Abstract
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.
Highlights
Recent genome-wide profiling of transcriptome has resulted in identification of many functional genes involved in pesticide accumulation, translocation, and degradation in plants[11]
There are reports indicating that ATR contamination of rice affects many aspects of physiological metabolisms[7,24] and cereal production as well[25], the epigenetic mechanism for DNA methylation regulated by organic toxicants in plants has not been described
The DNA methylation marks of the locus were well confirmed by the specific PCR (Supplementary Fig. S2)
Summary
Recent genome-wide profiling of transcriptome has resulted in identification of many functional genes involved in pesticide accumulation, translocation, and degradation in plants[11]. Using high-throughput RNA sequencing, we have identified hundreds of functional genes related to degradation and detoxification of ATR in rice[12] It is rarely known about the regulatory mechanism of gene expressions in response to ATR. There are reports indicating that ATR contamination of rice affects many aspects of physiological metabolisms[7,24] and cereal production as well[25], the epigenetic mechanism for DNA methylation regulated by organic toxicants in plants has not been described. The transcriptome of ATR-exposed rice was profiled to figure out the link between DNA methylation and gene expression. To our knowledge, this is the first report on global DNA methylation modified by organic toxicants in plants
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