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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Arabidopsis dark-induced senescence: wild type (Col-0) vs. pif quadruple (pif1pif3pif4pif5) mutant

ABSTRACT: Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence. Two-condition experiment, wild type vs. pif quadruple mutant. Biological replicates: 3 wild type replicates, 3 mutant replicates.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jinkil Jeong

PROVIDER: E-GEOD-52646 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Arabidopsis dark-induced senescence: wild type (Col-0) vs. pif quadruple (pif1pif3pif4pif5) mutant

Project description:Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence.

2014-08-04 | GSE52646 | GEO

Arabidopsis thaliana

Project description:Arabidopsis dark-induced senescence: wild type (Col-0) vs. pif quadruple (pif1pif3pif4pif5) mutant

| PRJNA229514 | ENA

Transcriptome-wide analysis of gene expression in dark-grown WT and pif mutant seedlings

Project description:We sequenced mRNA from WT and PhytochromeInteractingFactor (pif) mutant seedlings grown for 2d in darkness. Transcriptome profiles of the wild-type (WT), pif1, pif3, pif, pif5 monogenic mutants, pif3pif4pif5 (pif345), pif1pif4pif5(pif145), pif1pif3pif5 (pif135) and pif1pif3pif4 (pif134) triple mutants and pif1pif3pif4pif5 (pifq) quadruple mutant seedlings. Biological triplicate samples were analyzed from libraries constructed using a 3'-capture, 5' to 3' directional method.

2014-10-02 | E-GEOD-42665 | biostudies-arrayexpress

Expression data from WT (Columbia) and pifq (pif1pif3pif4pif5) mutant Arabidopsis seedlings

Project description:Plants respond to changes in the red:far red ratio (R:FR) of incident light. A reduction in this ratio (increase in FR) results in the Shade Avoidance Response (SAR) with associated changes in gene expression. The Phyotchrome-Interacting Factors (PIFs) are bHLH transcription factors known to be involved in the SAR. An analysis of changes in gene expression in WT and quadruple pif1pif3pif4pif5 (pifq; Leivar et al., 2008 (PMID 19920208)) mutant seedlings in response to an increase in FR should identify primary targets of PIF signaling.

2012-08-02 | GSE28297 | GEO

Transcription profiling of rice wild type and OsNOA1-RNAi plant

Project description:Rice genes regulated by OsNOA1 (Nitric oxide-associated protein1) profiled by comparing between wild-type and OsNOA1-RNAi plant at 22 degree centigrade for 6 days.

2011-05-25 | E-MEXP-3136 | biostudies-arrayexpress

The profiling of gene expression in pupa stage of Drosophila melanogaster: Wildtype vs. dicer-2 mutant

Project description:To investigate transcriptional effects caused by a severe defect in endo-siRNA production, a gene expression profiling was performed on Drosophila dicer-2 pupae compared to wild-type. Two-condition experiment, Wildtype pupa vs. dicer-2 mutant pupa. Biological replicates: each 3 replicates.

2012-05-20 | E-GEOD-35945 | biostudies-arrayexpress

Expression changes by Endodermal PIF1: SCR:PIF1/pifQ transgenic plant vs. pif1pif3pif4pif5 (pifQ) mutant

Project description:Transcriptional profiling of dark-grown Arabidopsis seedlings comparing SCR:PIF1/pifQ transgenic plant with pif1pif3pif4pif5 quadruple mutant (pifQ). Seedlings were grown under dark condition for 2.5 days. Goal was to determine the effects of endodermal PIF1 in dark-grown seedlings. Two-condition experiment, SCR:PIF1/pifQ vs. pifQ Biological replicates: 3 pifQ replicates, 3 SCR:PIF1 replicates.

2016-08-01 | E-GEOD-71918 | biostudies-arrayexpress

Expression data from epidermis specific phytochrome B or global phytochrome B line comparing to phyB-9 mutant.

Project description:Seedling hypocotyls display negative gravitropism in the dark but agravitropism in the light. The Arabidopsis thaliana pif quadruple mutant (pifQ), which lacks four PHYTOCHROME-INTERACTING FACTORS (PIFs), is agravitropic in the dark. Endodermis-specific expression of PIF1 rescues gravitropism in pifQ mutant seedlings. Since phytochromes induce light responses by inhibiting PIFs and the COP1-SPA ubiquitin E3 ligase complex in the nucleus, we asked whether phyB can cell autonomously inhibit hypocotyl negative gravitropism in the endodermis. We found that while epidermis-specific expression of PHYB rescues hypocotyl negative gravitropism and all other phyB mutant phenotypes, endodermis-specific expression of PHYB does not. Epidermal phyB induces the phosphorylation and degradation of endodermal PIFs in response to red light. This induces a global gene expression pattern similar to that induced by red light treatment of seedlings expressing PHYB under the control of its own endogenous promoter. Our results imply that epidermal phyB generates an unidentified mobile signal that travels to the endodermis where it promotes PIF degradation and inhibits hypocotyl negative gravitropism.

2017-02-08 | GSE87591 | GEO

Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PHYTOCHROME-INTERACTING FACTORS

Project description:Light-environment signals, sensed by plant phytochrome (phy) photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown “trans factors” modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of co-localization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade, and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator, to regulate the expression of PIF-DTGs, through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF signaling hub.

2020-09-01 | GSE136843 | GEO

A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1

Project description:Telomere erosion contributes to age-associated tissue dysfunction and senescence, and p53 plays a crucial role in this response. We undertook a genome-wide screen to identify gene deletions that sensitized p53-positive human cells to loss of telomere integrity, and uncovered a previously unannotated gene, C16ORF72, which we term Telomere Attrition and p53 Response 1: TAPR1. CRISPR-Cas9 mediated deletion of TAPR1 led to elevated p53 and induction of p53 transcriptional targets. TAPR1-disrupted cells exhibited a synthetic-sick relationship with the loss of telomerase, or treatment with the topoisomerase II inhibitor doxorubicin. Stabilization of p53 with nutlin-3a further decreased cell fitness in cells lacking TAPR1 or telomerase, whereas deletion of TP53 rescued the decreased fitness of TAPR1-deleted cells. We propose that TAPR1 regulates p53 turnover, thereby tapering the p53-dependent response to telomere erosion. We discuss the possible implications of such a mechanism in the preservation of genome integrity during senescence or aging.

2021-03-04 | PXD022128 | Pride

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