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ABSTRACT: Transcriptome Sequencing of amiR-BAK1 BKK1 SERK5 transgenic plants

PROVIDER: PRJNA1265463 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33638103_1.fastq.gz	Fastqsanger.gz
	SRR33638103_2.fastq.gz	Fastqsanger.gz
	SRR33638104_1.fastq.gz	Fastqsanger.gz
	SRR33638104_2.fastq.gz	Fastqsanger.gz
	SRR33638105_1.fastq.gz	Fastqsanger.gz

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Heterotrimeric G-protein interactions are conserved despite regulatory element loss in some plants

Project description:Purpose: To study the shared transcriptional network between suppression transgenic plants of BdG and overexpresssion plants of SiRGS in B. distachyon. Method: Total RNA was isolated from 2 independent transgenic lines of amiR-BdG and Bd-SiRGS-OE. RNA-seq library preparation, sequencing and initial quality control analysis were performed by Novogene Inc. The sequences were analyzed for quality using FastQC. Transcripts per million (TPM) abundance was estimated by pseudo-aligning the reads with that of the k-mer index available from the reference genome of B. distachyon from Phytozome using Kallisto. Differentially expressed genes were sorted using Sleuth program with likelihod ration cutoff of false discovery rate (FDR) < 0.05. The log2 fold change was calculated from the TPM values derived for the wild-type and transgenic plants. Result: The transcriptome data showed more that 60% of overlap between amiR-BdG and Bd-SiRGS-OE. Among common genes more than 90% showed similar expression pattern when screened for several developmental and hormonal signaling pathways.

2020-12-15 | GSE153188 | GEO

Invasion by diverse fungal pathogens in Arabidopsis thaliana commonly activates both tryptophan-dependent and independent defense pathways exhibiting distinct sensitivity to the bak1-5 mutation

Project description:Transcriptome analysis to identify genes up- and down-regulated genes in pen2 bak1-5 plants compared with pen2 plants in the case of Alternaria brassicicola (Ab) inoculation .

2020-01-31 | GSE124921 | GEO

Genome wide analysis of the chromatin state and gene expression in Wild-type, tor-es mutant, and fie mutants

Project description:Using Western blot, we found the level of H3K27me3, but not H3K4me3, H3K9me2 and H3K36me3, was specifically reduced in the tor-es mutant. To gain a genome-wide view of the effects of TOR activity on H3K27me3 distribution, we performed quantitative chromatin immunoprecipitation with an exogenous reference genome (ChIP-Rx) followed by deep-sequencing. We find a global reduction of H3K27me3 occupancy in tor-es, whereas the H3K9me2 level was largely unaffected. These results suggest that TOR may be a specific and direct regulator of global deposition of H3K27me3. To investigate the function of TOR phosphorylation of FIE, we complemented the heterozygous fie/+ plants with GFP-FIE or the phosphorylation site mutant (SSTS/AAAA) under the control of the FIE promoter. To provide a parallel comparison with SSTS/AAAA/fie, we generated estradiol-inducible fie-amiR-es transgenic lines, that eliminated FIE protein. Quantitative ChIP-seq analyses revealed greatly reduced H3K27me3 levels across the genome in SSTS/AAAA and fie-amiR-es mutants. And transcriptome profiling by RNA-Seq was conducted to globally identify thousands of genes coordinately dysregulated in the shoots of SSTS/AAAA and fie-amiR-es plants. Furthermore, gene Ontology analysis of 986 TOR-FIE-PRC2 target genes revealed significant enrichment for transcription factors/regulators controlling a broad spectrum of developmental programs.

2022-06-20 | GSE161807 | GEO

Control of lateral root formation by rapamycin-induced dimerization of engineered RGI/BAK1 and by BIR3 chimera

Project description:Leucine-rich repeat receptor kinases (LRR-RKs) play a pivotal role in diverse aspects of growth, development, and immunity in plants by sensing extracellular signals. Typically, LRR-RKs are activated through the ligand-induced interaction with a SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) coreceptor, triggering downstream signaling. ROOT MERISTEM GROWTH FACTOR1 (RGF1) INSENSITIVEs (RGIs) LRR-RLK receptors promote primary root meristem activity while inhibiting lateral root (LR) development in response to RGF peptide. In this study, we employed rapamycin-induced dimerization (RiD) and BAK1-INTERACTING RECEPTOR-LIKE KINASE3 (BIR3) chimera approaches to explore the gain-of-function of RGI1, RGI4, and RGI5. Rapamycin induced the association of cytosolic kinase domains (CKDs) of RGI1 and the BAK1 coreceptor, activating both mitogen-activated protein kinase 3 (MPK3) and MPK6. Rapamycin significantly inhibited LR formation in RiD-RGI1/RGI4/RGI5-BAK1 plants. Using transgenic Arabidopsis expressing RGI1CKD fused to the BIR3-LRR chimera under estradiol control, we observed a substantial reduction in LR density upon β-estradiol treatment. Additionally, we identified a decrease in root gravitropism in BIR3 chimera plants. In contrast, RiD-RGI/BAK1 plants did not exhibit defects in root gravitropism, implying the importance of combinatorial interactions between RGIs and SERK coreceptors in the inhibition of root gravitropism. Constitutive activation of RGIs with BAK1 in RiD-RGI/BAK1 plants by rapamycin treatment resulted in the inhibition of primary root growth, resembling the inhibitory effects observed with high concentrations of phytohormones on primary root elongation. Our findings highlight that the interactions between CKDs of RGIs and BAK1, constitutively induced by rapamycin or BIR3 chimera, efficiently control LR development.

2023-12-21 | GSE138627 | GEO

Identification of ORB1 target genes using inducible overexpression system

Project description:The aim was to identify genes associated to the down-regulation TARGET OF RAPAMYCIN (TOR) pathway in Arabidopsis. For this purpose, three independent amiR-tor lines (amiR-tor9, amiR-tor17 and amiR-tor 20) and EV lines 3 and 6 days after EST- or non-induction were used for expression profile analysis using Affymetrix microarray. Two weeks-old transgenic seedlings were transferred to MS plate with 20ÂµM estradiol to induce the overexpression of amiR-tor (consequently, repression of AtTOR levels) under the control of an estradiol-(EST) inducible promoter. Identically treated wild-type Col-0 and pER8 empty-vector (EV) transformed seedlings were served as controls. Seedlings were harvested after 3 and 6 (amiR-tor lines) days. genetic modification

2013-01-31 | E-GEOD-38878 | biostudies-arrayexpress

Identification of ORB1 target genes using inducible overexpression system

Project description:The aim was to identify genes associated to the down-regulation TARGET OF RAPAMYCIN (TOR) pathway in Arabidopsis. For this purpose, three independent amiR-tor lines (amiR-tor9, amiR-tor17 and amiR-tor 20) and EV lines 3 and 6 days after EST- or non-induction were used for expression profile analysis using Affymetrix microarray. Two weeks-old transgenic seedlings were transferred to MS plate with 20µM estradiol to induce the overexpression of amiR-tor (consequently, repression of AtTOR levels) under the control of an estradiol-(EST) inducible promoter. Identically treated wild-type Col-0 and pER8 empty-vector (EV) transformed seedlings were served as controls. Seedlings were harvested after 3 and 6 (amiR-tor lines) days.

2013-01-31 | GSE38878 | GEO

Molecular basis of GA-independent DELLA regulation by the VIH-type inositol pyrophosphate synthase in a non-vascular land plant

Project description:To study the functional relationship between MpVIH and MpDELLA at molecular level, the system-wide transcriptome profile of the following genotype were analysed: WT, CRISPR/Cas9 knockout lines of MpVIH (Mpvih) and independent Mpvih transgenic lines with reduced MpDELLA transcripts using an artificial microRNA (Mpvih::amiR-MpDELLA) technology.

2025-05-21 | GSE269387 | GEO

Microarray analysis of Psm-induced transcriptome changes in the systemic leaves of Arabidopsis plants

Project description:The goal of the microarray was to compare the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326 (Psm)-induced transcriptome changes in the systemic leaves of the wild-type Col-0, lecrk-VI.2-2, and bak1-5 plants. Results showed that local Psm inoculation induced dramatic transcriptional changes in Col-0, with 564 and 151 genes up- and down-regulated at least twofold with a low q value (≤ 0.05), respectively. However, only 55 and 26 genes in lecrk-VI.2-2 and 221 and 121 genes in bak1-5 were up- and down-regulated, respectively. The majority of the genes that were induced or suppressed twofold or more with a low q value (≤ 0.05) in Col-0 were induced or suppressed to a smaller extent in bak1-5 and the smallest extent in lecrk-VI.2-2. These results indicate that both lecrk-VI.2-2 and bak1-5 suppressed Psm-induced systemic signaling with the lecrk-VI.2-2 mutation having a stronger effect than bak1-5.

2019-10-29 | GSE121886 | GEO

bak1 bkk1 flg22 - Flagellin response in mpk mutants

Project description:au-09-01_mpk_flagellin_edu - bak1 bkk1 flg22 - Investigate flagellin mpk dependent genes. - 2 weeks Bak1bkk1 plants treated with flg22 1h 1 microM

2012-01-01 | GSE23184 | GEO

bak1 bkk1 flg22 - Flagellin response in mpk mutants

Project description:au-09-01_mpk_flagellin_edu - bak1 bkk1 flg22 - Investigate flagellin mpk dependent genes. - 2 weeks Bak1bkk1 plants treated with flg22 1h 1 microM 2 dye-swap - CATMA arrays

2012-01-01 | E-GEOD-23184 | biostudies-arrayexpress

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