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Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine
Atrazine (ATR) is a pesticide widely used for controlling weeds for crop production. Crop contamination with ATR negatively affects crop growth and development. This study presents the first genome-wide single-base-resolution maps of DNA methylation in ATR-exposed rice. Widespread differences were i...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704053/ https://www.ncbi.nlm.nih.gov/pubmed/26739616 http://dx.doi.org/10.1038/srep18985 |
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author | Lu, Yi Chen Feng, Sheng Jun Zhang, Jing Jing Luo, Fang Zhang, Shuang Yang, Hong |
author_facet | Lu, Yi Chen Feng, Sheng Jun Zhang, Jing Jing Luo, Fang Zhang, Shuang Yang, Hong |
author_sort | Lu, Yi Chen |
collection | PubMed |
description | Atrazine (ATR) is a pesticide widely used for controlling weeds for crop production. Crop contamination with ATR negatively affects crop growth and development. This study presents the first genome-wide single-base-resolution maps of DNA methylation in ATR-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between the ATR-exposed and ATR-free (control) rice. Most of DNA methyltransferases, histone methyltransferases and DNA demethylase were differentially regulated by ATR. We found more genes hypermethylated than those hypomethylated in the regions of upstream, genebody and downstream under ATR exposure. A stringent group of 674 genes (p < 0.05, two-fold change) with a strong preference of differential expression in ATR-exposed rice was identified. Some of the genes were identified in a subset of loss of function mutants defective in DNA methylation/demethylation. Provision of 5-azacytidine (AZA, inhibitor of DNA methylation) promoted the rice growth and reduced ATR content. By UPLC/Q-TOF-MS/MS, 8 degraded products and 9 conjugates of ATR in AZA-treated rice were characterized. Two of them has been newly identified in this study. Our data show that ATR-induced changes in DNA methylation marks are possibly involved in an epigenetic mechanism associated with activation of specific genes responsible for ATR degradation and detoxification. |
format | Online Article Text |
id | pubmed-4704053 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-47040532016-01-19 Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine Lu, Yi Chen Feng, Sheng Jun Zhang, Jing Jing Luo, Fang Zhang, Shuang Yang, Hong Sci Rep Article Atrazine (ATR) is a pesticide widely used for controlling weeds for crop production. Crop contamination with ATR negatively affects crop growth and development. This study presents the first genome-wide single-base-resolution maps of DNA methylation in ATR-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between the ATR-exposed and ATR-free (control) rice. Most of DNA methyltransferases, histone methyltransferases and DNA demethylase were differentially regulated by ATR. We found more genes hypermethylated than those hypomethylated in the regions of upstream, genebody and downstream under ATR exposure. A stringent group of 674 genes (p < 0.05, two-fold change) with a strong preference of differential expression in ATR-exposed rice was identified. Some of the genes were identified in a subset of loss of function mutants defective in DNA methylation/demethylation. Provision of 5-azacytidine (AZA, inhibitor of DNA methylation) promoted the rice growth and reduced ATR content. By UPLC/Q-TOF-MS/MS, 8 degraded products and 9 conjugates of ATR in AZA-treated rice were characterized. Two of them has been newly identified in this study. Our data show that ATR-induced changes in DNA methylation marks are possibly involved in an epigenetic mechanism associated with activation of specific genes responsible for ATR degradation and detoxification. Nature Publishing Group 2016-01-07 /pmc/articles/PMC4704053/ /pubmed/26739616 http://dx.doi.org/10.1038/srep18985 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Lu, Yi Chen Feng, Sheng Jun Zhang, Jing Jing Luo, Fang Zhang, Shuang Yang, Hong Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine |
title | Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine |
title_full | Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine |
title_fullStr | Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine |
title_full_unstemmed | Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine |
title_short | Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine |
title_sort | genome-wide identification of dna methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704053/ https://www.ncbi.nlm.nih.gov/pubmed/26739616 http://dx.doi.org/10.1038/srep18985 |
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