Gene expression in pif3 mutant under dark and in wt under Red 1h and Red 18h
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE30030 | GEO | 2012/01/03
SECONDARY ACCESSION(S): PRJNA144053
REPOSITORIES: GEO
Similar Datasets
Project description:PIF3 plays a role as repressor of photomorphogenesis in darkness. To identify PIF3-regulated genes that might be implementing this action, we have performed whole-genome expression analysis in the pif3 mutant. Seeds were surface-sterilized and plated on GM medium without sucrose, stratified at 4ºC in the dark for 4 days, exposed to white light for 3 hours to induce germination, and placed in a growth chamber at 21ºC in darkness for 4 days (D0h) and 4 days and 1 hour (D1h). For Rc treatments seedlings were moved to Rc growth chambers at 21ºC for 1 (R1h) and 18 (R18h) hours.
2012-01-03 | E-GEOD-30030 | biostudies-arrayexpress
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).
2009-11-01 | GSE17159 | GEO
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
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
Project description:Red light can affect a variety of responses in Arabidopsis. We characterize the early gene expression patterns of roots exposed to 1 hour of red light. Early genes indicate elements involved in photomorphogenesis, chloroplast development, PAL pathways, root hair development are regulated by 1 hour of red light We used microarrays to detail the gene expression underlying the effects of red light on roots. Keywords: treatment
2006-08-15 | GSE4933 | GEO
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. 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.
2014-06-01 | E-GEOD-43311 | biostudies-arrayexpress
Project description:Etiolated Arabidopsis seedlings open their cotyledons and halt rapid elongation of hypocotyl when exposed to light (de-etiolation). Major light responsive components in this process have been identified and signaling pathways revealed, yet how the organ-specific light responses are achieved remains unknown. Here we report that a developmental regulator TCP4 (TEOSINTE BRANCHED1, CYCLOIDEA, and PCF) participates in photomorphogenesis and facilitates light-induced cotyledon-opening. We demonstrate that TCP4-like transcriptional factors, which predominantly express in cotyledons of both light and dark seedlings, activate SAUR16 and SAUR50 in response to light. Light repressor PIF3 (or PIFs, phytochrome-interacting factors), which accumulates in etiolated seedlings and rapidly declines upon light exposure, inhibits TCP4 promoter-binding and prevents activation of SAUR16/50 in darkness. Our study reveals how an interplay between light responsive factors and developmental regulators leads to signal-dependent and tissue-specific regulation of gene expressions, which ultimately resulted in organ-specific light responses during de-etiolation.
2019-03-28 | GSE115584 | GEO
Project description:Etiolated Arabidopsis seedlings open their cotyledons and halt rapid elongation of hypocotyl when exposed to light (de-etiolation). Major light responsive components in this process have been identified and signaling pathways revealed, yet how the organ-specific light responses are achieved remains unknown. Here we report that a developmental regulator TCP4 (TEOSINTE BRANCHED1, CYCLOIDEA, and PCF) participates in photomorphogenesis and facilitates light-induced cotyledon-opening. We demonstrate that TCP4-like transcriptional factors, which predominantly express in cotyledons of both light and dark seedlings, activate SAUR16 and SAUR50 in response to light. Light repressor PIF3 (or PIFs, phytochrome-interacting factors), which accumulates in etiolated seedlings and rapidly declines upon light exposure, inhibits TCP4 promoter-binding and prevents activation of SAUR16/50 in darkness. Our study reveals how an interplay between light responsive factors and developmental regulators leads to signal-dependent and tissue-specific regulation of gene expressions, which ultimately resulted in organ-specific light responses during de-etiolation.
2019-03-28 | GSE115358 | GEO
Project description:To identify the genes regulated by PIF3 under higher temperatures in the endosperm and embryo, we performed an RNA-seq analysis. We compared the transcriptome of WT and pif3 endosperm from seeds imbibed for 24h and 48h at 30˚C, which is a time when WT and pif3 seeds have not yet germinated We also compared the transcriptome of WT and pif3 embryos, after removing their endosperm 4h upon seed imbibition, cultured for 24h and 48h at 30˚C, which are times when WT and pif3 hypocotyl length was comparable
2023-06-23 | GSE224926 | GEO
Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis. Four biological replicates data of PIF3-binding sites were collected by comparing the parallel ChIP samples from transgenic seedlings overexpressing Myc-epitope-tagged PIF3 (35S:PIF3-5xMyc, P3M) in pif3-3 null mutant background and the wild-type (WT) control.
2013-02-01 | E-GEOD-39215 | biostudies-arrayexpress