Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Bisulfite Sequencing Reveals that Aspergillus flavus Holds A Hollow in DNA Methylation

ABSTRACT: Aspergillus flavus first gained scientific attention for its production of aflatoxin, the most potent naturally occurring toxin and hepatocarcinogenic secondary metabolite. For several decades, The DNA methylation status of A. flavus remains to be controversial. We first applied bisulfite sequencing, the gold standard at present, in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Our results reveal that the DNA methylation level of this fungus turns out to be negligible, comparable to the unmethylated lambda DNA we set as the false positive control of our bisulfite experiments. When comparing the DNA methyltransferase homolog of A. flauvs with that from several selected hypermethylated speices, we find that the DNA methyltransferase homolog of A.flavus as well as the other Aspergillus members groups closely with the RID from Neurospora crassa and Masc1 from Ascobolus immerses, which has been reported as DMT-incapable, but it diverges distantly from the other capable DNA methyltransferases. We observe significant depletion of repeat components within the A. flavus, which may possibly explain the lack of DNA methylation in this fungus. What's more, the RIP-index of the repeat of A. flavus turns out to be higher than the fungi without RID-like enzyme, suggesting this asexual fungus may possibly possess RIP process during the obscure sexual-stage which is very evanescent and may potentially related to DNA methylation. This work contributes to our understanding on the DNA methylation status of A. flavus. Also, it reinforces our views on the DNA methylation in fungal species. What's more, our strategy of applying bisulfite sequencing to DNA methylation detection on species with low DNA methylation may serve as a reference for later scientific investigations on other hypomethylated species. Two replicates were subjected to bisulfite conversion independently, unmethylated lambda DNA as a false positive control is added to both replicates.

ORGANISM(S): Aspergillus flavus

SUBMITTER: Zhumei He

PROVIDER: E-GEOD-32177 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Liu Si-Yang SY Lin Jian-Qing JQ Wu Hong-Long HL Wang Cheng-Cheng CC Huang Shu-Jia SJ Luo Yan-Feng YF Sun Ji-Hua JH Zhou Jian-Xiang JX Yan Shu-Jing SJ He Jian-Guo JG Wang Jun J He Zhu-Mei ZM

PloS one 20120120 1

Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains to be controversial. Here, we applied bisulfite sequencing in conjunction with a biological replicate st ...[more]

PMID: 22276181

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Project description:Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: methylcytosine has been detected at very low levels in early embryos, but the genomic location and function of methylation has not been established. We have mapped cytosine methylation genomewide in Stage 5 Drosophila embryo DNA by combining immuno-enrichment for 5-methylcytosine, bisulfite conversion, and deep sequencing. Unlike methylation patterns observed in other eukaryotic species, methylation in Drosophila is punctate and highly strand-asymmetrical; we confirmed this by direct PCR amplification and sequencing of bisulfite-converted DNA. Despite the locally asymmetric nature of methylation, large-scale patterns of methylation are symmetric. Methylated regions make up ~1% of the genome, and within these regions methylation of individual cytosines averages 2-10%. Methylation is concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. It is depleted from promoters, coding sequences, and most retrotransposons, and enriched in introns and in certain simple sequence repeats containing the commonly methylated motifs. Comparison with available gene expression data indicates that methylation in a gene is associated with lower expression; the X chromosome, which is subject to gene dosage compensation, is more densely methylated than the autosomes. This study firmly establishes the presence of cytosine methylation in Drosophila; the temporal overlap of methylation with the maternal-zygotic transition raises the possibility that methylation participates in the transition to zygotic gene expression. To enrich for rare cytosine methylation in Drosophila at embryonic Stage 5 (2-3 hours post-fertilization), we enriched sonicated Stage 5 genomic DNA for methylcytosine by immunoprecipitation with antibody to 5-methylcytosine. The immunoprecipitated DNA was then bisulfite converted and Illumina sequenced to obtain direct evidence for the presence of methylation. The presence and extent of DNA methylation was confirmed by Illumina sequencing of bisulfite-converted PCR amplicons.

Dataset Information

Bisulfite Sequencing Reveals that Aspergillus flavus Holds A Hollow in DNA Methylation

Publications

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

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