Overexpression of OsTZF8, a CCCH-Tandem Zinc finger, increases drought tolerance in rice by regulating stress related genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE135940 | GEO | 2020/11/05
REPOSITORIES: GEO
Similar Datasets
Project description:Purpose: The goals of this study are to find putative target transcript regulated by OsGRP3 by comparing rice transcriptome between wild-type and OsGRP3 overexpressing (or Knock-down) plants. Methods: Total RNAs were extracted from the leaf tissues of OsGRP3OE, OsGRP3KD, and non-transgenic (NT) plants using the RNeasy plant mini kit (Qiagen, USA) according to the manufacturer’s instruction. cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (v2) (Macrogen, Korea). Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). After mapping reads to a reference genome, differentially expressed genes (DEGs) were selected using a cut-off change of at least 2-fold change and Student’s t-test (P < 0.05). The selected DEGs were grouped by hierarchical clustering analysis (Complete Linkage). Results: A cutoff change of at least two-fold was used to isolate up- and down-regulated genes by OsGRP3. The analysis revealed that OsGRP3OX plants contained 195 up-regulated and 190 down-regulated genes compared with WT plants. Among the 195 up-regulated transcripts, 45 genes belonged to the gene ontology (GO) category of response to abiotic and/or biotic stress and defense. The majority of these genes were categorized into defense- and stress-related genes and interestingly many PR genes were up-regulated. This high frequency of defense- and stress-related genes affected by OsGRP3 overexpression suggests that OsGRP3 is closely associated with biotic and abiotic stress responses. We then isolated genes showing opposite expression patterns between OsGRP3OX and OsGRP3KD plants as candidate genes directly regulated by OsGRP3. Through these criteria, we finally isolated 15 genes as target candidates in the OsGRP3-mediated drought tolerance pathway. Interestingly, six genes showing a positive correlation with the expression level of OsGRP3 were associated with plant stress responses. The list included four PR genes, LATE EMBRYOGENESIS ABUNDANT PROTEIN 17 (LEA17), and EXOCYST SUBUNIT EXO70 FAMILY PROTEIN FX1 (FX1). On the other hand, eight genes showing negative correlation with OsGRP3 expression level included PEROXIDASE 1 (POX11), METALLOTHIONEIN 1d (MT1d), CAROTENOID 9, 10-CLEAVAGE DIOXYGENASE 1 (CCD1), 4,5-DOPA DIOXYGENASE EXTRADIOL-LIKE PROTEIN (DOPA), LEUCINE-RICH REPEAT DOMAIN CONTAINING PROTEIN (LRR), LIPOXYGENASE (LOX) and S-ADENOSYLMETHOININE SYNTHETASE 1 (SAM1) that were mainly associated with plant metabolic regulations. Conclusions: OsGRP3 positively affects the expression of stress-responsive genes and negatively affected the expression of metabolic pathway genes.
2021-03-24 | GSE151351 | GEO
Project description:Purpose: The goals of this study are screening the putative target genes regulated by OsNF-YA5 using DEX(dexamethason) inducible system. Methods: 10-day-old GOS2::OsNF-YA5-GR plants grown on MS solid media were treated with 50 μM dexamethasone (DEX) solution containing 0.02% (w/v) Silwet L-77. For mock treatments, 0.02% Silwet L-77 was sprayed into rice plants. To minimize the effect by the treatment, plants were pre-treated with 0.02% Silwet L-77 3 hours before DEX treatment). Total RNAs were extracted using the RNeasy plant mini kit (Qiagen, USA) according to the manufacturer’s instruction. cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (v2) (Macrogen, Korea). Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). After mapping reads to a reference genome, differentially expressed genes (DEGs) were selected using a cut-off change of at least 2-fold change (DEX/mock) and Student’s t-test (P < 0.1). The selected DEGs were grouped by hierarchical clustering analysis (Complete Linkage). Results: RNA sequencing analysis revealed that 81 (3 hr DEX treatment) and 88 (9 hr DEX treatment) genes were up-regulated. In comparison, 61 (3 hr DEX treatment) and 45 (9 hr DEX treatment) genes were down-regulated in GOS2:OsNF-YA5-GR transgenic plants by DEX treatment compared to mock treatment. Among 161 up-regulated genes, 71 genes (44%) were also up-regulated in N starvation conditions. GO term analysis of up-regulated genes revealed that 59-76% of genes were involved in the metabolic process, and 10%-12% were transporter (Extended Data Fig. 4c). These results suggested that OsNF-YA5 regulated the genes involved in the metabolic process. Conclusions: OsNF-YA5 positively regulated the genes involved in the nitrogen metabolic process including amino acid and nitrate/peptide transporters.
2024-01-03 | GSE178682 | GEO
Project description:To identify the differetially expressed genes under nitrate stress, RNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were mapped to rice (IRGSP-1) genome.
2022-04-01 | GSE166667 | GEO
Project description:The general aim was to better understand the role of StTGA2.1 in plant immunity by transcriptional profiling of plants overexpressing the salicylic acid pathwas related TGA transcription factor StTGA2.1 after infection with potato virus Y (PVY). Potato non-transgenic cultivar Rywal (NT), Rywal-NahG (NahG), a transgenic line unable to accumulate SA due to salicylate hydroxylase expression, and a transgenic Rywal-NahG line inducibly overexpressing StTGA2.1 (TGA2.1-NahG) using the glucocorticoid-system, in which target gene expression can be controlled by external application of dexamethasone (DEX), were used. The leaves of three plants per genotype were infected with either PVY or mock-inoculum and subsequently treated with DEX. Additionally, three TGA2.1-NahG PVY-infected or mock-inoculated plants were not treated with DEX as control. After four days, PVY infection symtoms appeared as small regions of necrotic tissue called lesions. Tissue sections, containing lesions and their immediate surrounding area, were sampled, allowing us to focus on PVY-affected cells. Total RNA was isolated, DNase treated and sent for library prep and high-throughput sequencing.
2022-12-14 | GSE196078 | GEO
Project description:To understand downstream genes affected by overexpression of OsbHLH148, the Rice 3’-Tiling Microarray analysis (GreenGene Biotech, Yongin, Korea) was carried out to profile gene expression of OsCc1:OsbHLH148 transgenic plants in comparison with wild-type plants under normal growth conditions. RNA samples from these plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from two biological repeats with independent transgenic lines. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in OsCc1:OsbHLH148 transgenic and wild-type rice plants. Cy3-labeled target cDNA fragments were synthesized from two-week old seedlings using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment two times with independent transgenic lines, T-2 and T-9, and analyzed each data set statistically using one-way ANOVA.
2011-01-01 | E-GEOD-22676 | biostudies-arrayexpress
Project description:The goal of this study was to compare the transcriptional profile (RNA-seq) of seven-week-old auxin resistant pIAA26::IAA26-P108H-GFP transgenic plants to non-transformed control plants to identify candidate genes and pathways regulated by IAA26. RNA-seq analysis was performed with A. thaliana ecotype Shahdara seven-week-old leaves from auxin resistant pIAA26::IAA26-P108H-GFP transgenic plants or non-transformed controls. Four fully expanded leaves were collected from each test plant and total RNA from four to six individual test plants was pooled for each of the three biological replicates. Sequencing was carried out on an Illumina HiSeq 1500 platform using rapid run mode with 50 nt single end reads.
2016-04-14 | E-GEOD-75983 | biostudies-arrayexpress
Project description:For identification of genes up-regulated in RCc3:OsNAC5, GOS2:OsNAC5 plants, total RNA (100 μg) was prepared from root tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in RCc3:OsNAC5, GOS2:OsNAC5 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
2012-03-01 | E-GEOD-31856 | biostudies-arrayexpress
Project description:For identification of genes up-regulated in RCc3:OsNAC1, GOS2:OsNAC1 plants, total RNA (100 μg) was prepared from root tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in RCc3:OsNAC1, GOS2:OsNAC1 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
2012-03-01 | E-GEOD-31855 | biostudies-arrayexpress
Project description:For identification of genes up-regulated in RCc3:OsNAC6, GOS2:OsNAC6 plants, total RNA (100 μg) was prepared from root tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in RCc3:OsNAC6, GOS2:OsNAC6 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
2012-03-01 | E-GEOD-31857 | biostudies-arrayexpress
Project description:For identification of genes up-regulated in OsCc1:AP37, OsCc1:AP59 plants, total RNA (100 ?g) was prepared from leaf tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in OsCc1:AP37, OsCc1:AP59 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
2011-09-05 | E-GEOD-31859 | biostudies-arrayexpress