Expression data from 10-days old dark grown Arabidopsis seedlings of wild type (Col-0), sps1 line and L17 line.
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE36581 | GEO | 2012/07/01
SECONDARY ACCESSION(S): PRJNA153745
REPOSITORIES: GEO
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Project description:In the present work, experiments were carried out to understand the molecular mechanism underlying phyA’ silencing.The EMS-mutagenesis of phyA’ line, L17, generated suppressor mutations that activate phyA’ locus. Detailed study of one suppressor line, sps1, indicated that methylation of specific CG site within the phyA coding region is critical for maintaining phyA’ silencing. In order to study the possible genomic targets of the putative SPS1 factor, microarray analysis using ATH1 genome array chip was done on sps1, L17 and Col-0. 9 samples in total were analyzed. Each line (WT, sps1, L17) were analyzed in triplicate.
2012-06-30 | E-GEOD-36581 | biostudies-arrayexpress
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2021-12-28 | GSE97670 | GEO
Project description:Background: Photomorphogenesis is repressed in the dark mainly by an E3 ubiquitin ligase complex comprising CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and four homologous proteins called SUPPRESSOR OF PHYA-105 (SPA1-SPA4) in Arabidopsis. This complex induces the ubiquitination and subsequent degradation of positively acting transcription factors (e.g., HY5, HFR1, PAP1 and others) in the dark to repress photomorphogenesis. Genomic evidence showed a large number of genes regulated by COP1 in the dark, of which many are direct targets of HY5. However, the genomic bases for the constitutive photomorphogenic phenotypes of spaQ remain unknown. Results: Here, we show that >7200 genes are differentially expressed in the spaQ background compared to wild type in the dark. Comparison of the RNAseq data between cop1 and spaQ revealed a large overlapping set of genes regulated by the COP1-SPA complex. In addition, many of the genes coordinately regulated by the COP1-SPA complex are also regulated by HY5 directly and indirectly. Moreover, a large number of genes (~2790) are predominantly regulated by SPA proteins and not by COP1, suggesting that SPA proteins might regulate many biological processes independently of COP1. Conclusions: Taken together, our data reveal that SPA proteins repress photomorphogenesis by controlling expression of a large number of genes in concert with COP1, likely through regulating the abundance of downstream transcription factors in light signaling pathways. Moreover, SPA proteins may function both in a COP1-dependent and –independent manner in regulating many biological processes and developmental pathways in Arabidopsis.
2018-11-05 | GSE112662 | GEO
Project description:Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment. Experiment Overall Design: We analysed the transcriptome profile in dark grown seedlings of the WT, and phyA phyB photoreceptor mutants. All seedlings have the same treatment (3d grown in complete darkness). We have two samples for each genotype that represent two replicates in each case.
2008-06-12 | E-GEOD-3002 | biostudies-arrayexpress
Project description:Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer light-independent, constitutive photomorphogenic (cop) phenotypes to transgenic plants (Su & Lagarias 2007 Plant Cell 19, 2124-2139). In the present study, comparative transcript profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole genome transcriptional profiles of dark-grown phyAphyB seedlings expressing the Y276H mutant of phyB (YHB) revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to, but quantitatively greater than those of wild-type seedlings grown under 15 or 50 umol m-2 m-1 continuous red light (Rc). Among the 2977 genes statistically significant two-fold (SSTF) regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-modulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the majority of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway(s) strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion. Experiment Overall Design: 16 samples: 9 are dark-grown samples (3 samples x 3 replicates), 6 are continuous red light (Rc)-grown samples (3 samples x 2 replicates). Experiment Overall Design: wild type grown in darkness, three independent biological replicates; Experiment Overall Design: phyA-201phyB-5 mutant grown in darkness, three independent biological replicates; Experiment Overall Design: YHB (AtPHYB-YH/phyA-201phyB-5) grown in darkness, two independent transgenic lines, three independent biological replicates; Experiment Overall Design: wild type grown under 15 umol m-2 s-1 Rc, two independent biological replicates; Experiment Overall Design: wild type grown under 50 umol m-2 s-1 Rc, two independent biological replicates; Experiment Overall Design: YHB (AtPHYB-YH/phyA-201phyB-5) grown under 50 umol m-2 s-1 Rc, one transgenic line used, two independent biological replicates
2008-11-15 | E-GEOD-8951 | biostudies-arrayexpress
Project description:Molecular genetic analyses support important roles for the AtGATA2 gene in brassinolide (BR) and light regulation of plant development. The overexpression line 6-9 of AtGATA2 suppresses the etiolated phenotype of Col-0 grown in the dark. Using microarray analysis, we identified genes differentially expressed in the AtGATA2ox transgenic line 6-9 compared to wild type, and genes differentially expressed in the AtGATA2ox transgenic line 6-9 compared to the bri1-116 single mutant. Consistent with the phenotypic similarity of bri1-116 and AtGATA2, overall about 93% of the co-regulated genes were affected in the same way by GATA2-ox and bri1-116.
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Project description:To address the molecular mechanisms underlying environmental adaptation, we studied a Drosophila melanogaster line, termed Dark-fly, which has been maintained in constant dark conditions for 57 years (1400 generations).The structural gene copy number changes between the dark fly and its control were assessed by aCGH array. The comparison showed that hundreds of genes in the dark fly bear duplications or deletions relative to the control line.
2012-01-31 | GSE35418 | GEO
Project description:This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. However, genetic studies have indicated the existence of more than one plastid signalling pathway. We have recently investigated a phytochrome A-mediated, far-red (FR) input pathway which blocks subsequent chloroplast development under white light (WL). This has also been found to inhibit the transcription of a small group of known nuclear-encoded plastidic proteins. Here we wish to establish how wide-reaching this FR-effect is on nuclear transcription, and will directly compare the affected gene groups with those identified from our earlier (and other's) studies with a Norflurazon treatment. In this array experiment we will compare RNA from seedlings grown in complete darkness (D) before transfer to WL, with that of seedlings preconditioned under a restricted wavelength FR source before exposure to WL. This comparison of FR- and Norflurazon-affected gene groupings will indicate whether the plastid signalling pathways are likely to be the same, overlapping or highly divergent. As well as wild-type seedlings, the gun1,gun5 mutant line is to be used as both these alleles are well established as alleviating the Norflurazon-inhibited pathway, but their affect on the FR-pathway is less clear. A single replicate of a phyA-null mutant line will also be included in order to differentiate between specific phytochromeA-mediated responses and other FR effects. It is envisaged that, in general, D- and FR-treated samples of the phyA mutant line will respond in the same way as each other and as the wild-type D-treated samples and, thus, the lack of a biological repeat in this case is not a major short-fall. The proposed experiment will consist of: wild-type: D-pretreated (x2 biological replicates) wild-type: FR-preconditioned (x2) gun1,gun5: D-pretreated (x2) gun1,gun5: FR-preconditioned (x2) phyA: D-pretreated (x1) phyA: FR-preconditioned (x1) Experiment Overall Design: Number of plants pooled:300 seedlings
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2011-11-09 | E-GEOD-25396 | biostudies-arrayexpress