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MetabolomicsRibosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis

Translation fidelity is the limiting factor in the accuracy of gene expression. With an estimated frequency of 10-4, errors in mRNA decoding occur in a mostly stochastic manner. Little is known about the response of higher eukaryotes to chronic loss of ribosomal accuracy as per an increase in the...

2019-09-17 | MTBLS106 | MetaboLights
MetabolomicsBiosynthesis of Isonitrile Lipopeptides by Conserved Non-ribosomal Peptide Synthetase Gene Clusters in Actinobacteria
A putative lipopeptide biosynthetic gene cluster is conserved in many species of Actinobacteria, including Mycobacterium tuberculosis and Mycobacterium marinum, but the specific function of the encoding proteins has been elusive. Using both in vivo heterologous reconstitution and in vitro biochemica...
2017-07-18 | MTBLS454 | MetaboLights
TranscriptomicsRibosomal Protein Gene Deletions in Diamond Blackfan Anemia
Diamond Blackfan anemia is a congenital bone marrow failure syndrome characterized by hypoproliferative anemia, often with associated physical abnormalities. Perturbations of the ribosome appear critically important to the development of DBA, as alterations in 9 different ribosomal protein genes ha...
ORGANISM(S): Homo sapiens 
2012-01-15 | E-GEOD-31575 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of S. cerevisiae ribosomal protein knockouts
Duplicated genes escape gene loss by conferring a dosage benefit or evolving diverged functions. The yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins. Prior studies have suggested that these duplicated proteins are functionally redundant and affect cellular...
ORGANISM(S): Saccharomyces cerevisiae 
2008-06-16 | E-GEOD-8761 | biostudies-arrayexpress
TranscriptomicsGenome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was tr...
ORGANISM(S): Homo sapiens 
2012-08-08 | E-GEOD-39561 | biostudies-arrayexpress
GenomicsTwo distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription
In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, b...
ORGANISM(S): Saccharomyces cerevisiae 
2014-10-01 | E-GEOD-61596 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse embryonic stem cells transfected with miR-10a or miR-10a-MUT shows that miR-10a interacts with the 5 prime untranslated region of mRNAs encoding ribosomal proteins and enhances their translation
MicroRNAs (miRNAs) are small RNAs that function as post-transcriptional regulators of gene expression. miRNAs affect a variety of signaling pathways and impaired miRNA regulation may contribute to the development of cancer and other diseases. We show that miRNA miR-10a interacts with the 5' untransl...
ORGANISM(S): Mus musculus 
2008-11-08 | E-MEXP-1375 | biostudies-arrayexpress
TranscriptomicssiRNA knockdown of ribosomal protein gene RPL19 abrogates the aggressive phenotype of human prostate cancer
Ribosomal protein RPL19 is an integral component of eukaryotic ribosomes and universally involved in protein synthesis. Although consistently stableM-BM- in normal cells, RPL19 transcription is relatively elevated in prostate cancer. Using siRNA, we inhibited RPL19 transcription and demonstrated th...
ORGANISM(S): Homo sapiens 
2011-12-08 | E-GEOD-26774 | biostudies-arrayexpress
GenomicsDeconvolution ChIP-seq profiling of UBF and RPA194 in K562 cells to identify analogous enhancer structures on mouse and human ribosomal RNA genes
The combination of Chromatin Immunoprecipitation and Massively Parallel Sequencing, or ChIP-Seq, has greatly advanced our genome-wide understanding of chromatin and enhancer structures. However, its resolution at any given genetic locus is limited by several factors. In applying ChIP-Seq to study th...
ORGANISM(S): Homo sapiens 
2017-12-31 | E-MTAB-6032 | biostudies-arrayexpress
TranscriptomicsNew partners in regulation of gene expression: the Enhancer of Trithorax and Polycomb Corto interacts with methylated Ribosomal Protein L12 via its chromodomain.
Chromodomains are found in many regulators of chromatin structure. Most of them recognize methylated histones. Here, we investigate the role of the Corto chromodomain. This Drosophila melanogaster Enhancer of Polycomb and Trithorax is involved in both silencing and activation of gene expression. Ove...
ORGANISM(S): Drosophila melanogaster 
2012-09-05 | E-GEOD-38435 | biostudies-arrayexpress
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