Project description:Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830). 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.
Project description:Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830). 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.
Project description:Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830). 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.
Project description:Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830). 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.
Project description:Heat stress is one of the most prominent and deleterious environmental threads affecting plant growth and development. Upon high temperatures, plants launch specialized gene expression programs that promote stress protection and survival. These programs involve global and specific changes at the transcriptional and translational levels. However the coordination of these processes and their specific role in the establishment of the heat stress response is not fully elucidated. In this report, we have carried out a genome-wide analysis to simultaneously monitor the individual changes in the transcriptional and translational mRNA levels of Arabidopsis thaliana seedlings after the exposure to a heat shock stress. Our results demonstrated that, superimposed to transcription, translation exerts a wide but dual regulation of gene expression. For the majority of mRNAs, translation is severely repressed, causing a decreased of 50% of the association of the bulk of mRNAs to polysomes. However, some relevant mRNAs involved in different aspects of homeostasis maintenance follow a differential pattern of translation. Analysis of the sequence of the differentially translated mRNAs unravels that some features, like the 5´UTR G+C content and the cDNA length, may take part in the discrimination mechanisms for mRNA polysome loading. Among the differential translated genes stand out master regulators of the stress response, highlighting the main role of translation in the early establishment of physiological response of plants to elevated temperatures. In total 8 ATH1 Affymetrix GeneChips were hybridized with all combinations of two factors: total mRNA/polysome-bound-RNA; 22ºC/38ºC. Two biological replicates per sample type were performed.
Project description:Transcriptional profiling of rainbow trout liver and muscle cells comparing small fish with large fish within a population of neomale offspring. Small vs. large-fish liver and muscle cells from neomale offspring. Biological replicates: 4 small replicates, 4 large replicates.
Project description:Translational control is a key regulatory step in the expression of genes as proteins. In plant cells, translational efficiency of mRNAs differs on different mRNA species, and the efficiency dynamically changes in various conditions. To gain a global view of translational control throughout growth and development, we performed genome-wide analysis of polysome association of mRNA over growth and leaf development in Arabidopsis thaliana by applying the mRNAs in polysome to DNA microarray. This analysis revealed that the degree of polysome association of mRNA had different levels depending on mRNA species, and the polysome association changed greatly throughout growth and development for each. In the growth stage, transcripts showed varying changes in polysome association from strongly depressed to unchanged degree, with the majority of transcripts showing dissociation from ribosomes. On the other hand, during leaf development, the polysome association of transcripts showed a normal distribution from repressed to activated mRNAs when comparing between expanding and expanded leaves. In addition, functional category analysis of the microarray data suggested that translational control has a physiological significance in plant growth and development process, especially in category of signaling and protein synthesis. Besides this, we compared changes in polysome association of mRNAs between various conditions and characterized translational controls in each. This result suggested that mRNAs translation might be controlled by complicated mechanisms for response to each condition. Our results highlight the importance of dynamic changes in mRNA translation in plant development and growth. Experiment using two-flactionated mRNA in 4 developmental stages, Polysomal mRNA vs. total mRNA. Biological replicates: 2. Compared 2DAG and 21DAG, or Young leaves and Mature leaves.
Project description:We investigated genome-wide changes in mRNA translation in Arabidopsis thaliana T87 suspension cell cultures which thought to be one of the host materials for bioreactor. Global translational repression was observed in cells of 8 day after inoculation that is thought to be stressful condition by the nutrient deficiency and hypoxia. This suggested the negative effect of the global translational repression on transgene expression. On the other hand, previous study using heat stress showed that some mRNAs were actively translated under such stressful condition, suggesting the existence of mRNA that were actively translated in cells of 8 day after inoculations. To identify mRNAs that escape global translational repression on 8 day and its cis-elements would be the 1st step to make the system for higher transgene expression by the escaping global translational repression. To this end, we subjected polysomal RNA and non-polysomal RNA from sucrose gradient fractionated cell lysates to the co-hybridization on Agilent Arabidopsis 4 Oligo Microarrays. The ratio of signal intensities (polysomal RNA: total RNA) was used as an indicator of the translation state for each transcript. Experiment using two-fractionated mRNA, Polysomal mRNA vs. total mRNA. Biological replicates: 1
Project description:Transcriptional profiling of rainbow trout liver cells comparing liver cells from small fish with liver cells from large fish at two time periods. Two-condition experiment, small vs. large-fish liver cells. Sept. and Dec. spawning fish. Biological replicates: 4 small replicates, 4 large replicates for each time period.
Project description:Transcriptional profiling of rainbow trout muscle cells comparing muscle cells from small fish with muscle cells from large fish at two time periods. Two-condition experiment, small vs. large-fish muscle cells. Sept. and Dec. spawning fish. Biological replicates: 4 small replicates, 4 large replicates for each time period.