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Microarray analysis in wild type and hy5 plants

ABSTRACT: Gene expression profiles between wild type (WT) and hy5 were compared to know HY5-targets.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE62119 | GEO | 2015/01/06

SECONDARY ACCESSION(S): PRJNA263244

REPOSITORIES: GEO

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Microarray analysis in wild type and hy5 plants

Project description:Gene expression profiles between wild type (WT) and hy5 were compared to know HY5-targets. Gene expression profiles between wild type (WT) and hy5 were compared to known HY5-targets.

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Analysis of transcription factor HY5 genomic binding sites in Arabidopsis

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

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Project description:Purpose: The purpose of this RNA Sequencing project was to investigate the transcriptional regulatory relationship between NF-YC3/4/9 and HY5 Methods: Total RNA was isolated, and then poly-A purified. 100ng of starting RNA was used to generate RNASeq libraries using the NEXTflex Illumina qRNA-Seq Library Prep Kit, and sequenced on an Illumina HiSeq2500 machine. Results: NF-YC3/4/9 and HY5 have both shared and independent regulatory targets.

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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

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ELONGATED HYPOCOTYL 5 (HY5) and POPEYE (PYE) Regulate Intercellular Iron Transport in Plants

Project description:Plants maintain iron (Fe) homeostasis under varying environmental conditions by balancing processes such as Fe uptake, transport, and storage. In Arabidopsis, POPEYE (PYE), a basic helix-loop-helix (bHLH) transcription factor (TF), has been shown to play a crucial role in regulating this balance. In recent years, the mechanisms regulating Fe uptake have been well established but the upstream transcriptional regulators of Fe transport and storage are still poorly understood. In this study, we report that ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) TF which has recently been shown to play a crucial role in Fe homeostasis, interacts with PYE. Molecular, genetic and biochemical approaches revealed that PYE and HY5 have overlapping as well as some distinct roles in regulation of Fe deficiency response. We found that HY5 and PYE both act as a repressor of Fe transport genes such as YSL3, FRD3, NPF5.9, YSL2, NAS4, and OPT3. HY5 was found to directly bind on the promoter of these genes and regulate intercellular Fe transport. Further analysis revealed that HY5 and PYE directly interact at the same region on PYE and NAS4 promoter. Overall, this study revealed that HY5 regulates Fe homeostasis by physically interacting with PYE as well as independently.

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