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

Content Provider	Springer Nature Link
Author	Zong, Wei Zhong, Xiaochao You, Jun Xiong, Lizhong
Copyright Year	2012
Abstract	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.
Starting Page	175
Ending Page	188
Page Count	14
File Format	PDF
ISSN	01674412
Journal	Plant Molecular Biology
Volume Number	81
Issue Number	1-2
e-ISSN	15735028
Language	English
Publisher	Springer Netherlands
Publisher Date	2012-11-29
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Oryza H3K4me3 modification Drought stress Gene expression Plant Sciences Biochemistry Plant Pathology
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Medicine Agronomy and Crop Science

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