Zhi Min Yang
Nanjing Agricultural University, China
Title: New insights into genome-wide change of DNA methylation and its association with gene expression in cadmium-exposed rice (Oryza sativa)
Biography
Biography: Zhi Min Yang
Abstract
Plant exposure to cadmium (Cd) affects transcriptional responses. Whether Cd-modified DNA methylation marks are associated with transcription and functional consequences in plants remains unknown. We present the genome-wide single-base-resolution maps of methylated cytosines in Cd-exposed rice, along with global transcriptional change in mRNA. Widespread differences were identified in the composition and patterning of CG and non-CG methylation marks between Cd-exposed and control rice genomes. There are 2393 non-redundant differentially-methylated regions (DMRs). RNA-sequencing revealed that most of DNA methyltransferases, histone methyltransferases and DNA demethylases differentially changed in transcription under Cd exposure. By profiling global DNA methylation and gene transcription, we found more genes hypermethylated than those hypomethylated in CG, CHH and CHG (where H is A, C or T) contexts in the regions of upstream, genebody and downstream under Cd stress. Seventy-nine genes (p < 0.05, two-fold change) with a strong preference of differential expression in Cd-exposed rice plants was identified. Many of them were involved in stress response, metal transport, and transcription factors. A subset of loss of function mutants defective in DNA methylation/demethylation and histone modification activities were used to identify transcript abundance of selected genes. In most cases, genes in the mutants were repressed by Cd treatment. Provision of azacitidine (a global DNA methylation inhibitor) attenuated root growth inhibition, but promoted biomass and Cd accumulation under Cd exposure. Finally, we identified 108 transposons and 254 retrotransposons that were modificed by methylation, where transcriptional expressions of 30 neighboring genes were changed under Cd exposure.