||Roles of histone modifications in DNA damage response have been extensively studied in non-plant systems, including mammalian and yeast systems. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or a combined chromatin status, participate in regulating differentially expressed genes in plant DNA damage response. In this study, through applying RNA-seq and ChIP-seq assay, we found that differential expressed genes (DEGs) post ionizing radiation (IR) might be involved in different pathways responsible for DNA damage response. In addition, chromatin structures associated with promoters, exons and intergenic regions were significantly affected by IR. Especially, changes in H3K4/36me3 and H3K27ac related nucleosome positioning occurred in DEGs with FPKM between 10 and 50. Most importantly, either an individual mark or a certain chromatin status was found to be highly correlated with the expression of up-regulated genes, by contrast, only the chromatin status, instead of any individual mark tested, were related to the expression of down-regulated genes. Our findings demonstrate that IR related differentially expressed genes are modulated by distinct epigenetic mechanisms. Either chromatin status or distinct histone dynamics, including nucleosome positioning, may act sequentially or in combination in regulating up-regulated genes, but a complex chromatin structure is mainly responsible for expression of down-regulated genes. Thus, this study provides new insights in how up and down regulated genes are epigenetically regulated at chromatin levels, thereby helping us to understand distinct epigenetic mechanisms functioning in plant DNA damage response.