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Expression data of Arabidopsis thaliana (Ler accession) phytochrome phyABCDE quintuple mutant and phyABDE quadruple mutant in response to red light, and their comparison to WT expression data

ABSTRACT: Phytochromes are red/far-red light photoreceptors. We sought to test at the transcriptomic level if Arabidopsis mutants lacking all phytochromes (from phyA to phyE), or just retaining trace levels of phyC, had transcriptional response to red light exposure.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE31587 | GEO | 2012/04/01

SECONDARY ACCESSION(S): PRJNA145603

REPOSITORIES: GEO

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Expression data of Arabidopsis thaliana (Ler accession) phytochrome phyABCDE quintuple mutant and phyABDE quadruple mutant in response to red light, and their comparison to WT expression data

Project description:Phytochromes are red/far-red light photoreceptors. We sought to test at the transcriptomic level if Arabidopsis mutants lacking all phytochromes (from phyA to phyE), or just retaining trace levels of phyC, had transcriptional response to red light exposure. phyABCDE and phyABDE mutants were grown for 4 days in darkness (D), or under continuous red light at 50 µmol m-2 s-1 (R50), or in darkness followed by 2 hr of red light exposure on day 4 (DR2h). Differentially expressed genes of the mutants in response to red light were compared to those of wild type obtained previously {Hu et al. (2009) Molecular Plant, 2: 166-182}. Three biological replicates were employed for dark and Rc-grown samples, and 2 biological replicates for DR2h samples, thus 8 samples were used for each mutant genotype. It needs to be pointed out that 5 of the 6 WT samples (from WT-D-2 to WT-R50-2) had previously been deposited with GEO accessions GSM226267, GSM226268, GSM226269, GSM226278 and GSM226279. Their cRNA samples were synthesized and labeled with the Affymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents). They are included in this series of study for convenient comparison, with newly assigned accessions from GSM784837 to GSM784841. The more recent GeneChip 3' IVT Express Kit (Affymetrix) was used to synthesize and label aRNA for one new WT sample (WT-D-1)(GSM784836) and all mutant samples.

2012-03-31 | E-GEOD-31587 | biostudies-arrayexpress

Phytochrome C and Low Temperature Promote the Expression and Red Light Signaling of Phytochrome D

Project description:Light is an ever-changing environmental parameter affecting almost every aspects of plant growth and development. It is perceived by photoreceptors, among them phytochromes (PHY) are responsible for monitoring the red and far-red part of the spectrum. Arabidopsis thaliana possesses five phytochromes genes, named through phyA-phyE. Whereas the function of phyA and phyB – that mediate most of the phytochrome responses – is extensively studied, our knowledge on other phytochromes are still rudimentary. To analyze phyD function we expressed it at high levels in different phytochrome deficient genetic backgrounds. We found that overexpressed phyD governs effective light signaling at low temperatures but only in cooperation with functional phyC. Under these conditions, opposite to phyB, phyD accumulates to high levels and this pool is stable under light illumination. Furthermore, the detectable photoconvertible phyD amount is proportional with the available protein amount indicating that the phyD pool contains fully functional photoreceptors. The thermal reversion of phyD is very fast suggesting that the thermosensing of phyD is based on its protein amount and not on its Pfr conformer stability, which was described for phyB. We also found that phyD and phyB associate to identical genomic locations and mediate similar gene expression changes, however the efficiency of phyD is lower. Taken together our data suggest that under certain conditions synergistic interaction of phyD and phyC substitutes phyB function thus increases the ability of plants to respond more flexible to environmental changes.

2024-01-19 | GSE253236 | GEO

Phytochrome C And Low Temperature Promote The Expression And Red Light Signaling Of Phytochrome D

2024-01-19 | GSE253043 | GEO

Analyses of phyB-regulated genes by RNA-seq

Project description:The phytochrome family consists of five numbers (phyA-phyE) in Arabidopsis, of which phyB is the best characterized and shown to play a major role in mediating red light inhibition of hypocotyl elongation. In order to reveal the molecular basis for phyB-mediated red light signaling to promote photomorphogenesis, we analyzed the gene expression profile of red light-grown WT and phyB mutant seedlings by high throughput sequencing.

2020-07-25 | GSE101875 | GEO

PHYB and PHYC–mediated transcriptomic responses to short and long day photoperiods in wheat

Project description:The phytochromes (PHYs) are a family of photoreceptors which absorb red and far-red light to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in tetraploid wheat and performed RNA-seq studies to analyze and compare the regulons of each phytochrome under short day photoperiods.

2019-11-26 | GSE141000 | GEO

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways

Project description:The phytochromes (PHYs) are a family of photoreceptors which absorb light of red and far-red wavelengths to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in wheat and performed replicated RNA-seq studies to analyze and compare the regulons of each phytochrome under long day photoperiods.

2016-06-29 | GSE79049 | GEO

Phytochrome Interacting Factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

Project description:Phytochromes are red/far red photosensors regulating numerous developmental programs in plants. Among them phytochrome A (phyA) is essential to enable seedling de-etiolation in continuous far-red (FR) light a condition mimicking the environment under a dense canopy. The ecological relevance of this response is demonstrated by the high mortality rate of phyA mutants germinating in deep vegetational shade. phyA signaling involves a direct interaction of the photoreceptor with members of the bHLH transcription factor family, PIF1 and PIF3 (Phytochrome Interacting Factor). Here we investigated the involvement of PIF4 and PIF5 in phyA signaling and found that they redundantly control de-etiolation in FR light. The pif4pif5 double mutant is hypersensitive to low fluence rates of FR light. This phenotype is dependent on FR light perception by phyA but does not rely on alterations of the phyA level. Our microarrays analysis shows that PIF4 and PIF5 are part of an inhibitory mechanism repressing the expression of some light-responsive genes in the dark and are also needed for full expression of several growth-related genes in the light. Unlike PIF1 and PIF3, PIF4 and PIF5 are not degraded in response to FR light indicating that they are light-regulated by a different mechanism. Our genetic analysis suggests that this is achieved through the sequestration of these PIFs by the closely related bHLH transcription factor HFR1 (long Hypocotyl in FR light).

2009-08-19 | GSE16333 | GEO

Transcription profiling of Arabidopsis thaliana phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

2009-09-17 | E-GEOD-16333 | biostudies-arrayexpress

The roles of red light and phytochrome A/B in photomorphogenesis

Project description:Analysis of etiolated seedlings exposed for 1hr to red light. Phytochromes are red/far-red light receptors, palying important roles in photomorphogenesis. Results suggest that red light and phytochromes regulate a set of genes' expression in seedlings.

2021-03-01 | GSE111380 | GEO

mRNA-seq of Physcomitrella protonema responding to 1 hr red light in wild type and the phytochrome-deficient mutant

Project description:The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. For details, please see PMID: .

2012-05-08 | GSE36274 | GEO

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