Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray radiation in rice

BMC Genomics

Research Article

Kai Wang¹  Hengxiu Yu²  Xueming Yang³  Xiucai Pan⁴  Lei Wang⁴  Jin Xiao⁴  Yuan Fang⁴  Lifen Chen⁴  Xiu-e Wang⁴  Dongyang Zheng⁴  Wenli Zhang⁵  Zhukuan Cheng⁶ 

[1] Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, 35002, Fuzhou, Fujian, China;Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, China;Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, China;State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, 210095, Nanjing, Jiangsu, China;State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, 210095, Nanjing, Jiangsu, China;JiangSu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agriculture University, 210095, Nanjing, Jiangsu, China;State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China;

关键词: Gene expression;    Histone modifications;    Chromatin states;    Ionizing radiation;    Oryza sativa;   

DOI  :  10.1186/s12864-017-4172-x

 received in 2017-04-18, accepted in 2017-10-05,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response.ResultsIn this study, we used RNA-seq and ChIP-seq to show that differentially expressed genes (DEGs), in response to ionizing radiation (IR), might be involved in different pathways responsible for the DNA damage response. Moreover, chromatin structures associated with promoters, exons and intergenic regions are significantly affected by IR. Most importantly, either an individual mark or a certain chromatin state was found to be highly correlated with the expression of up-regulated genes. In contrast, only the chromatin states, as opposed to any individual marks tested, are related to the expression of the down-regulated genes.ConclusionsOur findings demonstrate that IR-related DEGs are modulated by distinct epigenetic mechanisms. Either chromatin states or distinct histone dynamics may act sequentially or in combination in regulating up-regulated genes, but the complex chromatin structure is mainly responsible for the expression of down-regulated genes. Thus, this study provides new insights into how up- and down-regulated genes are epigenetically regulated at the chromatin levels, thereby helping us to understand distinct epigenetic mechanisms that function in the plant DNA damage response.

【 授权许可】

CC BY   
© The Author(s). 2017