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| Status |
Public on Jun 19, 2019 |
| Title |
Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [RNA-Seq] |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.
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| Overall design |
mRNA profiles of two-week old leaf and root of rice were generated by deep sequencing, in duplicate, using Illumina Hiseq2500 platform
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| Contributor(s) |
Zheng D, Wang L, Pan X, Zhang w |
| Citation(s) |
31111914 |
| |
| Submission date |
Jan 25, 2018 |
| Last update date |
Jun 19, 2019 |
| Contact name |
Zheng dong yang |
| Organization name |
NJAU
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| Department |
college of agronomy
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| Lab |
wenlizhang
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| Street address |
weigang NO.1
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| City |
Nanjing |
| ZIP/Postal code |
210000 |
| Country |
China |
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| Platforms (1) |
| GPL19290 |
Illumina HiSeq 2500 (Oryza sativa) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE109618 |
Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice |
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| Relations |
| BioProject |
PRJNA431539 |
| SRA |
SRP131218 |
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