Whole-genome transcriptome profiling of dark-grown cryptochrome 2 over-expressing indica rice seedlings
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ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Indica Group
PROVIDER: GSE200963 | GEO | 2025/04/02
REPOSITORIES: GEO
Similar Datasets
Project description:Whole-genome transcriptome profiling of dark-grown cryptochrome 2 over-expressing indica rice seedlings
| PRJNA827771 | ENA
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:The transition between growth in the dark (skotomorphogenesis) and growth in the light (photomorphogenesis) is one of the most critical in plant development. Here the newly identified mutant dez is photomorphogenic in the dark and is strongly enhanced in high Zn. dez displays a shortened hypocotyl, expanded cotyledons, an elongated root and differentiated plastids in the dark contrast to wild-type seedlings that are typically skotomorphogenic, with a long hypocotyl and unexpanded cotyledons protected by an apical hook, and undifferentiated etioplasts We used microarrays to identify transcripts regulated in dez in high-Zn relative to wild-type in high-Zn, and dez in high-Zn relative to dez in control conditions.
2017-11-02 | GSE96589 | GEO
Project description:Photomorphogenesis is a critical developmental process bridging light-regulated transcriptional reprogramming with morphological changes in organisms. Strikingly, the chromatin-based transcriptional control of photomorphogenesis remains poorly understood. Here, we show that both light-induced genes and dark-induced genes were affected in the atino80 mutant. Genome-wide occupancy of the H2A.Z histone variant and levels of histone H3 were reduced in atino80.
2020-11-30 | GSE150114 | GEO
Project description:Circadian rhythms are daily oscillations in metabolism and physiology and are generated by the circadian clock. In fruit fly Drosophila, the circadian clock is generated by a transcription-translation feedback loop in which the positive arm components Clock and Cycle activate the expression of the Period and Timeless genes of negative arm, as well as other circadian clock-regulated genes. After being retained in the cytoplasm, the Period and Timeless proteins then migrate to the nucleus to inhibit the Clock/Cycle transactivity by protein-protein interactions (PPIs). The endogenous circadian clock is synchronized with the geological (solar) clock via photoreceptors. Drosophila Cryptochrome protein functions as a circadian photoreceptor. In the early morning, exposure of Cryptochrome to light causes a conformational change in it which results in the formation of new PPIs. Light-activated Cryptochrome interacts with the core clock protein Timeless and the E3 ubiquitin ligase-substrate adaptor protein Jetlag, which results in the ubiquitylation of Timeless by Jetlag-E3 ligase complex and then degradation of Timeless within minutes by proteasome system. Rapid degradation of Timeless and then its partner protein Period, because of its instability in the absence of Timeless, relieves the inhibition on the Clock/Cycle transcription factors suddenly. Therefore, Clock/Cycle-driven expression of circadian clock-regulated genes are induced again, which is the restart of the circadian oscillation or the resetting of the clock. Following Timeless degradation, Cryptochrome is also degraded so the photoreceptor mechanism does not start a new resetting signal until all the required factors are re-synthesized in a circadian manner. Light-dependent degradation of Drosophila Cryptochrome can be observed in Drosophila S2 cell line in culture. In this project, we aimed at finding the interactome of Cryptochrome protein in Drosophila S2 cell line under light and in the dark using proximity labeling method. Because of the fast kinetics of Cryptochrome degradation, we chose the enzymes that can saturate in less than one hour. TurboID (TID) and APEX2 enzymes label proteins with biotin in the proximity even though they work with different mechanisms. They were fused to Cryptochrome protein, and proximity labeling was performed in the dark or under light. We have identified novel light-dependent or -independent interactors of Drosophila Cryptochrome and confirmed some of them using classical coimmunoprecipitation technique.
2024-02-05 | PXD038052 | Pride
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. Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses
2005-09-04 | GSE3038 | 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. Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses
2005-09-04 | GSE3002 | GEO
Project description:To cover a comprehensive understanding of the complex regulatory networks controlling cryptochrome 1(CRY1)-mediated photomorphogenic response in Brassica, a genome-wide differential expression analysis was performed for the 5-day-old T3 BnCRY1-OE and wild type seedlings grown under white light (100 µmol m–2s–1) on 0.8% agar-gelled MS (Murashige and Skoog) medium containing 2% sucrose. Total RNA was extracted and cleaned up with the Qiagen RNeasy Plant Mini Prep Kit as per the manufacturer’s instructions (Qiagen). The yield and RNA purity were determined spectrophotometrically. Integrity of the RNA was checked using Agilent Bioanalyzer (Agilent Technologies, USA). 500 ng RNA of each of the sample was processed for microarray analysis according to Agilent protocol. Keywords: Cryptochrome, Brassica, photomorphogenesis, differential expression.
2014-01-10 | GSE26797 | GEO
Project description:To cover a comprehensive understanding of the complex regulatory networks controlling cryptochrome 1(CRY1)-mediated photomorphogenic response in Brassica, a genome-wide differential expression analysis was performed for the 5-day-old T3 BnCRY1-OE and wild type seedlings grown under white light (100 M-BM-5mol mM-bM-^@M-^S2sM-bM-^@M-^S1) on 0.8% agar-gelled MS (Murashige and Skoog) medium containing 2% sucrose. Total RNA was extracted and cleaned up with the Qiagen RNeasy Plant Mini Prep Kit as per the manufacturerM-bM-^@M-^Ys instructions (Qiagen). The yield and RNA purity were determined spectrophotometrically. Integrity of the RNA was checked using Agilent Bioanalyzer (Agilent Technologies, USA). 500 ng RNA of each of the sample was processed for microarray analysis according to Agilent protocol. Keywords: Cryptochrome, Brassica, photomorphogenesis, differential expression. Agilent one-color experiment, Organism: B. napus (Brassica) Oligo Microarray, Agilent-022520 B. napus (Brassica) Oligo Microarray 4x44K, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
2014-01-10 | E-GEOD-26797 | biostudies-arrayexpress
Project description:Arabidopsis seed lings were grown in dark for 10 days on MS media and treated with DMSO (control) or 1 µM of BA for either 45 or 120 minutes to look for changes in genes profiles
2013-03-28 | E-MTAB-1597 | biostudies-arrayexpress