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Gene expression in hemera mutants in red light condition

ABSTRACT: The hemera (hmr) mutant was identified as the first photomorphogenetic mutant with the combination of long hypocotyl and albino phenotypes in the light. Phytochrome-Interacting bHLH transcription Factors (PIFs), which are repressors of photomorphogenesis accumulate in darkness and are degraded in the light in a phytochrome-dependent manner. Two PIFs, PIF1 and PIF3 accumulated in the light in hmr mutants. In order to determine the gene expression of PIF-dependent genes in hmr mutants in the light, we have performed whole-genome expression analysis on two hmr mutants: a null allele, hmr-5; and a weak allele, hmr-22. Wild-type (Col-0) and hmr mutant seeds were surface-sterilized and plated on half-strength Murashige and Skoog (MS) growth medium without sucrose. The seeds were stratified in the dark at 4ºC for 4d. Seedlings were grown in constant red light (Rc, 10?mol/m2/s) at 21°C for 4d.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Meina Li

PROVIDER: E-GEOD-43311 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression in hemera mutants in red light condition

Project description:The hemera (hmr) mutant was identified as the first photomorphogenetic mutant with the combination of long hypocotyl and albino phenotypes in the light. Phytochrome-Interacting bHLH transcription Factors (PIFs), which are repressors of photomorphogenesis accumulate in darkness and are degraded in the light in a phytochrome-dependent manner. Two PIFs, PIF1 and PIF3 accumulated in the light in hmr mutants. In order to determine the gene expression of PIF-dependent genes in hmr mutants in the light, we have performed whole-genome expression analysis on two hmr mutants: a null allele, hmr-5; and a weak allele, hmr-22.

2014-06-01 | GSE43311 | GEO

Gene expression in pif1pif3pif4pif5 mutant under dark or red light conditions

Project description:Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq). Wild-type and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, induced to germinate with a 5-min red pulse (Rp) (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before exposure to a terminal 5-min far red pulse (FRp) (58 μmol/m2/s) to suppress pseudo-dark effects. Seeds were then placed in either dark (D) or constant red light (Rc) (6.7 μmol/ m2/s) at 21°C for 45h (2d-old seedlings). Alternatively, 2d-old dark-grown seedlings were treated with 1h of red light (R1) (7.5 μmol/m2/s). Seed samples were harvested after stratification (5d stratified seeds).

2009-10-31 | E-GEOD-17159 | biostudies-arrayexpress

Gene expression in the rcb (regulator for chloroplast biogenesis) mutant in red light conditions

Project description:The regulator for chloroplast biogenesis (rcb) mutant was identified as a mutant defective in phytochrome-mediated chloroplast biogenesis. The rcb mutant has long hypocotyl and albino phenotypes. RCB initiates chloroplast biogenesis in the nucleus by promoting the degradation of the master repressors for chloroplast biogenesis, the PIFs (Phytochrome Interacting Factors). To understand how RCB regulates the expression of PIF-regulated genes, we performed genome-wide expression analysis of RCB-dependent genes using a rcb-10 null allele.

2019-06-20 | GSE122351 | GEO

Gene expression in pif1pif3pif4pif5 mutant under dark or red light conditions

2009-11-01 | GSE17159 | GEO

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

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. We used microarrays to examine the SAR in WT (Columbia) and pifq mutant Arabidopsis seedlings. Arabidopsis WT and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure, the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, and then grown in WL (19 umol/m2/s, R/FR ratio of 6.48) for 2 days at 21°C (WL0 samples). Two-day-old WL-grown seedlings were then maintained in the same fluence rate of WL supplemented with far-red light (WL-FR, R/FR ratio of 0.006) for 1 (FR1), 3 (FR3) or 24 (FR24) hours before harvesting. Control seedlings were also maintained in parallel in the same fluence rate of WL for 24h (WL24) before harvesting. Three different biological replicates of each treatment were grown separately and extracted, processed, and analyzed independently.

2012-08-01 | E-GEOD-28297 | biostudies-arrayexpress

Expression data from Col-0 and pil5 imbibed seeds after far-red or far-red/red light irradiation.

Project description:PIL5 is a key negative regulator of phytochrome mediated seed germination and PIL5 protein is degraded by red light irradiation through phytochrome. The microarray aimed to find various red light-regulated genes and PIL5-regulated genes in the imbibed seeds. Keywords: genetic modification

2010-01-12 | GSE14374 | GEO

The JA-pathway MYC transcription factors regulate photomorphogenic responses by modulating the expression of HY5 and PIF targets

Project description:Jasmonates are key regulators of the balance between defence and growth in plants. However, the molecular mechanisms by which activation of defences reduces growth are not yet understood. Here, we analyze the role of MYC transcription factors (TFs) and JA in photomorphogenic growth. We found that multiple myc mutants share light-related phenotypes with mutants of the phytochrome B photoreceptor, regarding seed germination and hypocotyl growth. Over-expression of MYC2 in a phyB background partially suppressed its long hypocotyl phenotype. We show that the activity of MYC TFs is partially independent of COI1 and that JA inhibition of hypocotyl growth acts through alteration of auxin homeostasis and is partially independent of the classical JA signalling pathway. Transcriptomic analysis of multiple myc mutants confirmed that MYCs are required for full expression of R-light regulated genes, including the master regulator HY5. ChIP-Seq analyses revealed that MYC2 and MYC3 directly bind to the promoter of HY5 and that HY5 gene expression and protein levels are compromised in multiple myc mutants. Moreover, MYC2 and MYC3 share a high amount of direct targets with PIFs, and have an opposite effect on gene expression of these targets. Altogether, our results pinpoint MYCs as photomorphogenic TFs that regulate phytochrome responses by regulating PIFs targets and activating HY5 expression. This has important implication to understand the trade-off between growth and defence, since the same TFs that activate defence responses are photomorphogenic growth regulators.

2019-07-31 | GSE114590 | 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