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Arabidopsis thaliana

ABSTRACT: In vitro gennomic DNA binding assay and sequencing using recombinant HYH, GBF1, GBF2,GBF3, GBF4 and EEL(bzip12) proteins.

PROVIDER: PRJNA610701 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11266700.fastq.gz	Fastqsanger.gz
	SRR11266700_1.fastq.gz	Fastqsanger.gz
	SRR11266700_2.fastq.gz	Fastqsanger.gz
	SRR11266701_1.fastq.gz	Fastqsanger.gz
	SRR11266701_2.fastq.gz	Fastqsanger.gz

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ChIP-chip analysis of GBF1 in the presence and absence of its heterodimerizing partners, HY5 and HYH

Project description:Transcription factors are key components of light signalling as they amplify the signal, which results in massive changes in genome-wide expression during photomorphogenesis. Three bZIP transcription factors (TFs), namely GBF1, HY5, and HYH, form heterodimers with each other and regulate photomorphogenesis in an interdependent manner. GBF1 acts as both a positive and negative regulator of photomorphogenesis, whereas HY5 and HYH mainly act as positive regulators of photomorphogenesis. In this study, the impact of heterodimerization of GBF1 with HY5 and HYH was analyzed for genome-wide binding of GBF1 through ChIP-chip in GBF1. We identified more than 2000 direct targets of GBF1 in the presence of HY5 and HYH. However, in the absence of HY5, very few binding sites were found, and in the absence of functional HYH protein, the number of GBF1 direct targets reduced to only half compared to when functional HYH was present.

2014-03-24 | GSE36965 | GEO

ChIP-chip analysis of GBF1 in the presence and absence of its heterodimerizing partners, HY5 and HYH

2014-03-24 | E-GEOD-36965 | biostudies-arrayexpress

Expression data from gbf1, gbf1 hy5, and gbf1 hyh mutants

2016-04-01 | GSE36964 | GEO

Expression data from gbf1, gbf1 hy5, and gbf1 hyh mutants

Project description:Three bZIP transcription factors (TFs), namely GBF1, HY5, and HYH, form heterodimers with each other and regulate photomorphogenesis in an interdependent manner. GBF1 acts as both a positive and negative regulator of photomorphogenesis, whereas HY5 and HYH mainly act as positive regulators of photomorphogenesis. To study the effect of HY5 and HYH on GBF1-mediated genome-wide expression, transcript profiling was performed in the gbf1 single mutant and gbf1hy5 and gbf1hyh double mutants. Our study revealed that GBF1 mainly acts antagonistic to HY5 and HYH for genome-wide expression. Four-day-old constant white-light grown Arabidipsis seedlings of wild-type (Col-0), gbf1 mutant, gbf1 hy5 double mutant and gbf1 hyh double mutant were harvested for total RNA extraction and Affymetrix microarray hybridisation. Two biological replicates of each sample were used for hybridisation and data analysis. Data were analysed using GeneSpring software by utilising the RMA algorithm. To draw the conclusions from this study, probe level intensity of gbf1, gbf1 hy5, and gbf1 hyh was normalised against the probe level intensity of wild-type, and also the probe level intensity of gbf1 hy5 and gbf1 hyh double mutants was normalised against the probe level intensity of the gbf1 single mutant.

2016-04-01 | E-GEOD-36964 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Expression data from gbf1, gbf1 hy5, and gbf1 hyh mutants

| PRJNA157297 | ENA

Arabidopsis thaliana

Project description:In vitro gennomic DNA binding assay and sequencing using recombinant HY5 protein.

| PRJNA263309 | ENA

Arabidopsis thaliana

Project description:ChIP-chip analysis of GBF1 in the presence and absence of its heterodimerizing partners, HY5 and HYH

| PRJNA157299 | ENA

Project description:Heterodimerization of GBF1 with HY5 and HYH is crucial for its genome wide binding and target gene regulation

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Hevea brasiliensis cultivar:RRIM 600

Project description:RNA-seq of rubber-cultured cells supplemented with 2 kinds of chemicals and in vitro gennomic DNA binding assay and sequencing using 4 kinds of recombinant proteins.

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DAP-seq Analysis of Transcription Factors Associated with Maize Endosperm Development

Project description:Transcription factors (TFs) play an important role in maize endosperm development regulation. The temporal RNA-seq and co-expression network analysis of maize endosperm reveals a hiararchical regulatory network architechture modulating the endosperm development. In the network, NKD1 and NKD2 are central regulators, and GBF1, HSFTF10, NACTF49 and HB115 are secondary regulators downstream of NKD1 and 2. To further test the relationship between these TFs, a DNA affinity purification and sequencing (DAP-seq) assay was performed. The result shows that the assay on NKD1 and NKD2 called 1,951 and 56,855 peaks, and 93 and 1,692 peaks are located within 3 kb distance to transcription starting site (TSS), respectively. And assays on GBF1, HSFTF10, NACTF49 and HB115 called 15,543; 38,147; 7,388 and 936 peaks, respectively.

2023-10-09 | GSE214166 | GEO

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