The spatial organization of chromatin, the methylome, and histone modifications represents epigenetic layers that greatly intersect each other, influencing genome regulation and allowing high flexibility in stress response. Although changes in specific histone modification marks could be extensively associated with transcriptional regulation of stress-responsive genes, a link between specific epigenetic signatures and plant stress tolerance has not yet been established. This chapter includes some examples of the associations found between fluctuations in these marks and regulation of plant stress-responsive genes. Chromatin immunoprecipitation (ChIP) has been widely used to uncover the landscape of histone modifications. However, ChIP involves multiple steps and requires optimizations targeting the tissue and the plant species. Here, we detail the ChIP procedure currently used in our laboratory, for leaf tissues of young rice seedlings, to decipher the dynamic feature of specific chemical modifications of histones that may influence the expression of stress-responsive genes. We show the success achieved after introducing specific optimizations and highlight the key critical steps and trouble shootings that may occur. A thorough understanding of stress-induced fluctuations of specific histone modifications may unveil new strategies to improve plant adaptation and performance in suboptimal conditions
