E-GEOD-35057
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ABSTRACT:
PROVIDER: E-GEOD-35057 | ExpressionAtlas | 2015-12-01
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE35057: Phytochrome Interacting Factor 4 and 5 regulate different set of genes in high and low red/far-red light GSE35059: ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition Refer to individual Series
2012-05-02 | E-GEOD-35062 | biostudies-arrayexpress
Project description:Phytochrome Interacting Factor 4 and 5 regulate different set of genes in high and low red/far-red light
| PRJNA156177 | ENA
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
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). Experiment Overall Design: he pif4pif5 double mutant were compared to wild-type plants when kept in the dark or subjected to 1 or 24 hours of 0.5 or 5 µmol/m2/s far-red light respectively.
2009-09-17 | E-GEOD-16333 | biostudies-arrayexpress
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
Project description:The goal of this work was to investigate the influence of low red to far-red (R:FR) signals generated by a biological weedy and an artificial source of far-red light on the nitrate assimilation pathway in maize. In the absence of direct resource competition, far-red light reflected from neighboring weeds compromises light quality (red to far-red ratio; R/FR) and causes a wide range of morphological and physiological responses at early growth stages of crop plants. This study has investigated the effects of low R/FR light signals on nitrate assimilation in maize seedlings. The transcript levels of genes, metabolites, and activities of enzyme in the nitrate assimilation pathway under a biological and a simulated low R:FR light environment were compared with a high R:FR control environment. Low R:FR signals stimulated nitrate accumulation in maize leaves, which did not appear to result from the upregulation of nitrate transporter genes. A significant reduction in ferredoxin-dependent glutamine:2-oxoglutarate aminotransferase activity appears to play a major role in nitrate accumulation under low R:FR light environments, while activities of other enzymes of the nitrate assimilation pathway remain unchanged.
2022-09-27 | GSE213949 | GEO
Project description:To study the transcriptomic profile of wt and brc1 mutant axillary buds during the shade avoidance response, we simulated a canopy shade with a low R/FR light ratio. We treated plants with white light supplemented with far-red light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 146 μeinstein · m-2 seg-1) for 8 hours. Control plants were left for 8 hours in white light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 2.2 μeinstein · m-2 seg-1) .
2013-02-28 | GSE27273 | GEO
Project description:The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths, but show little or no response to the more attenuated red/far-red wavelengths. Here we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared to other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.
2016-05-09 | GSE73915 | GEO
Project description:The purpose of this experiment was to identify genes responding differently to a 24 h low red to far red ratio (R:FR) treatment in plants grown at 16 and 22 degrees Keywords: Light treatment
2007-10-28 | GSE8745 | GEO
Project description:UV-A mediated regulation of anthocyanin biosynthesis was investigated in swollen hypocotyls of the red turnip ‘Tsuda’. The shaded swollen hypocotyls which contained negligible anthocyanin were exposed to artificial light sources including low fluence UV-B, UV-A, blue, red, far-red, red plus UV-A, far-red plus UV-A, and blue plus red. Among these lights, only UV-A induced anthocyanin biosynthesis and co-irradiation of red or far-red with UV-A did not affect the extent of UV-A induced anthocyanin accumulation. The expression of phenylalanine ammonia lyase (PAL; EC 4.3.1.5), chalcone synthase (CHS; EC 2.3.1.74), flavanon 3-hydrocylase (F3H; EC 1.14.11.9), dihydroflavonol 4-reductase (DFR; EC 1.1.1.219) and anthocyanidin synthase (ANS; EC 1.14.11.-) genes were increased with time during a 24 hour exposure of UV-A. In contrast, irradiation of red, blue, UV-B, and a combination of blue with red failed to induce CHS expression. Microarray analysis showed that only a few genes, including chalcone synthase and flavanon 3-hydroxylase were induced significantly by UV-A, while a separate set of many genes was induced by low fluence UV-B. The UV-A specific induction of anthocyanin biosynthesis and the unique gene expression profile upon UV-A irradiation as compared with blue and UV-B demonstrated that the observed induction of anthocyanin biosynthesis in red turnips was mediated by a distinct UV-A specific photoreceptor, but not by phytochromes, UV-A/blue photoreceptors, or UV-B photoreceptors. Keywords: light response
2007-02-22 | GSE6876 | GEO