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28 results for “stop codon”
Stop-codon recoding in bacteriophages may regulate translation of lytic genes
<p><strong>This has some basic datasets for bacteriophages that use alternative genetic codes, and their close standard code relatives. </strong></p> <p>I have included the following:</p> <p>- Genomes for all alternatively coded phages and their relatives</p> <p>- Predicted proteins all alternatively coded phages and their relatives</p> <p>- A sheet with some basic information about these phages</p> <p>- Terminase treefile (Figure 2A) </p> <p>- Genomes for crAss-like phages used in the alternative code bias analysis (Figure 4)</p> <p>- Genomes for Agate phages used in the alternative code bias analysis (Figure 4) as well as the ANI analysis (Figure 3A)</p> <p>- Untrimmed lysogenic contigs for prophages (Like those shown in Figure 5)</p> <p> </p>
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.
Six Month Study of Gentamicin in Duchenne Muscular Dystrophy With Stop Codons
ClinicalTrials.gov study NCT00451074. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
Open the record for dataset details and reuse information.
Data from: Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster
Open the record for dataset details and reuse information.
Erythromycin Treatment for Readthrough of APC Gene Stop Codon Mutation in Familial Adenomatous Polyposis-minors' Adjusted Version
ClinicalTrials.gov study NCT02354560. IPD Sharing: Not stated. Countries: 0. Publications: 11.
Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 1]
GEO Series GSE138638. Homo sapiens. 26 samples. Type: Expression profiling by high throughput sequencing.
Mechanisms of stop codon readthrough mitigation reveal principles of GCN1 mediated translational quality control
GEO Series GSE214396. Caenorhabditis elegans; Homo sapiens. 66 samples. Type: Expression profiling by high throughput sequencing.
Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 3]
GEO Series GSE138640. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons
GEO Series GSE29714. Homo sapiens; Mus musculus. 11 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides
GEO Series GSE138643. Homo sapiens. 41 samples. Type: Expression profiling by high throughput sequencing.
Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 2]
GEO Series GSE138639. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 4]
GEO Series GSE138641. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages
<p><strong>Abstract</strong></p> <p>Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero- organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of Bacteria and Eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.</p> <p><strong>Repository Contents</strong></p> <p>00.description of MAGs.xlsx</p> <p>01.MAGs.zip<br> A collection of Asgardarchaeota genomes recovered in this study, i.e. The original contigs for each of the 71 MAGs (.fa files).</p> <p>02.MAG_genes.zip<br> A collection of Asgardarchaeota genome annotations (translated CDS / proteins) recovered in this study, i.e. The prokka output for each MAG (faa files)</p> <p>03.trees.zip<br> A collection of Newick tree files included in figures and supplementary figures in this study.</p> <p>04.Prokka_annotations.tar.gz (Added in 5 Aug, 2021)</p> <p>Prokka annotation files for the 71 Asgard genomes.</p>
Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
<p>Genomes and supplementary materials for Borges et al. 2021 (<strong>Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes) </strong></p>
Azithromycin Treatment for Readthrough of APC Gene Stop Codon Mutations in Familial Adenomatous Polyposis
ClinicalTrials.gov study NCT04454151. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Erythromycin Treatment for Readthrough of APC Gene Stop Codon Mutations in Familial Adenomatous Polyposis
ClinicalTrials.gov study NCT02175914. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae
GEO Series GSE162780. Saccharomyces cerevisiae W303. 16 samples. Type: Expression profiling by high throughput sequencing; Other.
Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 5]
GEO Series GSE138642. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
ENVIRONMENT MODULATES PROTEIN HETEROGENEITY THROUGH TRANSCRIPTIONAL AND TRANSLATIONAL STOP CODON RECODING
GEO Series GSE226936. Escherichia coli str. K-12 substr. MG1655. 13 samples. Type: Other.
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