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Comparison analysis of rice and Arabidopsis photomorphogenesis

ABSTRACT: 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

ORGANISM(S): Arabidopsis thaliana Oryza sativa

PROVIDER: GSE2360 | GEO | 2005/05/02

SECONDARY ACCESSION(S): PRJNA91207

REPOSITORIES: GEO

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Comparison analysis of rice and Arabidopsis photomorphogenesis

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

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Project description:Light, an important environmental factor regulates most of plant physiology and development. In the photomorphogenic stage, light globally enhances translation status in de-etiolating Arabidopsis seedlings. More than 1500 genes showed increased translation but not transcription in this developmental process. This implies these mRNAs are translationally repressed in dark-grown seedlings. Through transcriptome and translatome comparisons, we revealed that p-bodies attenuate the translation of mRNAs in the etiolated seedlings. We found hundreds of mRNAs accumulated and also increased translation for thousands of genes in dark-grown dcp5-1, including genes known to regulate the transition from skotomorphogenesis to photomorphogenesis. Our data reports p-bodies regulate both RNA stability and attenuation of translation for specific mRNAs in the dark.

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Arabidopsis De-etiolated 1 Represses Photomorphogenesis by Positively Regulating Phytochrome Interacting Factors in the Dark

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.

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Translational control: a new dimension in the regulation of Arabidopsis photomorphogenesis

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.

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Project description:Intron retention (IR) is the most common alternative splicing (AS) event in Arabidopsis. Increasing studies have demonstrated a major role of IR in gene expression regulation. The impacts of IR on plant growth and development, and response to environments remains under explored. Here, we found that IR functions directly in gene expression regulation on a genome-wide scale through detainment of the intron-retained transcripts (IRTs) in the nucleus. Through this mechanism, nuclear-retained IRTs can be kept away from translation. COP1-dependent light modulation of IRTs of light signaling genes, such as PIF4, RVE1, and ABA3, contribute to seedling morphological development in responding to changing light conditions. Further, light-induced IR changes are under the control of the spliceosome, and in part through COP1-dependent ubiquitination and degradation of DCS1, a plant-specific spliceosomal component. Our data suggests that light regulates the activity of the spliceosome and the consequent IRTs nucleus detainment to modulate photomorphogenesis through COP1.

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