메뉴 건너뛰기




Volumn 7, Issue 1, 2012, Pages

Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA METHYLTRANSFERASE; FUNGAL DNA; GENOMIC DNA; HYDROGEN SULFITE; SULFITE;

EID: 84856062466     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030349     Document Type: Article
Times cited : (56)

References (49)
  • 1
    • 75149119849 scopus 로고    scopus 로고
    • Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters
    • Georgianna DR, Fedorova ND, Burroughs JL, Dolezal AL, Bok JW, et al. (2010) Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters. Mol Plant Pathol 11: 213-226.
    • (2010) Mol Plant Pathol , vol.11 , pp. 213-226
    • Georgianna, D.R.1    Fedorova, N.D.2    Burroughs, J.L.3    Dolezal, A.L.4    Bok, J.W.5
  • 2
    • 79952088976 scopus 로고    scopus 로고
    • Aflatoxin: a 50-year odyssey of mechanistic and translational toxicology
    • Kensler TW, Roebuck BD, Wogan GN, Groopman JD, (2011) Aflatoxin: a 50-year odyssey of mechanistic and translational toxicology. Toxicol Sci 120 (Suppl 1): S28-48.
    • (2011) Toxicol Sci , vol.120 , Issue.SUPPL. 1
    • Kensler, T.W.1    Roebuck, B.D.2    Wogan, G.N.3    Groopman, J.D.4
  • 3
    • 60349103334 scopus 로고    scopus 로고
    • Potential of Aspergillus flavus genomics for applications in biotechnology
    • Cleveland TE, Yu J, Fedorova N, Bhatnagar D, Payne GA, et al. (2009) Potential of Aspergillus flavus genomics for applications in biotechnology. Trends Biotechnol 27: 151-157.
    • (2009) Trends Biotechnol , vol.27 , pp. 151-157
    • Cleveland, T.E.1    Yu, J.2    Fedorova, N.3    Bhatnagar, D.4    Payne, G.A.5
  • 5
    • 4143090400 scopus 로고    scopus 로고
    • LaeA, a regulator of secondary metabolism in Aspergillus spp
    • Bok JW, Keller NP, (2004) LaeA, a regulator of secondary metabolism in Aspergillus spp. Eukaryot Cell 3: 527-535.
    • (2004) Eukaryot Cell , vol.3 , pp. 527-535
    • Bok, J.W.1    Keller, N.P.2
  • 6
    • 38649139072 scopus 로고    scopus 로고
    • Improved protocols for functional analysis in the pathogenic fungus Aspergillus flavus
    • He ZM, Price MS, Obrian GR, Georgianna DR, Payne GA, (2007) Improved protocols for functional analysis in the pathogenic fungus Aspergillus flavus. BMC Microbiol 7: 104.
    • (2007) BMC Microbiol , vol.7 , pp. 104
    • He, Z.M.1    Price, M.S.2    Obrian, G.R.3    Georgianna, D.R.4    Payne, G.A.5
  • 7
    • 58849163072 scopus 로고    scopus 로고
    • Genetic regulation of aflatoxin biosynthesis: from gene to genome
    • Georgianna DR, Payne GA, (2009) Genetic regulation of aflatoxin biosynthesis: from gene to genome. Fungal Genet Biol 46: 113-125.
    • (2009) Fungal Genet Biol , vol.46 , pp. 113-125
    • Georgianna, D.R.1    Payne, G.A.2
  • 8
    • 1842816643 scopus 로고    scopus 로고
    • Influence of white light, near-UV irradiation and other environmental conditions on production of aflatoxin B1 by Aspergillus flavus and ochratoxin A by Aspergillus ochraceus
    • Aziz NH, Moussa LA, (1997) Influence of white light, near-UV irradiation and other environmental conditions on production of aflatoxin B1 by Aspergillus flavus and ochratoxin A by Aspergillus ochraceus. Nahrung 41: 150-154.
    • (1997) Nahrung , vol.41 , pp. 150-154
    • Aziz, N.H.1    Moussa, L.A.2
  • 9
    • 73949102298 scopus 로고    scopus 로고
    • Epigenome manipulation as a pathway to new natural product scaffolds and their congeners
    • Cichewicz RH, (2010) Epigenome manipulation as a pathway to new natural product scaffolds and their congeners. Nat Prod Rep 27: 11-22.
    • (2010) Nat Prod Rep , vol.27 , pp. 11-22
    • Cichewicz, R.H.1
  • 10
    • 0035960702 scopus 로고    scopus 로고
    • DNA from Aspergillus flavus contains 5-methylcytosine
    • Gowher H, Ehrlich KC, Jeltsch A, (2001) DNA from Aspergillus flavus contains 5-methylcytosine. FEMS Microbiol Lett 205: 151-155.
    • (2001) FEMS Microbiol Lett , vol.205 , pp. 151-155
    • Gowher, H.1    Ehrlich, K.C.2    Jeltsch, A.3
  • 12
    • 0021060841 scopus 로고
    • High-frequency conversion to a "fluffy" developmental phenotype in Aspergillus spp. by 5-azacytidine treatment: evidence for involvement of a single nuclear gene
    • Tamame M, Antequera F, Villanueva JR, Santos T, (1983) High-frequency conversion to a "fluffy" developmental phenotype in Aspergillus spp. by 5-azacytidine treatment: evidence for involvement of a single nuclear gene. Mol Cell Biol 3: 2287-2297.
    • (1983) Mol Cell Biol , vol.3 , pp. 2287-2297
    • Tamame, M.1    Antequera, F.2    Villanueva, J.R.3    Santos, T.4
  • 13
    • 33646346836 scopus 로고    scopus 로고
    • Evidence of RIP (repeat-induced point mutation) in transposase sequences of Aspergillus oryzae
    • Montiel MD, Lee HA, Archer DB, (2006) Evidence of RIP (repeat-induced point mutation) in transposase sequences of Aspergillus oryzae. Fungal Genet Biol 43: 439-445.
    • (2006) Fungal Genet Biol , vol.43 , pp. 439-445
    • Montiel, M.D.1    Lee, H.A.2    Archer, D.B.3
  • 14
    • 49649120660 scopus 로고    scopus 로고
    • A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans
    • Lee DW, Freitag M, Selker EU, Aramayo R, (2008) A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans. PLoS One 3: e2531.
    • (2008) PLoS One , vol.3
    • Lee, D.W.1    Freitag, M.2    Selker, E.U.3    Aramayo, R.4
  • 15
    • 43749098985 scopus 로고    scopus 로고
    • DNA methylation landscapes: provocative insights from epigenomics
    • Suzuki MM, Bird A, (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-476.
    • (2008) Nat Rev Genet , vol.9 , pp. 465-476
    • Suzuki, M.M.1    Bird, A.2
  • 16
    • 77957932941 scopus 로고    scopus 로고
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    • Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28: 1097-1105.
    • (2010) Nat Biotechnol , vol.28 , pp. 1097-1105
    • Harris, R.A.1    Wang, T.2    Coarfa, C.3    Nagarajan, R.P.4    Hong, C.5
  • 17
    • 77952123054 scopus 로고    scopus 로고
    • Single base-resolution methylome of the silkworm reveals a sparse epigenomic map
    • Xiang H, Zhu JD, Chen Q, Dai FY, Li X, et al. (2010) Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 28: 516-520.
    • (2010) Nat Biotechnol , vol.28 , pp. 516-520
    • Xiang, H.1    Zhu, J.D.2    Chen, Q.3    Dai, F.Y.4    Li, X.5
  • 18
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3    Hawkins, R.D.4    Hon, G.5
  • 19
    • 77952355762 scopus 로고    scopus 로고
    • Genome-wide evolutionary analysis of eukaryotic DNA methylation
    • Zemach A, McDaniel IE, Silva P, Zilberman D, (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328: 916-919.
    • (2010) Science , vol.328 , pp. 916-919
    • Zemach, A.1    McDaniel, I.E.2    Silva, P.3    Zilberman, D.4
  • 20
    • 0037172977 scopus 로고    scopus 로고
    • A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa
    • Freitag M, Williams RL, Kothe GO, Selker EU, (2002) A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa. Proc Natl Acad Sci USA 99: 8802-8807.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8802-8807
    • Freitag, M.1    Williams, R.L.2    Kothe, G.O.3    Selker, E.U.4
  • 21
  • 22
    • 0025641736 scopus 로고
    • Premeiotic instability of repeated sequences in Neurospora crassa
    • Selker EU, (1990) Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet 24: 579-613.
    • (1990) Annu Rev Genet , vol.24 , pp. 579-613
    • Selker, E.U.1
  • 23
    • 4143050271 scopus 로고    scopus 로고
    • RIP: the evolutionary cost of genome defense
    • Galagan JE, Selker EU, (2004) RIP: the evolutionary cost of genome defense. Trends Genet 20: 417-423.
    • (2004) Trends Genet , vol.20 , pp. 417-423
    • Galagan, J.E.1    Selker, E.U.2
  • 24
    • 67650221600 scopus 로고    scopus 로고
    • Sexual reproduction in Aspergillus flavus
    • Horn BW, Moore GG, Carbone I, (2009) Sexual reproduction in Aspergillus flavus. Mycologia 101: 423-429.
    • (2009) Mycologia , vol.101 , pp. 423-429
    • Horn, B.W.1    Moore, G.G.2    Carbone, I.3
  • 25
    • 0035839126 scopus 로고    scopus 로고
    • Epigenetic reprogramming in mammalian development
    • Reik W, Dean W, Walter J, (2001) Epigenetic reprogramming in mammalian development. Science 293: 1089-1093.
    • (2001) Science , vol.293 , pp. 1089-1093
    • Reik, W.1    Dean, W.2    Walter, J.3
  • 26
    • 22844457491 scopus 로고    scopus 로고
    • DNA methylation and human disease
    • Robertson KD, (2005) DNA methylation and human disease. Nat Rev Genet 6: 597-610.
    • (2005) Nat Rev Genet , vol.6 , pp. 597-610
    • Robertson, K.D.1
  • 27
    • 3342927934 scopus 로고    scopus 로고
    • Role of transposable elements in heterochromatin and epigenetic control
    • Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
    • (2004) Nature , vol.430 , pp. 471-476
    • Lippman, Z.1    Gendrel, A.V.2    Black, M.3    Vaughn, M.W.4    Dedhia, N.5
  • 28
    • 77953809924 scopus 로고    scopus 로고
    • DNA methylation and the formation of heterochromatin in Neurospora crassa
    • Rountree MR, Selker EU, (2010) DNA methylation and the formation of heterochromatin in Neurospora crassa. Heredity 105: 38-44.
    • (2010) Heredity , vol.105 , pp. 38-44
    • Rountree, M.R.1    Selker, E.U.2
  • 29
    • 67349217819 scopus 로고    scopus 로고
    • Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2
    • Phalke S, Nickel O, Walluscheck D, Hortig F, Onorati MC, et al. (2009) Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2. Nat Genet 41: 696-702.
    • (2009) Nat Genet , vol.41 , pp. 696-702
    • Phalke, S.1    Nickel, O.2    Walluscheck, D.3    Hortig, F.4    Onorati, M.C.5
  • 30
    • 0034672095 scopus 로고    scopus 로고
    • DNA of Drosophila melanogaster contains 5-methylcytosine
    • Gowher H, Leismann O, Jeltsch A, (2000) DNA of Drosophila melanogaster contains 5-methylcytosine. EMBO J 19: 6918-6923.
    • (2000) EMBO J , vol.19 , pp. 6918-6923
    • Gowher, H.1    Leismann, O.2    Jeltsch, A.3
  • 31
    • 78649955848 scopus 로고    scopus 로고
    • The honey bee epigenomes: differential methylation of brain DNA in queens and workers
    • Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, et al. (2010) The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol 8: e1000506.
    • (2010) PLoS Biol , vol.8
    • Lyko, F.1    Foret, S.2    Kucharski, R.3    Wolf, S.4    Falckenhayn, C.5
  • 32
    • 0024554833 scopus 로고
    • DNA methylation in fungi
    • Magill JM, Magill CW, (1989) DNA methylation in fungi. Dev Genet 10: 63-69.
    • (1989) Dev Genet , vol.10 , pp. 63-69
    • Magill, J.M.1    Magill, C.W.2
  • 33
    • 0042386500 scopus 로고    scopus 로고
    • DNA methylation analysis techniques
    • Dahl C, Guldberg P, (2003) DNA methylation analysis techniques. Biogerontology 4: 233-250.
    • (2003) Biogerontology , vol.4 , pp. 233-250
    • Dahl, C.1    Guldberg, P.2
  • 34
    • 0033287156 scopus 로고    scopus 로고
    • Sex brings transposons and genomes into conflict
    • Bestor TH, (1999) Sex brings transposons and genomes into conflict. Genetica 107: 289-295.
    • (1999) Genetica , vol.107 , pp. 289-295
    • Bestor, T.H.1
  • 35
    • 78751621346 scopus 로고    scopus 로고
    • Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes
    • Clutterbuck AJ, (2011) Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes. Fungal Genet Biol 48: 306-326.
    • (2011) Fungal Genet Biol , vol.48 , pp. 306-326
    • Clutterbuck, A.J.1
  • 36
    • 77954688477 scopus 로고    scopus 로고
    • 5-azacytidine treatment reorganizes genomic histone modification patterns
    • Komashko VM, Farnham PJ, (2010) 5-azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics 5: 229-240.
    • (2010) Epigenetics , vol.5 , pp. 229-240
    • Komashko, V.M.1    Farnham, P.J.2
  • 37
    • 46249124364 scopus 로고    scopus 로고
    • Internuclear gene silencing in Phytophthora infestansis established through chromatin remodelling
    • van West P, Shepherd SJ, Walker CA, Li S, Appiah AA, et al. (2008) Internuclear gene silencing in Phytophthora infestansis established through chromatin remodelling. Microbiology 154: 1482-1490.
    • (2008) Microbiology , vol.154 , pp. 1482-1490
    • van West, P.1    Shepherd, S.J.2    Walker, C.A.3    Li, S.4    Appiah, A.A.5
  • 38
    • 0032817359 scopus 로고    scopus 로고
    • Effect of interaction between 5-azacytidine and DNA (cytosine-5) methyltransferase on C-to-G and C-to-T mutations in Escherichia coli
    • Doiron KM, Lavigne-Nicolas J, Cupples CG, (1999) Effect of interaction between 5-azacytidine and DNA (cytosine-5) methyltransferase on C-to-G and C-to-T mutations in Escherichia coli. Mutat Res 429: 37-44.
    • (1999) Mutat Res , vol.429 , pp. 37-44
    • Doiron, K.M.1    Lavigne-Nicolas, J.2    Cupples, C.G.3
  • 39
    • 36048997460 scopus 로고    scopus 로고
    • Does urea promote the bisulfite-mediated deamination of cytosine in DNA? Investigation aiming at speeding-up the procedure for DNA methylation analysis
    • Hayatsu H, Tsuji K, Negishi K, (2006) Does urea promote the bisulfite-mediated deamination of cytosine in DNA? Investigation aiming at speeding-up the procedure for DNA methylation analysis. Nucleic Acids SympSer (Oxf) 50: 69-70.
    • (2006) Nucleic Acids SympSer (Oxf) , vol.50 , pp. 69-70
    • Hayatsu, H.1    Tsuji, K.2    Negishi, K.3
  • 40
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: an improved ultrafast tool for short read alignment
    • Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3    Lam, T.W.4    Yiu, S.M.5
  • 41
    • 33750831582 scopus 로고    scopus 로고
    • Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
    • Kohany O, Gentles AJ, Hankus L, Jurka J, (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7: 474.
    • (2006) BMC Bioinformatics , vol.7 , pp. 474
    • Kohany, O.1    Gentles, A.J.2    Hankus, L.3    Jurka, J.4
  • 42
    • 84860513986 scopus 로고    scopus 로고
    • PILER: identification and classification of genomic repeats
    • Edgar RC, Myers EW, (2005) PILER: identification and classification of genomic repeats. Bioinformatics 21 (Suppl 1): i152-158.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Edgar, R.C.1    Myers, E.W.2
  • 43
    • 34547592867 scopus 로고    scopus 로고
    • LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
    • Xu Z, Wang H, (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35: W265-268.
    • (2007) Nucleic Acids Res , vol.35
    • Xu, Z.1    Wang, H.2
  • 44
    • 0031927613 scopus 로고    scopus 로고
    • A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation
    • Margolin BS, Garrett-Engele PW, Stevens JN, Fritz DY, Garrett-Engele C, et al. (1998) A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation. Genetics 149: 1787-1797.
    • (1998) Genetics , vol.149 , pp. 1787-1797
    • Margolin, B.S.1    Garrett-Engele, P.W.2    Stevens, J.N.3    Fritz, D.Y.4    Garrett-Engele, C.5
  • 46
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan-an integration platform for the signature-recognition methods in InterPro
    • Zdobnov EM, Apweiler R, (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
    • (2001) Bioinformatics , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 48
    • 59449110909 scopus 로고    scopus 로고
    • DOG 1.0: illustrator of protein domain structures
    • Ren J, Wen L, Gao X, Jin C, Xue Y, et al. (2009) DOG 1.0: illustrator of protein domain structures. Cell Res 19: 271-273.
    • (2009) Cell Res , vol.19 , pp. 271-273
    • Ren, J.1    Wen, L.2    Gao, X.3    Jin, C.4    Xue, Y.5
  • 49
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
    • (2007) Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.