNA;

ANIMALIA; EUKARYOTA; FILOBASIDIELLA NEOFORMANS; FUNGI; MAMMALIA;

EID: 84871537672     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052734     Document Type: Article

References (44)

1. Ambros V, (2003) MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113: 673-676.
2. Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
3. Carrington JC, Ambros V, (2003) Role of microRNAs in plant and animal development. Science 301: 336-338.
4. Ghildiyal M, Zamore PD, (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10: 94-108.
5. Wang L, Wang MB, Tu JX, Helliwell CA, Waterhouse PM, et al. (2007) Cloning and characterization of microRNAs from Brassica napus. FEBS Letters 581: 3848-3856.
6. Carthew RW, Sontheimer EJ, (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
7. Halic M, Moazed D, (2010) Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell 140: 504-516.
8. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
9. Benfey PN, (2003) MicroRNA is here to stay. Science 425: 244-245.
10. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, et al. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106: 23-34.
11. Hyun S, Lee JH, Jin H, Nam JW, Namkoong B, et al. (2009) Conserved microRNA miR-8/miR-200 and its target USH/FOG2 control growth by regulating PI3K. Cell 139: 1096-1108.
12. Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I, (2008) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455: 1124-1128.
13. 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.
14. Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, et al. (2010) Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 38: 803-814.
15. Buhler M, Moazed D, (2007) Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14: 1041-1048.
16. Catalanotto C, Nolan T, Cogoni C, (2006) Homology effects in Neurospora crassa. FEMS Microbiol Lett 254: 182-189.
17. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, et al. (2009) RNAi in budding yeast. Science 326: 544-550.
18. Liu H, Cottrell TR, Pierini LM, Goldman WE, Doering TL, (2002) RNA interference in the pathogenic fungus Cryptococcus neoformans. Genetics 160: 463-470.
19. Wang X, Hsueh YP, Li W, Floyd A, Skalsky R, et al. (2010) Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi. Genes Dev 24: 2566-2582.
20. Idnurm A, Bahn YS, Nielsen K, Lin X, Fraser JA, et al. (2005) Deciphering the model pathogenic fungus Cryptococcus neoformans. Nat Rev Microbiol 3: 753-764.
21. Dang Y, Yang Q, Xue Z, Liu Y, (2011) RNA interference in fungi: pathways, functions, and applications. Eukaryot Cell 10: 1148-1155.
22. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, et al. (2005) The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307: 1321-1324.
23. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ, (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432: 231-235.
24. Jones-Rhoades MW, Bartel DP, Bartel B, (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
25. Kim VN, Han J, Siomi MC, (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10: 126-139.
26. Edman JC, Kwon-Chung KJ, (1990) Isolation of the URA5 gene from Cryptococcus neoformans var. neoformans and its use as a selective marker for transformation. Mol Cell Biol 10: 4538-4544.
27. Williamson PR, Wakamatsu K, ITO S, (1998) Melanin Biosynthesis in Cryptococcus neoformans. J Bacteriol 180: 1570-1572.
28. Zhu X, Williamson PR, (2003) A CLC-type chloride channel gene is required for laccase activity and virulence in Cryptococcus neoformans. Mol Microbiol 50: 1271-1281.
29. Zhu X, Williamson PR, (2004) Role of laccase in the biology and virulence of Cryptococcus neoformans. FEMS Yeast Res 5: 1-10.
30. Janbon G, Maeng S, Yang DH, Ko YJ, Jung KW, et al. (2010) Characterizing the role of RNA silencing components in Cryptococcus neoformans. Fungal Genet Biol 47: 1070-1080.
31. Marchler-Bauer A, Lu S, Anderson SL, Chitsaz F, Derbyshire MK, et al. (2011) "CDD: a Conserved Domain Database for the functional annotation of proteins.". Nucleic Acids Res 39: 225-229.
32. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 22DDCT method. Methods 25: 402-408.
33. Piriyapongsa J, Jordan IK, (2007) A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS ONE 2: e203.
34. Piriyapongsa J, Marino-Rami{dotless}rez L, Jordan IK, (2007) Origin and evolution of human microRNAs from transposable elements. Genetics 176: 1323-1337.
35. Piriyapongsa J, Jordan IK, (2008) Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14: 814-821.
36. Yu S, Li J, Luo L, (2010) Complexity and Specificity of Precursor microRNAs Drivenby Transposable Elements in Rice. Plant Mol Biol Rep 28: 502-511.
37. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, et al. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumor biology. Nature 465: 1033-1040.
38. Swami M, (2010) Pseudogenes act as microRNA decoys. Nat Rev Genet 11: 530-531.
39. Drivinya A, Shimizu K, Takeo K, (2004) Construction of a complete URA5 deletion strain of a human pathogenic yeast Cryptococcus neoformans. Nihon Ishinkin Gakkai Zasshi 45: 1-6.
40. Williamson PR, (1994) Biochemical and molecular characterization of the diphenol oxidase of Cryptococcus neoformans: identification as a laccase. J Bacteriol 176: 656-664.
41. Pall GS, Codony-Servat C, Byrne J, Ritchie L, Hamilton A, (2007) Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Res 35: e60.
42. Wigkes BL, Edman JC (1994) Development of a transformation system for Cryptococcus neoformans. In Molecular biology of Pathogenic Fungi (Maresca, B. & Kobayashi, G.S., eds). New York: Telos Press. pp. 309-313.
43. Jiang N, Xiao D, Zhang D, Sun N, Yan B, et al. (2009) Negative roles of a novel nitrogen metabolite repression-related gene, TAR1, in laccase production and nitrate utilization by the basidiomycete Cryptococcus neoformans. Appl Environ Microbiol 75: 6777-6782.
44. Jiang N, Sun N, Xiao D, Pan J, Wang Y, et al. (2009) A copper-responsive factor gene CUF1 is required for copper induction of laccase in Cryptococcus neoformans. FEMS Microbiol Lett 296: 84-90.