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Experiment: Seedling transcriptome affected by Norflurazon-induced photobleaching of chloroplasts
Experiment Description
NASCArrays Experiment Reference Number: NASCARRAYS-51
Regulation of expression of genes encoding chloroplast components is critical to the autotrophic plant and never more so than in the cotyledons of the de-etiolating seedling. Many chloroplast proteins are nuclear-encoded and a retrograde signal from the chloroplasts (the Plastid Signal) modulates nuclear transcription. However, not all chloroplast-targeted genes are subject to this control and not all plastid-dependent nuclear genes are chloroplast-targeted. We therefore aim to provide the most comprehensive screen yet of which genes are affected by plastid-signalling. To specifically knock-out positive plastid signalling in light-grown cotyledons, the herbicide Norflurazon (NF) is supplied in the growth medium, causing a carotenoid deficiency that leaves the chloroplasts vulnerable to photobleaching. This blocks the expression of a subset of nuclear genes, such as Lhcb and HEMA1.
Two pairs of RNAs will directly compare the transcription in seedlings grown under continuous white light with and without NF. A third RNA will also be compared from a mutant that shows a degree of constitutive positive plastid signalling. These two mutants act synergistically to counteract the effect of NF on nuclear transcription. The gun1,gun5 double mutant maintains a significantly higher level of Lhcb and HEMA1 expression in the presence of photobeached chloroplasts than the NF-treated wild-type. This transcriptome set will therefore complement RNA1 (wild-type+NF) and indicate which of the genes identified from the RNA1/RNA2 comparison are subject to the particular gun1/gun5 plastid signalling pathway(s).
The growth of conditions of the seedlings (namely on MS medium supplemented with 1.5% sucrose, for 3 days under continuous WL following 2 days germination in darkness) has been chosen from the results of our own recent studies using Northern blotting techniques that show these conditions to maximise the respective NF and gun mutant effects on Lhcb and HEMA1 gene expression. This experiment is part one of a two-part study to compare the transcriptional output of this NF-affected pathway with that of a newly discovered FR-mediated pathway. A subsequent array experiment will assess the nuclear response as affected by this FR/ phyA-input pathway and the two sets of array data will be compared and contrasted.
Note:
Col-0 wild-type (NASC code N1092). gun1,gun5 double mutant(obtained from Enriquez Lopez-Juez, Royal Holloway, University of London.(Mochizuki et al. 2001 PNAS 98: 2053-2058). This line cannot be donated by us as it is the IP of Joanne Chory (SALK Institute, USA). Treatment = a herbicide (Norflurazon) application which leads to chloroplast photobleaching and hence down regulation of nuclear genes dependent on plastid signalling from intact chloroplasts.
About the ExperimenterName: | Dr Alex McCormac |
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Head of Lab Name: | Dr Matthew Terry |
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Lab:
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Institute:
| University of Southampton |
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Address: | School of Biological Sciences Division of Cell Sciences University of Southampton Bassett Crescent East Southampton
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Postcode:
| SO16 7PX |
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Country:
| UK |
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| Telephone Number:
| 023 80594297 |
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Fax Number:
| 023 80594319 |
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are free to do whatever you please with it. If you intend to publish
work based on any of this data, please acknowledge us, contact the
experimenter above, and either acknowledge them or use them as
co-authors in the work.
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| About this ExperimentExperiment Type:
| genetic_modification_design; compound_based_treatment_design |
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Number of Slides: | 6 |
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| Experimental Parameters:
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parameter | gene_knock_out |
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parameter | compound_based_treatment |
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Quality Control Measures Taken:
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no-plants-pooled | 100 seedlings |
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References:
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| Other Information:
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ArrayExpressAccession | E-NASC-40 |
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Slides in this Experiment
Hybridisation Set: McCormac_genome_Exp1_Rep1
Slide: McCormac_1-1_wildtype-NFtreated_Rep1_ATH1 | | |
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Tissue:
| whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). |
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Diseased:
| Normal |
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in vivo Treatment:
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treament | WT seedlings treated with the herbicide Norflurazon. |
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Other Information:
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Protocols for BioSource 1 |
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Slide: McCormac_1-2_wildtype-Contrl_Rep1_ATH1 | | |
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Tissue:
| whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). |
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Diseased:
| Normal |
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in vivo Treatment:
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treament | WT seedlings which had not been treated with Norflurazon and therefore are the control sample. |
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Other Information:
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Protocols for BioSource 1 |
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Slide: McCormac_1-3_mutant-NFtreated_Rep1_ATH1 | | |
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Tissue:
| whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). |
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Diseased:
| Normal |
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in vivo Treatment:
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treament | Seedlings of a double mutant line gun1,gun5 which had been treated with Norflurazon. |
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Other Information:
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Protocols for BioSource 1 |
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Hybridisation Set: McCormac_genome_Exp1_Rep2
Slide: McCormac_1-4_wildtype-NFtreated_Rep2_ATH1 | | |
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Tissue:
| whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). |
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Diseased:
| Normal |
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in vivo Treatment:
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treament | Seedlings of WT which had been treated with Norflurazon. |
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Other Information:
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Protocols for BioSource 1 |
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Slide: McCormac_1-5_wildtype-Contrl_Rep2_ATH1 | | |
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Tissue:
| whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). |
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Diseased:
| Normal |
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in vivo Treatment:
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treament | Seedlings of WT which had not been treated with Norflurazon. |
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Other Information:
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Protocols for BioSource 1 |
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Slide: McCormac_1-6_mutant-NFtreated_Rep2_ATH1 | | |
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Tissue:
| whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). |
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Diseased:
| Normal |
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in vivo Treatment:
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treament | Seedlings of a double mutant line gun1,gun5 treated with Norflurazon. |
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Other Information:
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Protocols for BioSource 1 |
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Problems? Comments? Suggestions? Contact the Affymetrix Team