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Experiment: Genes co-regulated by the NMD factors UPF2 and SMG5
Experiment Description
NASCArrays Experiment Reference Number: NASCARRAYS-418
Eukaryotic cells have evolved a mechanism called nonsense mediated mRNA decay (NMD) that detects and degrades aberrant mRNAs that contain premature termination codons (PTCs). NMD has recently acquired broader importance as it has been found to regulate not only aberrant mRNAs but also a great diversity of transcripts, including wild type genes in mammals, Drosophila and yeast. Seven proteins are the core of the NMD complex: SMG1, SMG2 (UPF1), SMG3 (UPF2), SMG4 (UPF3), SMG5, SMG6 and SMG7. Plants have orthologues of most of these proteins. We have identified and characterized a number of alleles of UPF1, UPF3 and SMG5 and made 35S:UPF2 RNAi (upf2i) transgenic plants, all of which share some phenotypic characteristics. Transcriptome analysis of upf1 and upf3 mutants has identified a subset of genes coregulated by UPF1 and UPF3 and, therefore, by NMD (unpublished data). By doing further transcriptome analysis on smg5 mutants and upf2i plants we aim to build a more robust subset of NMD targets in Arabidopsis. RNA will be extracted from 17 day-old mutant, transgenic and wild type seedlings grown at 22-24 C under constant light.
About the ExperimenterName: | Dr Luis Arciga-Reyes |
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Head of Lab Name: | Prof Brendan Davies |
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Lab:
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Address: | Centre for Plant Sciences Institute of Integrative and Comparative Biology University of Leeds Leeds
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Postcode:
| LS2 9JT |
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Country:
| UK |
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All of the data available in this website/database is free, and you
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:
| strain_or_line_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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Quality Control Measures Taken:
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References:
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Slides in this Experiment
Hybridisation Set: Arciga-Reyes: Genes co-regulated by the NMD factors UPF2 and SMG5_genome
Slide: Arciga-Reyes_2-6_smg5-2-2_Rep2_ATH1 | | |
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Tissue:
| whole plant |
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Diseased:
| Normal |
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Other Information:
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Protocols for BioSource 1 |
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Slide: Arciga-Reyes_2-5_smg5-2-1_Rep1_ATH1 | | |
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Tissue:
| whole plant |
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Diseased:
| Normal |
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Other Information:
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Protocols for BioSource 1 |
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Slide: Arciga-Reyes_2-4_upf2i-2_Rep2_ATH1 | | |
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Tissue:
| whole plant |
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Diseased:
| Normal |
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Other Information:
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Protocols for BioSource 1 |
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Slide: Arciga-Reyes_2-3_upf2i-1_Rep1_ATH1 | | |
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Tissue:
| whole plant |
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Diseased:
| Normal |
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Other Information:
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Protocols for BioSource 1 |
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Slide: Arciga-Reyes_2-2_wildtype-2_Rep2_ATH1 | | |
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Tissue:
| whole plant |
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Diseased:
| Normal |
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Other Information:
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Protocols for BioSource 1 |
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Slide: Arciga-Reyes_2-1_wildtype-1_Rep1_ATH1 | | |
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Tissue:
| whole plant |
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Diseased:
| Normal |
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Other Information:
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Protocols for BioSource 1 |
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