Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Enzyme-Like Domain of Arabidopsis Nuclear Beta-Amylases is Critical During DNA Sequence Recognition and Transcriptional Activation

ABSTRACT: Plant BZR1-BAM transcription factors contain a β-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be non-catalytic, but determine the function of the Arabidopsis thaliana BZR1-BAMs (BAM7 and BAM8) during transcriptional initiation. Microarray experiments with plants overexpressing different mutant versions of the proteins show that only functional BZR1-BAM variants deregulate gene expression and cause leaf developmental abnormalities. Transcriptional changes caused by overexpression of the BZR1 domain alone indicate that the BAM domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE58370 | GEO | 2014/06/10

SECONDARY ACCESSION(S): PRJNA252366

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

The Enzyme-Like Domain of Arabidopsis Nuclear Beta-Amylases is Critical During DNA Sequence Recognition and Transcriptional Activation

Project description:Plant BZR1-BAM transcription factors contain a M-NM-2-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be non-catalytic, but determine the function of the Arabidopsis thaliana BZR1-BAMs (BAM7 and BAM8) during transcriptional initiation. Microarray experiments with plants overexpressing different mutant versions of the proteins show that only functional BZR1-BAM variants deregulate gene expression and cause leaf developmental abnormalities. Transcriptional changes caused by overexpression of the BZR1 domain alone indicate that the BAM domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes. Arabidopsis thaliana (accession Columbia) were grown in a nutrient-rich, medium-grade, peat-based compost in Percival AR95 growth chambers (CLF Plant Climatics) at a constant temperature of 20M-BM-0C, 70% humidity and a 12-h light period with constant, uniform light intensity of 150 M-NM-<molM-bM-^@M-"m-2M-bM-^@M-"s-1. Three-week-old plants were harvested 4 h after onset of the light period and immediately frozen in liquid nitrogen. Fourteen individual plants were pooled per replicate.

2014-06-10 | E-GEOD-58370 | biostudies-arrayexpress

Gene expression over the course of xylem tracheary element formation in cell suspension cultures of Arabidopsis thaliana

2015-09-18 | GSE73146 | GEO

The Arabidopsis GAGA-binding factor BPC6 recruits PRC1 component LHP1 to GAGA DNA-motifs

2015-04-30 | GSE68437 | GEO

Genome-wide binding sites for Arabidopsis ATH1

Project description:The Arabidopsis thaliana ATH1 encodes a BEL1-like TALE homeodomain (BLH) transcription factor that controls the development of shoot organ boundaries. As part of a screen for genes that mediate the function of ATH1 in shoot development, we performed ChIP-seq to identify genome-wide ATH1 binding sites in developing seedlings.

2021-03-31 | GSE157332 | GEO

Transcription profiling of Arabidopsis Brassinosteroid mutant (bzr1-1D and det2) analysis

Project description:Brassinosteroid (BR) homeostasis and signaling are crucial for normal growth; and development of plants. BR signaling through cell-surface receptor; kinases and intracellular components leads to dephosphorylation and; accumulation of the nuclear protein BZR1. How BR signaling regulates gene; expression, however, remains unknown. Here we show that BZR1 is a; transcriptional repressor that has a previously unknown DNA binding domain; and binds directly to the promoters of feedback-regulated BR biosynthetic; genes. To identify additional BZR1-regulated genes and to understand the; BR-regulated transcriptional pathways, we examined the effects of bzr1-1D; and det2 mutations on the expression of BR-regulated genes by using the; Arabidopsis full-genome oligo microarray (Affymetrix). Microarray analyses; identified additional potential targets of BZR1 and illustrated, together; with physiological studies, that BZR1 coordinates BR homeostasis and; signaling by playing dual roles in regulating BR biosynthesis and downstream; growth responses.

2008-06-12 | E-GEOD-2696 | biostudies-arrayexpress

The Arabidopsis GAGA-binding factor BPC6 recruits PRC1 component LHP1 to GAGA DNA-motifs

Project description:Plant BBR/BPC transcription factors contain the conserved Basic-Pentacystein (BPC) DNA-binding domain. Arabidopsis group II BBR/BPC proteins interact with PRC1 component LHP1 in vivo. Microarray experiments with Arabidopsis bpc4 bpc6, lhp1-4 and lhp1-4 bpc4 bpc6 suggest an importance of this interaction in the concerted repression of homeotic genes. In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes. Arabidopsis thaliana (accession Columbia) were grown in the greenhouse under constant temperature of 20°C, 35% humidity and a 18-h light period. 18 days old plants were harvested and immediately frozen in liquid nitrogen. Six individual plants were pooled per replicate.

2015-04-30 | E-GEOD-68437 | biostudies-arrayexpress

Brassinosteroid mutant (bzr1-1D and det2) analysis

Project description:Brassinosteroid (BR) homeostasis and signaling are crucial for normal growth and development of plants. BR signaling through cell-surface receptor kinases and intracellular components leads to dephosphorylation and accumulation of the nuclear protein BZR1. How BR signaling regulates gene expression, however, remains unknown. Here we show that BZR1 is a transcriptional repressor that has a previously unknown DNA binding domain and binds directly to the promoters of feedback-regulated BR biosynthetic genes. To identify additional BZR1-regulated genes and to understand the BR-regulated transcriptional pathways, we examined the effects of bzr1-1D and det2 mutations on the expression of BR-regulated genes by using the Arabidopsis full-genome oligo microarray (Affymetrix). Microarray analyses identified additional potential targets of BZR1 and illustrated, together with physiological studies, that BZR1 coordinates BR homeostasis and signaling by playing dual roles in regulating BR biosynthesis and downstream growth responses. Keywords: other

2005-05-24 | GSE2696 | GEO

BIC1 acts as a transcriptional coactivator to promote brassinosteroid signaling and plant 14 1 growth

Project description:The BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor family plays an essential role in plant brassinosteroid (BR) signaling, but the signaling mechanism through which BZR1 and its homologs cooperate with certain coactivators to facilitate transcription of target genes remains incompletely understood. In this study, we used an efficient protein interaction screening system to identify blue-light inhibitor of cryptochromes 1 (BIC1) as a new BZR1-interacting protein in Arabidopsis thaliana. We show that BIC1 positively regulates BR signaling and acts as a transcriptional coactivator for BZR1-dependent activation of BR-responsive genes. Simultaneously, BIC1 interacts with the transcription factor PIF4 to synergistically and interdependently activate expression of downstream genes including PIF4 itself, and to promote plant growth. Chromatin immunoprecipitation assays demonstrate that BIC1 and BZR1/PIF4 interdependently associate with the promoters of common target genes. In addition, we show that the interaction between BIC1 and BZR1 is evolutionally conserved in the model monocot plant Triticum aestivum (bread wheat). Together, our results reveal mechanistic details of BR signaling mediated by a transcriptional activation module BIC1/BZR1/PIF4 and thus provide new insights into the molecular mechanisms underlying the integration of BR and light signaling in plants.

2020-07-14 | GSE150362 | GEO

Gene expression over the course of xylem tracheary element formation in cell suspension cultures of Arabidopsis thaliana

Project description:Transcriptomic analysis of gene expression during the differentiation of cell suspension cultures into tracheary elements using the biological system published by Pesquet et al., Current Biology (2010): tracheary element differentiation was triggered by externally supplying hormone-free habituated cell suspension cultures of Arabidopsis thaliana Col-0 with auxin, cytokinin and epibrassinolides; RNA samples extracted from 3 independent time-courses every 12h from 0h to 4 days were analyzed using ATH1 Arabidopsis Affymetrix micro-array Time-course design during tracheary element differentiation (3 independepent time-course were harvested from initiation 0h to 4 days every 12h) - total of 27 samples corresponding to the 3 replicates of 9 time point time-courses - gene expression was monitored along the time-course compared to 0h

2015-09-18 | E-GEOD-73146 | biostudies-arrayexpress

Transcription profiling by array of Arabidopsis transgenic plants overexpressing YFP and VND7-YFP

Project description:The Arabidopsis thaliana NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), acts as a master regulator for differentiation of xylem vessels. In order to identify a set of genes regulated by VND7, we carried out a microarray experiment with the Arabidopsis full-genome GeneChip array ATH1 (Affymetrix) for transgenic Arabidopsis roots overexpressing VND7. Experiment Overall Design: Total RNAs were isolated from roots of 5-day-old seedling of transgenic plants overexpressing YFP and VND7-YFP under control of Cauliflower mosaic virus 35S promoter. Three independent biological replicates were performed for each sample.

2010-04-30 | E-MEXP-1876 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data