Plant Molecular Biology

, Volume 81, Issue 1, pp 175–188

Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress


DOI: 10.1007/s11103-012-9990-2

Cite this article as:
Zong, W., Zhong, X., You, J. et al. Plant Mol Biol (2013) 81: 175. doi:10.1007/s11103-012-9990-2


Histone modifications affect gene expression level. Several studies have shown that they may play key roles in regulating gene expression in plants under abiotic stress, but genome-wide surveys of such stress-related modifications are very limited, especially for crops. By using ChIP-Seq and RNA-Seq, we investigated the genome-wide distribution pattern of histone H3 lysine4 tri-methylation (H3K4me3) and the pattern’s association with whole genome expression profiles of rice (Oryza sativa L.) under drought stress, one of the major and representative abiotic stresses. We detected 51.1 and 48 % of annotated genes with H3K4me3 modification in rice seedlings under normal growth (control) and drought stress conditions, respectively. By RNA-Seq, 76.7 and 79 % of annotated genes were detected with expression in rice seedlings under the control and drought stress conditions, respectively. Furthermore, 4,837 genes were differentially H3K4me3-modified (H3M), (3,927 genes with increased H3M; 910 genes with decreased H3M) and 5,866 genes were differentially expressed (2,145 up-regulated; 3,721 down-regulated) in drought stress. Differential H3K4me3 methylation only affects a small proportion of stress-responsive genes, and the H3K4me3 modification level was significantly and positively correlated with transcript level only for a subset of genes showing changes both in modification and expression with drought stress. Moreover, for the H3K4me3-regulated stress-related genes, the H3K4me3 modification level was mainly increased in genes with low expression and decreased in genes with high expression under drought stress. The comprehensive data of H3K4me3 and gene expression profiles in rice under drought stress provide a useful resource for future epigenomic regulation studies in plants under abiotic stresses.


OryzaH3K4me3 modificationDrought stressGene expression



Chromatin immunoprecipitation sequencing


Differentially expressed genes


Differentially H3K4me3-modified


False discovery rate


H3K4me3 modification levels


RNA sequencing


Reads per kb per million reads


Transcription start site

Supplementary material

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Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Wei Zong
    • 1
  • Xiaochao Zhong
    • 1
  • Jun You
    • 1
  • Lizhong Xiong
    • 1
  1. 1.National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanPeople’s Republic of China