Genome-wide identification of SNAC1-targeted genes involved in drought response in rice
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ABSTRACT:
PROVIDER: PRJNA527848 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8746730_1.fastq.gz | Fastqsanger.gz | |||
| SRR8746730_2.fastq.gz | Fastqsanger.gz | |||
| SRR8746740_1.fastq.gz | Fastqsanger.gz | |||
| SRR8746740_2.fastq.gz | Fastqsanger.gz | |||
| SRR8746750_1.fastq.gz | Fastqsanger.gz |
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Project description:Drought stress can cause huge crop production losses. Drought resistance consists of complex traits, and is regulated by arrays of unclear networks at the molecular level. A stress-responsive NAC transcription factor gene SNAC1 has been reported for its function in the positive regulation of drought resistance in rice, and several downstream SNAC1 targets have been identified. However, a complete regulatory network mediated by SNAC1 in drought response remains unknown. In this study, we performed Chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq of SNAC1-overexpression transgenic rice (SNAC1-OE) lines and wild-type under normal and moderate drought stress conditions, to identify all SNAC1 target genes at a genome-wide scale by RNA-Seq analyses. We detected 980 differentially expressed genes (DEGs) in the SNAC1-OE lines compared to the wild-type control under drought stress conditions. By ChIP-Seq analyses, we identified 4,339 SNAC1-binding genes under drought stress conditions (SNAC1BGDs). By combining the DEGs and SNAC1BGDs, we identified 93 SNAC1-targeted genes involved in drought responses (SNAC1TGDs). Most SNAC1TGDs are involved in transcriptional regulation, response to water loss, and other processes related to stress responses. Moreover, the major motifs in the SNAC1BGDs promoters include a NAC recognition sequence (NACRS) and an ABA responsive element (ABRE). SNAC1-OE lines are more sensitive to ABA than wild-type. SNAC1 can bind to the OsbZIP23 promoter, an important ABA signaling regulator, and positively regulate the expression of several ABA signaling genes.
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Project description:The severity of impact of drought on crops is contingent on the developmental stage of the plant, with the most sensitive stage being the reproductive stage. Hence, gene expression profiling has been used to understanding drought response and resistance mechanism in rice. Here we present drought transcriptomes of rice in three developmental stages and gain insights into the processes and regulatory mechanisms involved in common and stage specific drought responses.
2016-07-20 | GSE81253 | GEO
Project description:Drought stress can cause huge crop production losses. Drought resistance consists of complex traits, and is regulated by arrays of unclear networks at the molecular level. A stress-responsive NAC transcription factor gene SNAC1 has been reported for its function in the positive regulation of drought resistance in rice, and several downstream SNAC1 targets have been identified. However, a complete regulatory network mediated by SNAC1 in drought response remains unknown. In this study, we performed Chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq of SNAC1-overexpression transgenic rice (SNAC1-OE) lines and wild-type under normal and moderate drought stress conditions, to identify all SNAC1 target genes at a genome-wide scale by RNA-Seq analyses. We detected 980 differentially expressed genes (DEGs) in the SNAC1-OE lines compared to the wild-type control under drought stress conditions. By ChIP-Seq analyses, we identified 4,339 SNAC1-binding genes under drought stress conditions (SNAC1BGDs). By combining the DEGs and SNAC1BGDs, we identified 93 SNAC1-targeted genes involved in drought responses (SNAC1TGDs). Most SNAC1TGDs are involved in transcriptional regulation, response to water loss, and other processes related to stress responses. Moreover, the major motifs in the SNAC1BGDs promoters include a NAC recognition sequence (NACRS) and an ABA responsive element (ABRE). SNAC1-OE lines are more sensitive to ABA than wild-type. SNAC1 can bind to the OsbZIP23 promoter, an important ABA signaling regulator, and positively regulate the expression of several ABA signaling genes.
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Project description:Three rice major tissues, namely flag leaf, shoot and panicle, were involved in this study. Each tissue had two kinds stress treatment, drought and high salinity, in 3 different time courses. For drought treated samples, an additional water recovery was applied. Each experiment had three replicates. Keywords: Comparison of gene expression in three tissues with stress treatment and without treatment To globally elucidate potential genes involved in drought and high-salinity stresses responses in rice, an oligomer microarray covering 37,132 genes including cDNA or EST supported and putative genes was applied to study the expression profiling of shoot, flag leaf, and panicle under drought or high-salinity treatment. Three rice major tissues, namely flag leaf, shoot and panicle, were involved in this study. Each tissue had two kinds stress treatment, drought and high salinity, in 3 different time courses. For drought treated samples, an additional water recovery was applied. Each experiment had three replicates.
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Project description:Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling. The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H2O2 (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403. We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.
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Project description:Transcriptional profiling of rice shootunder drought condition. Goal was to determine the effects of drought on changes in gene expression.
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Project description:The severity of impact of drought on crops is contingent on the developmental stage of the plant, with the most sensitive stage being the reproductive stage. Hence, gene expression profiling has been used to understanding drought response and resistance mechanism in rice. Here we present drought transcriptomes of rice in three developmental stages and gain insights into the processes and regulatory mechanisms involved in common and stage specific drought responses. Total RNA was isolated from the rice seedlings, vegetative (V4) and reproductive (R4) tissues of both control and stress treated plants for hybridization on Affymetrix microarrays. Two independent replicates for seedling and reproductive stages, and three replicates for vegetative stages were generated, for both control and stress samples. For drought treatments, plants were gradually subjected to field drought conditions in order to reach 50% field capacity (FC) by regulating water supply, whereas control plants were maintained at 100% FC.
2016-07-20 | E-GEOD-81253 | biostudies-arrayexpress
Project description:Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements.
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Project description:Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. The direct target genes were related to transmembrane/transporter activity, vesicle, plant hormone, carbohydrate metabolism, and transcription factors. The direct targets of each OsNAC are in a range of 4.0 to 8.7% of the genes up-regulated in RNA-Seq data sets. Thus, each OsNAC up-regulates of corresponding direct target genes that alters root system architectures of RCc3:OsNACs for drought tolerance. Our results provide valuable resources for functional dissection of the molecular mechanisms for plant drought tolerance.
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Project description:Three rice major tissues, namely flag leaf, shoot and panicle, were involved in this study. Each tissue had two kinds stress treatment, drought and high salinity, in 3 different time courses. For drought treated samples, an additional water recovery was applied. Each experiment had three replicates. Keywords: Comparison of gene expression in three tissues with stress treatment and without treatment
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