Comparison analysis of rice and Arabidopsis photomorphogenesis
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ABSTRACT:
PROVIDER: PRJNA91207 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Long oligonucleotide microarrays were used for the study of expression profile changes during seedling photomorphogenesis in rice and in Arabidopsis. Different light quality treatments were applied to seedlings. To dissect organ-specific light effects, we further profiled shoot and root organs in both species. Keywords = rice Keywords = Arabidopsis Keywords = photomorphogenesis Keywords: ordered
2005-05-02 | GSE2360 | GEO
Project description:Long oligonucleotide microarrays were used for the study of expression profile changes during seedling photomorphogenesis in rice and in Arabidopsis. Different light quality treatments were applied to seedlings. To dissect organ-specific light effects, we further profiled shoot and root organs in both species. Keywords = rice Keywords = Arabidopsis Keywords = photomorphogenesis Keywords: ordered
2010-06-10 | E-GEOD-2360 | biostudies-arrayexpress
Project description:The environmental “light” plays a vital role in regulating the plant growth and development. Transcriptomic profilings were widely used to examine how light regulates the changes of mRNA populations at a genome-wide scale. However, it remains unclear if translational regulation represents a new dimension of gene expression regulation in response to the light signal. Through a transcriptomic comparison of steady-state and polysome-bound mRNAs, we revealed an increased translational efficiency in de-etiolating Arabidopsis seedlings. Over 3,500 genes are subjected to translational regulation whereas only about 770 genes have increased mRNA abundances in response to the light signal. This result suggests a stronger impact of translational control over transcriptomic changes during photomorphogenesis. Genes encoding ribosomal protein are preferentially regulated at the translational level, possibly contributing to the enhancement of translation efficiency as observed. We also uncovered mRNAs regulated at the translational level share characteristics of longer half-lives and shorter cDNA length. The presence of a cis-element, TAGGGTTT, in the 5’untranslated region of a transcript renders its translational regulation by light signals. Taken together, our study revealed a previously neglected aspect of gene expression regulation during Arabidopsis photomorphogenesis. The identities and molecular signatures associated with mRNAs regulated at the translational level also offer new directions to perform mechanistic studies of light-trigged translational enhancement in Arabidopsis.
2012-07-11 | GSE29657 | GEO
Project description:Arabidopsis seedlings undergo photomorphogenic development even in darkness when the function of De-etiolated 1 (DET1), a repressor of photomorphogenesis, is disrupted. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genomic analysis also revealed that DET1 may control the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs.
2015-03-19 | GSE60835 | GEO
Project description:Plant photomorphogenesis is a light-induced developmental switch combining rapid enrichment in RNA Polymerase II activity and massive gene expression reprogramming. Yet, all former transcriptome analyses of this transition detected no average tendency toward gene upregulation. By applying a spike-in RNA-seq approach, we solved this conundrum and reconciled transcriptome dynamics with epigenomic and cytogenetic data. This further unveiled that Arabidopsis cotyledon photomorphogenesis involves a ~2-fold expansion of the transcriptome, a trend that we reproducibly observed in datasets from independent laboratories upon normalization using a set of stable genes defined ad hoc. This new standpoint enabled us to reinterpret light-mediated gene regulatory paths and unveil a quasi-exclusive positive effect of light-induced transcription factors on target genes. Collectively, this study reveals how environmentally controlled variations of the transcriptional regime can functionally impact plant genome expression. It further establishes a framework for investigating the mechanisms of global genome regulation in these organisms.
2025-10-16 | GSE191042 | GEO
Project description:Plant photomorphogenesis is a light-induced developmental switch combining rapid enrichment in RNA Polymerase II activity and massive gene expression reprogramming. Yet, all former transcriptome analyses of this transition detected no average tendency toward gene upregulation. By applying a spike-in RNA-seq approach, we solved this conundrum and reconciled transcriptome dynamics with epigenomic and cytogenetic data. This further unveiled that Arabidopsis cotyledon photomorphogenesis involves a ~2-fold expansion of the transcriptome, a trend that we reproducibly observed in datasets from independent laboratories upon normalization using a set of stable genes defined ad hoc. This new standpoint enabled us to reinterpret light-mediated gene regulatory paths and unveil a quasi-exclusive positive effect of light-induced transcription factors on target genes. Collectively, this study reveals how environmentally controlled variations of the transcriptional regime can functionally impact plant genome expression. It further establishes a framework for investigating the mechanisms of global genome regulation in these organisms.
2025-10-16 | GSE275426 | GEO
Project description:The environmental “light” plays a vital role in regulating the plant growth and development. Transcriptomic profilings were widely used to examine how light regulates the changes of mRNA populations at a genome-wide scale. However, it remains unclear if translational regulation represents a new dimension of gene expression regulation in response to the light signal. Through a transcriptomic comparison of steady-state and polysome-bound mRNAs, we revealed an increased translational efficiency in de-etiolating Arabidopsis seedlings. Over 3,500 genes are subjected to translational regulation whereas only about 770 genes have increased mRNA abundances in response to the light signal. This result suggests a stronger impact of translational control over transcriptomic changes during photomorphogenesis. Genes encoding ribosomal protein are preferentially regulated at the translational level, possibly contributing to the enhancement of translation efficiency as observed. We also uncovered mRNAs regulated at the translational level share characteristics of longer half-lives and shorter cDNA length. The presence of a cis-element, TAGGGTTT, in the 5’untranslated region of a transcript renders its translational regulation by light signals. Taken together, our study revealed a previously neglected aspect of gene expression regulation during Arabidopsis photomorphogenesis. The identities and molecular signatures associated with mRNAs regulated at the translational level also offer new directions to perform mechanistic studies of light-trigged translational enhancement in Arabidopsis. Three biological replicates for 4-d-old etiolated seedlings with or without 0. 5 h or 4 h of white-light treatment.
2012-07-10 | E-GEOD-29657 | biostudies-arrayexpress
Project description:Light-induced phosphorylation is necessary and essential for the degradation of phytochrome-interacting factors (PIFs), the central repressors of photomorphogenesis. Although the kinases responsible for PIF phosphorylation have been extensively studied, the phosphatases underlying PIF dephosphorylation are largely unknown. Here, we real that mutation of FyPP1 and FyPP3, two catalytic subunits of PP6 phosphatases, promoted photomorphogenesis of seedlings in the dark. PP6 and PIFs functioned synergistically to repress photomorphogenesis. FyPP1 and FyPP3 directly interacted with and dephosphorylated PIF3 and PIF4. The light-induced degradation of PIF4 and the PIF transcriptional activities were dependent on PP6 activity. These data demonstrate that PP6 phosphatases repress photomorphogenesis through regulation of PIF phosphorylation, protein stability and transcriptional activity.
2019-09-04 | GSE128498 | GEO
Project description:Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis
| PRJNA789498 | ENA
Project description:Arabidopsis seedlings undergo photomorphogenic development even in darkness when the function of De-etiolated 1 (DET1), a repressor of photomorphogenesis, is disrupted. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genomic analysis also revealed that DET1 may control the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs. Total of twelve samples, two treatments and three genotypes, and each have three replicates.
2015-03-19 | E-GEOD-60835 | biostudies-arrayexpress