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ABSTRACT:
PROVIDER: PRJNA213670 | ENA |
REPOSITORIES: ENA
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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
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. ChIPed DNA with GBF1 antibody from GBF1OE, hy5 GBF1OE, and hyh GBF1OE lines vs. ChIPed DNA with GBF1 antibody from wild-type.
2014-03-24 | E-GEOD-36965 | biostudies-arrayexpress
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.
2016-04-01 | GSE36964 | GEO
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
Project description:Expression data from gbf1, gbf1 hy5, and gbf1 hyh mutants
| PRJNA157297 | ENA
Project description:We show that longer-term inhibition of shade avoidance in Arabidopsis is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOG (HYH) which, together, regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification.
2023-06-07 | GSE192469 | GEO
Project description:The transcription factor HY5 acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. Coupled with DNA chip hybridization using high density 60-nucleotide oligomer microarray that contains one probe for every 500 nucleotides over the entire Arabidopsis genome, we mapped genome wide in vivo HY5 binding sites. This analysis showed that HY5 binds preferentially to promoter regions in vivo and revealed over 3 thousand chromosomal sites as putative HY5 binding targets. HY5 binding targets tend to be enriched in the early light responsive genes and transcription factor genes. Our data thus supports a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis. Keywords: ChIP-chip
2007-03-01 | GSE6510 | GEO
Project description:ChIP-chip analysis of GBF1 in the presence and absence of its heterodimerizing partners, HY5 and HYH
| PRJNA157299 | ENA
Project description:Arabidopsis thaliana seedlings comprising hy5 single mutant , hyh single mutant, hy5 hyh double mutant and wild-type plants were germinated in the dark on agar medium on usual Murashig and Skoog medium (pH 5.8) without sucrose. After 3 days of germination, etiolated seedlings were transfered to light conditions in liquid media similar to previous one but without agar . After 5 hours, auxin (10 micromolar IAA) was added to all treated samples except to controls (Mock treatment). all samples were harvested after one-hour treatment and frozen for further RNA extraction. Aim of the project was to detect impact of exogenous auxin treatment on each genotype
2006-11-08 | E-MEXP-715 | biostudies-arrayexpress
Project description:To determine the functional relevance of the HY5 binding sites to the transcriptional regulation, we performed genome wide expression analysis using WT and hy5 grown in continuous white light for 4 days. Keywords: mutant/widetype comparative
2007-03-01 | GSE6517 | GEO