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Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [ChIP-Seq]

ABSTRACT: Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [ChIP-Seq]

PROVIDER: PRJNA431540 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6510890_1.fastq.gz	Fastqsanger.gz
	SRR6510890_2.fastq.gz	Fastqsanger.gz
	SRR6510900_1.fastq.gz	Fastqsanger.gz
	SRR6510900_2.fastq.gz	Fastqsanger.gz
	SRR6510891_1.fastq.gz	Fastqsanger.gz

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Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [ChIP-Seq]

Project description: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.

2019-06-19 | GSE109616 | GEO

Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [RNA-Seq]

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Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice

Project description:Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice

| PRJNA431536 | ENA

Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [RNA-Seq]

Project description:Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [RNA-Seq]

| PRJNA431539 | ENA

Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-06-19 | GSE109618 | GEO

Ethylene Responsive Factor 34 (ERF34) negatively mediates salt stress-induced leaf senescence by regulating the expression of salt stress-responsive genes in Arabidopsis

Project description:Leaf senescence, the last step of leaf development which is important for plant’s fitness, proceeds with age but is modulated by various environmental stresses and hormones. Salt stress is one of the well-known environmental stresses that accelerate leaf senescence. However, the molecular mechanisms how the signal of salt stress is integrated into leaf senescence programs are still elusive. In this study, we characterized the function of an Arabidopsis APETALA 2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factor, ERF34, in salt stress-induced leaf senescence. ERF34 was differentially expressed under leaf senescence-inducing conditions including age, dark, and high salt. ERF34 negatively regulated salt stress-induced leaf senescence as well as promoted salt stress tolerance at diverse developmental stages. Analysis of genome-wide targets of ERF34 revealed that the overexpression of ERF34 could alter salt-responsive gene expression. Moreover, ERF34 directly bound to the promoters of EARLY RESPONSIVE TO DEHYDRATION 10 and RESPONSE TO DESICCATION 29A and activated their expression. Our findings imply that ERF34 is a key regulator in the convergence of salt stress response with the regulatory programs of leaf senescence and is a potential candidate for crop improvement, particularly by enhancing salt stress tolerance.

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Project description:Sodium-lithium countertransport activity (SLC) is an intermediate phenotype for salt sensitive hypertension; elevated SLC corresponds to increased risk of hypertension. Genetic epidemiology studies indicate that SLC is heritable in humans and nonhuman primates; however, little is known about genetic determinants explaining variation in SLC. In this study we identified dietary salt-responsive gene networks in baboon kidneys and salt-responsive networks that differ between baboons with normal and high blood pressure phenotypes.

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Project description:In order to screening the responsive miRNAs and target genes of willow under salt stress, the 30-day-old plants were exposed to the salt solution (100 mmol L-1 NaCl) for 0 h and 2 d. then RNA isolated from root and stem tissues for the same time point were mixed respectively in equal amounts for small RNA (sRNA) sequencing. sRNAs with 16–30 nt were separated from 1 µg total RNA by size fractionation. Subsequently, the selected sRNA fragments were ligated with specialized adaptors to the 5’ and 3’ ends (Illumina) using T4 RNA ligase. Then, the ligated RNAs were reverse transcribed and amplified for sequencing using Illumina Hiseq2500 (LC Sciences, Hangzhou, China). Salt stress-responsive miRNAs were identified by comparing the expression levels of miRNAs between the two libraries. Equal amounts of all 2 RNA samples were mixed together to construct one degradome library, and then sent to Hangzhou LC-Bio Co., Ltd (Hangzhou, China) for sequencing by Illumina Genome Analyzer GA-I (Illumina, San Diego, CA, USA).

2018-07-06 | GSE116625 | GEO

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