Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (ChIP-seq dataset). Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (ChIP-seq dataset)

Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. 8798 soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots. Overall design: Examination of histone modifications in control and salt-treated soybean roots.

大豆是一类重要的经济作物，因其富含蛋白质与油脂，可广泛应用于人类膳食、动物饲料及生物柴油生产。盐胁迫会通过影响基因表达（部分依赖染色质状态的表观遗传修饰）损害植物生长发育，进而显著抑制大豆生产力。然而，目前对于大豆根系胁迫响应的表观遗传调控机制仍知之甚少。本研究利用RNA测序（RNA-seq）与染色质免疫共沉淀测序（ChIP-seq）技术，解析了盐胁迫下大豆根系全基因组转录组与组蛋白甲基化模式的动态变化。研究共鉴定到8798个在盐胁迫处理下表达发生显著改变的大豆基因。针对表观遗传抑制性修饰标记——组蛋白H3赖氨酸27三甲基化（H3K27me3）的全基因组ChIP-seq分析，揭示了盐胁迫响应过程中H3K27me3沉积的动态变化。出乎意料的是，盐胁迫下大部分基因的失活，与对照组中原本不存在H3K27me3的启动子或编码区各区域内H3K27me3的从头建立存在显著相关性。此外，本研究还鉴定出若干可能参与盐胁迫下组蛋白从头甲基化与基因沉默过程的大豆组蛋白修饰调控因子。综上，为响应盐胁迫，大豆靶位点的染色质动态调控（即活性与非活性状态间的切换）会发生改变。本研究结果表明，组蛋白甲基化修饰与大豆根系中盐诱导基因的激活或失活密切相关。整体实验设计：对对照组与盐处理组大豆根系的组蛋白修饰进行检测分析。