MOE Key Laboratory of Aquatic Product Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
PLoS One. 2012;7(1):e30349. doi: 10.1371/journal.pone.0030349. Epub 2012 Jan 20.
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 strategy to investigate the DNA methylation profiling of A. flavus genome. Both the bisulfite sequencing data and the methylome comparisons with other fungi confirm that the DNA methylation level of this fungus is negligible. Further investigation into the DNA methyltransferase of Aspergillus uncovers its close relationship with RID-like enzymes as well as its divergence with the methyltransferase of species with validated DNA methylation. The lack of repeat contents of the A. flavus' genome and the high RIP-index of the small amount of remanent repeat potentially support our speculation that DNA methylation may be absent in A. flavus or that it may possess de novo DNA methylation which occurs very transiently during the obscure sexual stage of this fungal species. This work contributes to our understanding on the DNA methylation status of A. flavus, as well as reinforces our views on the DNA methylation in fungal species. In addition, our strategy of applying bisulfite sequencing to DNA methylation detection in species with low DNA methylation may serve as a reference for later scientific investigations in other hypomethylated species.
黄曲霉最初因其产生黄曲霉毒素而引起科学界的关注。黄曲霉毒素生物合成的基础调控机制一直是其他微生物次生代谢物生物合成的理论模型。然而，几十年来，涉及基因调控的重要表观遗传修饰之一的 DNA 甲基化状态在黄曲霉中仍然存在争议。在这里，我们应用亚硫酸氢盐测序结合生物重复策略来研究黄曲霉基因组的 DNA 甲基化谱。亚硫酸氢盐测序数据和与其他真菌的甲基组比较都证实了该真菌的 DNA 甲基化水平可以忽略不计。对曲霉 DNA 甲基转移酶的进一步研究揭示了它与 RID 样酶的密切关系，以及与具有验证 DNA 甲基化的物种的甲基转移酶的分化。黄曲霉基因组中没有重复内容，少量残留重复的 RIP-index 很高，这可能支持我们的推测，即黄曲霉中可能不存在 DNA 甲基化，或者它可能具有从头 DNA 甲基化，这种甲基化在该真菌种属的模糊有性阶段非常短暂。这项工作有助于我们了解黄曲霉的 DNA 甲基化状态，并加强我们对真菌物种中 DNA 甲基化的看法。此外，我们应用亚硫酸氢盐测序检测低甲基化物种中 DNA 甲基化的策略可能为以后在其他低甲基化物种中的科学研究提供参考。
