Ontology highlight
ABSTRACT:
PROVIDER: PRJNA822702 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18595284_1.fastq.gz | Fastqsanger.gz | |||
| SRR18595284_2.fastq.gz | Fastqsanger.gz | |||
| SRR18595285_1.fastq.gz | Fastqsanger.gz | |||
| SRR18595285_2.fastq.gz | Fastqsanger.gz | |||
| SRR18595286_1.fastq.gz | Fastqsanger.gz |
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Project description: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.
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Project description:Salt stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of salt stress RSA3 and used the Affymetrix whole-genome arrays to study the effect of rsa3-1 mutation on global gene expression under salt stress. A set of genes differentially expressed in rsa3-1 under salt stress are identified.
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Project description:Salinity is a pressing issue causing widespread crop loss, prompting plants to adapt through changes in gene expression. This study investigated the role of the non-tandem CCCH zinc finger protein gene AtC3H3 in Arabidopsis in response to salt stress. AtC3H3, a gene from the non-TZF gene family and known for its RNA-binding and ribonuclease activity, was found to be upregulated under osmotic stresses such as high salt and drought. When overexpressed in Arabidopsis, AtC3H3 led to increased tolerance to salt stress, not drought stress. qRT-PCR analysis showed that the expression of both well-known ABA-dependent salt stress-responsive genes, such as RAB18, RD29B, and RD22, and representative ABA-independent salt stress-responsive genes, such as DREB2A and DREB2B, was significantly higher in AtC3H3 OXs than WT under NaCl treatment, indicating its involvement in both ABA-dependent and ABA-independent signaling pathways. mRNA-Seq analysis using NaCl-treated WT and AtC3H3 OXs revealed no potential target mRNAs of the RNase function of AtC3H3, suggesting that the potential targets of AtC3H3 might be non-coding RNAs, not mRNAs. The study conclusively demonstrates that AtC3H3 plays a crucial role in salt stress tolerance by influencing the expression of salt stress-responsive genes. These findings have opened a new avenue for understanding plant stress mechanisms and suggest potential strategies for enhancing crop resilience to salinity.
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Project description: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.
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Project description:This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.
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