Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-Wide Direct Target Identification Reveals the transcriptional regulatory Framework of WOX11 in Root Development in Rice

ABSTRACT: WUSCHEL-related homeobox domain trancription factor WOX11 is a key regulator of crown root growth and development in rice (Oryza sativa. L). However, the gene regulatory network downstream of WOX11 remains largely unknown. To dissect WOX11 transcriptional regulatory framework, we determined the transcriptome of wox11 mutants and corresponding wild type (Hwayoung) by using RNA-seq technology.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE84933 | GEO | 2017/06/21

SECONDARY ACCESSION(S): PRJNA335701

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Histone acetyltransferase OsGCN5 palys an important role in establishing programs of cell proliferation of crown root meristem

Project description:Shoot-borne crown roots are the major root system in cereals. Previous work has shown that the Wuschel-related homeobox gene WOX11 is necessary and sufficient to promote rice crown root emergence and elongation. Here, we show that WOX11 recruits the ADA2-GCN5 histone acetyltransferase (HAT) module to activate downstream target genes in crown root meristem. OsGCN5 and OsADA2 are highly expressed in root meristem. Knockdown of OsGCN5 and OsADA2 affects crown root initiation and elongation. Here we sought to find the downstream genes of OsGCN5 in rice crown root tip.

2017-03-28 | GSE95481 | GEO

The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions [DAP-seq]

Project description:Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. We found that phenotypic variations were explained by four principal components and that tiller numbers and crown root diameters could summarize admixture groups. Transcriptome analysis revealed that admixture-group-associated differentially expressed genes were enriched with stress response related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin inducible genes, suggesting the association between auxin signaling and mild drought stress. Negative correlation between crown root diameters and stress response related genes suggested that thicker crown root diameter is associated with mild drought stress tolerance. Finally co-expression network analysis implemented with DAP-seq analysis identified phytohormone signaling network and key transcription factors negatively regulating crown root diameters. Our datasets would serve as an important resource for understanding genomic and transcriptomic basis of phenotypic variations under the upland-field condition.

2021-03-07 | GSE162312 | GEO

The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions [RNA-seq]

2021-03-07 | GSE162311 | GEO

Transcriptional profiling during OSH1 induction

Project description:In flowering plants, knotted1-like homeobox (KNOX) transcription factors play crucial roles in establishment and maintenance of the shoot apical meristem (SAM), from which aerial organs such as leaves, stems and flowers initiate. We report that a rice (Oryza Sativa) KNOX gene Oryza sativa homeobox1 (OSH1) represses the brassinosteroid (BR) phytohormone pathway through activation of BR catabolism genes. Inducible overexpression of OSH1 caused brassinosteroid insensitivity, whereas loss-of-function showed a BR-overproduction phenotype. Genome-wide identification of loci bound and regulated by OSH1 revealed hormonal and transcriptional regulation as the major function of OSH1. Among these targets, BR catabolism genes CYP734A2, CYP734A4 and CYP734A6 were rapidly up-regulated by OSH1-induction. Furthermore, RNAi knockdown plants of CYP734A genes arrested growth of the SAM and mimicked some osh1 phenotypes. Thus, we suggest that local control of BR levels by KNOX genes is a key regulatory step in SAM function.

2014-08-07 | E-MTAB-4316 | biostudies-arrayexpress

RNA-Seq of various rice tissues (Root hair, Collar, Leaf sheath, Ligule, Anther wall)

Project description:Various rice tissues were collected and immediately frozen from Dongin cultivar (Oryza sativa L. japonica).

2022-12-31 | E-MTAB-11005 | biostudies-arrayexpress

Transcriptome analysis of Azospirillum lipoferum 4B during its interaction with rice roots

Project description:Investigation of whole genome gene expression level changes in a Azospirillum lipoferum 4B associated to artificial roots, Oryza sativa japonica cv. Cigalon roots and Oryza sativa japonica cv. Nipponbare roots, compared to the strain grown in liquid culture.

2014-01-01 | GSE42450 | GEO

Expression analysis of genes affected by dehydration-responsive transcription factor Os02g31890 from rice.

Project description:Os02g31890 encodes a dehydration-responsive transcription factor (named ´ARID´) from rice (Oryza sativa, cv. Dongjin). Expression profiling was performed 90 min after the start of dehydration stress in roots of Oryza sativa wild-type plants (cv. Dongjin) and a knock-out (i.e. arid) mutant.

2013-11-30 | GSE42683 | GEO

Dynamic Profiles of transcriptome in Oryza sativa leaf

Project description:To evaluate the roles of gene regulation in Oryza sativa leaf, dynamic profiles of transcriptome were investigated in Oryza sativa L. spp. indica with different treatments, the aerial tissues of one-month-old plants from four different areas (groups 1–4) were treated with 0, 40 mL of 25% azoxystrobin, 0.01 g of VdAL, or 40 mL of 25% azoxystrobin plus 0.01 g VdAL, respectively.

2018-12-18 | GSE108204 | GEO

Insights into the influence of culture systems on maximum root length of rice (Oryza sativa L.) through phosphoproteomics analysis

Project description:To investigate the root system, three indoor cultivation systems, including water agar, deep water, and vermiculite-based hydroponics, are commonly used. However, their effects on the root development of rice (Oryza sativa L.) remain unknown. In this study, we assessed the effect of these indoor cultivation systems on the maximum root length (MRL) and examined the changes in phosphorylated protein profiles by LC-MS/MS.

2024-09-28 | PXD050876 | JPOST Repository

Characterize novel lncRNAs responding to stresses in Oryza sativa at transcriptional and post-transcriptional levels

Project description:We performed poly(A)+, poly(A)-, nuclear, small RNA-seq analysis on Oryza sativa japonica WT plants.

2018-06-13 | GSE86215 | GEO