Transcriptomic Analysis of the Zebrafish Prion Mutants Supports Conserved Cross-Species Function of the Cellular Prion Protein
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ABSTRACT:
PROVIDER: PRJNA690588 | ENA |
REPOSITORIES: ENA
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Project description:Wild-type zebrafish larvae and our prp1ua5003/ua5003;prp2ua5001/ua5001 mutant zebrafish larvae at 3 days post fertilisation were pooled into three biological replicates each of 50 larvae. Each replicate underwent paired end 100-125 and Illumina HiSeq2500 sequencing to a depth of 40 million reads, carried out by Otogenetics (Atlanta, GA). Samples were subsequently processed using the TopHat/Cufflinks bioinformatics pipeline. Alignments were mapped to the zebrafish reference genome, GRCz10. A small amount of wild-type reads were found to contaminate two of the pooled mutant samples and were not included in subsequent analysis. In total there were 1249 genes showing at least a 50% increase (745) in transcript abundance or 50% decrease (504) decrease in transcript abundance in wild-type zebrafish larvae compared to double mutant zebrafish larvae. Subsequent gene ontology analysis shows the biological process showing genes with the biggest decrease in transcript abundance was cell adhesion, and the process with the most genes showing an increase in transcript abundance was Oxidation/Reduction. Our study finds the processes affected by prion knockdown in zebrafish is remarkably similar to other studies in early mice embryos, suggesting a conserved function of the cellular prion protein in the early development of organisms.
2021-01-08 | GSE164423 | GEO
Project description: Not available
| S-EPMC8216189 | biostudies-literature
Project description:[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability.
2012-01-01 | GSE26612 | GEO
Project description:[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability.
2012-01-01 | GSE26613 | GEO
Project description:[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability.
2012-01-01 | GSE26611 | GEO
Project description:While prion infections have been extensively characterized in the laboratory mouse, little is known regarding the molecular responses to prions in other rodents. To explore these responses and make comparisons, we generated a prion disease in the laboratory rat by successive passage of mouse RML prions. Here we describe the accumulation of prions and associated pathology in the rat and describe the transcriptional impact throughout prion disease. Comparative transcriptional profiling between laboratory mice and rats suggests that similar molecular processes are unfolding in response to prion infection. At the level of individual transcripts, however, variability exists between mice and rats and many genes deregulated in mouse scrapie are not affected in rats. Notwithstanding these differences, many transcriptome responses are conserved between mice and rats infected with scrapie. Our findings highlight the usefulness of comparative approaches to understanding neurodegeneration and prion diseases in particular.
2015-09-01 | GSE63930 | GEO
Project description:[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability. Two groups (WT and ure2 mutant) consisted of 4 biological replicates in which a ure2 deleted strain sample was paired with the wild type strain sample. Each group included 1 reciprocally labeled sample.
2012-01-01 | E-GEOD-26611 | biostudies-arrayexpress
Project description:[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability. Two groups (Wild type and ure2 mutants) consisted of 4 biological replicates in which a Ure2 mutant sample was paired with the wild type strain BG14 sample. Each group included 1 reciprocally labeled sample.
2012-01-01 | E-GEOD-26612 | biostudies-arrayexpress
Project description:[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability. Two groups (WT and ure2 mutants) consisted of 4 biological replicates in which a ure2 deleted strain sample was paired with the wild type strain sample. Each group included 1 reciprocally labeled sample.
2012-01-01 | E-GEOD-26613 | biostudies-arrayexpress
Project description:While prion infections have been extensively characterized in the laboratory mouse, little is known regarding the molecular responses to prions in other rodents. To explore these responses and make comparisons, we generated a prion disease in the laboratory rat by successive passage of mouse RML prions. Here we describe the accumulation of prions and associated pathology in the rat and describe the transcriptional impact throughout prion disease. Comparative transcriptional profiling between laboratory mice and rats suggests that similar molecular processes are unfolding in response to prion infection. At the level of individual transcripts, however, variability exists between mice and rats and many genes deregulated in mouse scrapie are not affected in rats. Notwithstanding these differences, many transcriptome responses are conserved between mice and rats infected with scrapie. Our findings highlight the usefulness of comparative approaches to understanding neurodegeneration and prion diseases in particular. We Adapted RML Mouse Scrapie into Rats and measured the resulting gene expression changes in brain as a result of disease progression. Rats were infected by intracranial inoculation with prion isolates obtained by adaptation of mouse RML scrapie prions into rats. Brain samples were collected from third and fourth passage infected rats and age-matched controls at specified timepoints and gene expression profiles obtained. For each time point, 3 diseased and control brain samples were profiled.
2015-09-01 | E-GEOD-63930 | biostudies-arrayexpress