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The novel transcription factor, POPEYE, regulates response to iron deficiency in Arabidopsis roots

ABSTRACT: ChIP-chip analysis was used to identify direct targets of the transcription factor POPEYE (PYE) ChIP was performed on ProPYE:PYE:GFP plants and on wt plants as a control. The two samples were amplified and hybridized on Agilent arrays. Dye swap was performed for two biological replicates.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Wolfgang Busch

PROVIDER: E-GEOD-21625 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots.

Long Terri A TA Tsukagoshi Hironaka H Busch Wolfgang W Lahner Brett B Salt David E DE Benfey Philip N PN

The Plant cell 20100730 7

Global population increases and climate change underscore the need for better comprehension of how plants acquire and process nutrients such as iron. Using cell type-specific transcriptional profiling, we identified a pericycle-specific iron deficiency response and a bHLH transcription factor, POPEYE (PYE), that may play an important role in this response. Functional analysis of PYE suggests that it positively regulates growth and development under iron-deficient conditions. Chromatin immunoprec ...[more]

PMID: 20675571

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Transcriptional regulation of ROS controls the transition from proliferation to differentiation in the root

Project description:ChIP-chip analysis was used to identify direct targets of the transcription factor UPBEAT1 (UPB1) ChIP was performed on ProUPB1:UPB1:GFP plants and on wt plants as a control. The two samples were amplified and hybridized on Agilent arrays. Dye swap was performed for two biological replicates.

2010-11-12 | E-GEOD-21741 | biostudies-arrayexpress

The bacterial cell-cycle regulator GcrA is a Ï70 co-factor that drives gene expression from a subset of methylated promoters.

Project description:Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we find that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. GcrA forms a stable complex with RNA polymerase and localizes to almost all active Ï70-dependent promoters in vivo, but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact Ï70 interact with domain 4, GcrA interfaces with domain 2, the region that binds the -10 element during strand separation. Using kinetic analyses and a reconstituted in vitro transcription assay, we demonstrate that GcrA can stabilize RNA polymerase binding and directly stimulate open complex formation to activate transcription. Guided by these studies, we identify a regulon of ~200 genes, providing new insight into the essential functions of GcrA. Collectively, our work reveals a new mechanism for transcriptional regulation, and we discuss the potential benefits of activating transcription by promoting RNA polymerase isomerization rather than exclusively recruitment. Examination of GcrA, RNAP, Sigma70 ChIP in PYE and in PYE + rifampicin-treated for 30 min; sigma32 and sigma54 in PYE + rifampicin-treated for 30 min

2015-11-10 | E-GEOD-73925 | biostudies-arrayexpress

Effects of SocB toxin on genome-wide expression in Caulobacter crescentus

Project description:Caulobacter cells were grown to exponential phase in rich PYE medium. At time zero, expression of socB-M2 was induced by the addition of 0.3% xylose. A reference sample was also collected at this time point. Atter 1.5 hours, the experimental sample was then collected. RNA was extracted from the reference and experimental samples, reverse transcribed into Cy3- or Cy5-labeled cDNA, and then hybridized to Agilent 4x44K Caulobacter arrays. <br><br>

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Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (expression)

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The novel transcription factor, POPEYE, regulates response to iron deficiency in Arabidopsis roots

Project description:ChIP-chip analysis was used to identify direct targets of the transcription factor POPEYE (PYE)

2010-11-22 | GSE21625 | GEO

Expression analysis of the response to wild-type and pye-1 mutants to iron sufficient or iron deficient conditions

Project description:Transcriptional profile of whole roots of wild-type and pye-1 mutants exposed to 24 hours -Fe were generated Global population increases and climate change underscore the need for better comprehension of how plants acquire and process nutrients such as iron. A systems biology approach was taken to elucidate novel regulatory mechanisms involved in plant responses to iron deficiency (-Fe). Using cell-type specific transcriptional profiling we identified a pericycle-specific iron deficiency response, and a previously uncharacterized transcription factor, POPEYE (PYE), that plays an important role in this response. Functional analysis of PYE suggests that it positively regulates growth and development under iron deficient conditions. ChIP-on-chip analysis and transcriptional profiling reveal that PYE helps maintain iron homeostasis by directly and indirectly regulating the expression of ferric reductases, metal ion transporters, iron storage proteins, and other key iron homeostasis genes. In addition to PYE, we also identified a second protein BRUTUS (BTS), which appears to negatively regulate the response to iron deficiency. BTS is a unique putative E3 ligase protein, with metal ion binding and DNA binding domains. PYE and BTS are tightly co-regulated and physically interact with PYE paralogs, one of which is thought to positively regulate expression of genes involved in iron homeostasis. We propose that iron content is sensed within the pericycle where PYE, perhaps in conjunction with BTS and other regulatory proteins, is then activated to control a regulatory network involved in maintaining proper iron distribution in plants. Keywords: Expression analysis

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Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci

Project description:Identifying cis-regulatory elements is important to understand how human pancreatic islets modulate gene expression in physiologic or pathophysiologic (e.g., diabetic) conditions. We conducted genome-wide analysis of DNase I hypersensitive sites, histone H3 lysine methylation marks (K4me1, K4me3, K79me2), and CCCTC factor (CTCF) binding in human islets. This identified ~18,000 putative promoters (several hundred novel and islet-active). Surprisingly, active promoter marks were absent at genes encoding islet-specific hormones, suggesting a distinct regulatory mechanism. Of 34,039 distal (non-promoter) regulatory elements, 47% are islet-unique and 22% are CTCF-bound. These findings present a global snapshot of the human islet epigenome and should provide functional context for non-coding variants emerging from genetic studies of T2D and other pancreatic islet disorders. Three different islet samples were tested for DNase I hypersensitivity by DNase-Seq. Five different primary pancreatic islet samples were evaluated for several chromatin modifications (H3K4me3, H3K4me1, H3K79me2) by ChIP-seq. One islet sample was evaluated for CTCF binding via ChIP-seq, All ChIP-seq samples have both non-specific IP (GFP) and input DNA controls.

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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.

2024-09-02 | E-MTAB-14365 | biostudies-arrayexpress

Expression analysis of root pericycle cell-types after iron deficiency (-Fe) treatment

Project description:Pericycle specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) of roots that express a pericycle-specific GFP-reporter. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transferred to -Fe media for 24 hours. Global population increases and climate change underscore the need for better comprehension of how plants acquire and process nutrients such as iron. A systems biology approach was taken to elucidate novel regulatory mechanisms involved in plant responses to iron deficiency (-Fe). Using cell-type specific transcriptional profiling we identified a pericycle-specific iron deficiency response, and a previously uncharacterized transcription factor, POPEYE (PYE), that plays an important role in this response. Functional analysis of PYE suggests that it positively regulates growth and development under iron deficient conditions. ChIP-on-chip analysis and transcriptional profiling reveal that PYE helps maintain iron homeostasis by directly and indirectly regulating the expression of ferric reductases, metal ion transporters, iron storage proteins, and other key iron homeostasis genes. In addition to PYE, we also identified a second protein BRUTUS (BTS), which appears to negatively regulate the response to iron deficiency. BTS is a unique putative E3 ligase protein, with metal ion binding and DNA binding domains. PYE and BTS are tightly co-regulated and physically interact with PYE paralogs, one of which is thought to positively regulate expression of genes involved in iron homeostasis. We propose that iron content is sensed within the pericycle where PYE, perhaps in conjunction with BTS and other regulatory proteins, is then activated to control a regulatory network involved in maintaining proper iron distribution in plants. Keywords: Cell-type specific analysis of stress response using FACS

2010-10-12 | GSE21553 | GEO

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