Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress.
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.
- SourceAvailable from: Stefan A Rensing[Show abstract] [Hide abstract]
ABSTRACT: The moss P. patens is an important model organism for evo-devo studies. Here, we determined the genome-wide chromatin landscape of five important histone three (H3) modifications (H3K4me3, H3K27me3, H3K27Ac, H3K9Ac and H3K9me2) and describe the changes to these histone marks in two contrasted situations, developmental transition and abiotic (drought) stress. Integrative analysis of these histone H3 modifications revealed their preferential association into fifteen chromatin states (CS) in genic regions of the P. patens genome. Synergistic relationships influencing expression levels were revealed for the three activating marks H3K4me3, H3K27Ac and H3K9Ac, while an antagonistic relationship was found between CS containing the H3K27me3 and H3K27Ac marks, suggesting that H3K27 is a key indexing residue regarding transcriptional output. Concerning the alteration of histone marks in response to developmental transition (juvenile to adult) and drought stress, the three activating marks H3K4me3, H3K27Ac and H3K9Ac show significant changes in both situations. However, changes to H3K27me3 are central only for genes differentially expressed during development. Interestingly, genes induced during drought stress show significant histone mark toggling during developmental transition. This suggests that drought induced adult (gametophore expressed) genes are primed to respond to this stress during the juvenile to adult transition.This article is protected by copyright. All rights reserved.The Plant Journal 04/2014; · 6.58 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: Histone H3 lysine 4 trimethylation (H3K4me3) has been shown to be involved in stress-responsive gene expression and gene priming in plants. However, the role of H3K4me3 resetting in the processes is not clear. In this work we studied the expression and function of Arabidopsis H3K4 demethylase gene JMJ15. We show that the expression of JMJ15 was relatively low and was limited to a number of tissues during vegetative growth but was higher in young floral organs. Over-expression of the gene in gain-of-function mutants reduced the plant height with accumulation of lignin in stems, while the loss-of-function mutation did not produce any visible phenotype. The gain-of-function mutants showed enhanced salt tolerance, whereas the loss-of-function mutant was more sensitive to salt compared to the wild type. Transcriptomic analysis revealed that over-expression of JMJ15 down-regulated many genes which are preferentially marked by H3K4me3 and H3K4me2. Many of the down-regulated genes encode transcription regulators involved in stress responses. The data suggest that increased JMJ15 levels may regulate the gene expression program that enhances stress tolerance.Frontiers in Plant Science 01/2014; 5:290. · 3.60 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: Several eukaryotic Heme-associated proteins (HAPs) have been reported to bind specifically to DNA fragments containing CCAAT-box; however, the physiological functions and direct targets of these HAP proteins in plants remain unclear.In this study, we showed that AtHAP5A as a transcription factor interacted with CCAAT motif in vivo, and AtXTH21, one direct target of AtHAP5A, was involved in freezing stress resistance. The AtHAP5A overexpressing plants were more tolerant, whereas the loss-of-function mutant of AtHAP5A was more sensitive to freezing stress than wild-type plants. Chromatin immunoprecipitation (ChIP) assay demonstrated that AtHAP5A could bind to five fragments that contained CCAAT motifs in the AtXTH21 promoter.Similarly, the AtXTH21 overexpressing plants exhibited improved freezing resistance, while xth21 knockdown mutants displayed decreased freezing resistance. Notably, the modulated freezing resistance of AtHAP5A overexpressing plants and knockout mutant could be reversed by the xth21 mutant and AtXTH21 overexpressing plants, respectively, indicating that AtHAP5A might act upstream of AtXTH21 in freezing stress. Additionally, modulation of AtHAP5A and AtXTH21 expression had the same effects on abscisic acid (ABA) sensitivity and reactive oxygen species (ROS) metabolism.Taken together, these results demonstrated that AtHAP5A modulates freezing stress resistance in Arabidopsis through binding to the CCAAT motif of AtXTH21.New Phytologist 04/2014; · 6.74 Impact Factor