Cargando…
Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation
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,...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262820/ https://www.ncbi.nlm.nih.gov/pubmed/22276181 http://dx.doi.org/10.1371/journal.pone.0030349 |
_version_ | 1782221775869837312 |
---|---|
author | Liu, Si-Yang Lin, Jian-Qing Wu, Hong-Long Wang, Cheng-Cheng Huang, Shu-Jia Luo, Yan-Feng Sun, Ji-Hua Zhou, Jian-Xiang Yan, Shu-Jing He, Jian-Guo Wang, Jun He, Zhu-Mei |
author_facet | Liu, Si-Yang Lin, Jian-Qing Wu, Hong-Long Wang, Cheng-Cheng Huang, Shu-Jia Luo, Yan-Feng Sun, Ji-Hua Zhou, Jian-Xiang Yan, Shu-Jing He, Jian-Guo Wang, Jun He, Zhu-Mei |
author_sort | Liu, Si-Yang |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3262820 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-32628202012-01-24 Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation Liu, Si-Yang Lin, Jian-Qing Wu, Hong-Long Wang, Cheng-Cheng Huang, Shu-Jia Luo, Yan-Feng Sun, Ji-Hua Zhou, Jian-Xiang Yan, Shu-Jing He, Jian-Guo Wang, Jun He, Zhu-Mei PLoS One Research Article 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. Public Library of Science 2012-01-20 /pmc/articles/PMC3262820/ /pubmed/22276181 http://dx.doi.org/10.1371/journal.pone.0030349 Text en Liu et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Liu, Si-Yang Lin, Jian-Qing Wu, Hong-Long Wang, Cheng-Cheng Huang, Shu-Jia Luo, Yan-Feng Sun, Ji-Hua Zhou, Jian-Xiang Yan, Shu-Jing He, Jian-Guo Wang, Jun He, Zhu-Mei Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation |
title | Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation |
title_full | Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation |
title_fullStr | Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation |
title_full_unstemmed | Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation |
title_short | Bisulfite Sequencing Reveals That Aspergillus flavus Holds a Hollow in DNA Methylation |
title_sort | bisulfite sequencing reveals that aspergillus flavus holds a hollow in dna methylation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262820/ https://www.ncbi.nlm.nih.gov/pubmed/22276181 http://dx.doi.org/10.1371/journal.pone.0030349 |
work_keys_str_mv | AT liusiyang bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT linjianqing bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT wuhonglong bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT wangchengcheng bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT huangshujia bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT luoyanfeng bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT sunjihua bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT zhoujianxiang bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT yanshujing bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT hejianguo bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT wangjun bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation AT hezhumei bisulfitesequencingrevealsthataspergillusflavusholdsahollowindnamethylation |