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MetabolomicsEpigenetic coordination of transcriptional and translational programs in hypoxia

Adaptation to cellular stresses entails an incompletely understood coordination of transcriptional and post-transcriptional gene regulation. Here, we quantified hypoxia-dependent transcriptomes, epigenomes and translatomes in T47D breast cancer cells and H9 human embryonic stem cells. This reveal...

2025-06-09 | MTBLS12086 | MetaboLights
TranscriptomicsDeep sequencing reveals mRNA recruitment in translation initiation
We studied the initiation signals located in the translational initiation region (TIR) and identified the role for recognition of the initiation signals in each individual stage during formation of the initiation complexes. Sequencing the randomized mRNA libraries captured by translation initiation ...
ORGANISM(S): Escherichia coli 
2016-07-27 | E-GEOD-69782 | biostudies-arrayexpress
TranscriptomicsCoding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
It is well established that small noncoding RNAs (sRNAs) of bacteria recognize the 5â?? regions of target mRNAs, generally at the ribosome binding site. Until now, the translated coding sequence (CDS) of mRNA appeared to be refractory to sRNA interactions. We have discovered that Salmonella MicC RNA...
ORGANISM(S): Salmonella enterica 
2010-05-16 | E-GEOD-16540 | biostudies-arrayexpress
TranscriptomicsThe C-Terminal Domain of RNA Polymerase II is Modified by Site-Specific Methylation
The Carboxy-terminal domain (CTD) of RNA Polymerase II (RNAPII) in mammals undergoes extensive post-translational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the transcriptional co-...
ORGANISM(S): Homo sapiens 
2011-04-01 | E-GEOD-27315 | biostudies-arrayexpress
TranscriptomicsThe translational landscape of mTOR signaling steers cancer initiation and metastasis
The mammalian target of rapamycin (mTOR) kinase is a master regulator of protein synthesis that couples nutrient sensing to cell growth and cancer. However, the downstream translationally regulated nodes of gene expression that may direct cancer development are poorly characterized. Employing riboso...
ORGANISM(S): Homo sapiens 
2012-02-28 | E-GEOD-35469 | biostudies-arrayexpress
TranscriptomicsRibosome profiling data obtained from HEK293T cells 30 minutes after treatment with arsenite to a final concentration of 40 M-BM-5M
Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eIF2. However, the persistent translation of certain mRNAs is required for deployment of an adequate s...
ORGANISM(S): Homo sapiens 
2015-01-27 | E-GEOD-55195 | biostudies-arrayexpress
ProteomicsPositional proteomics reveals differences in N-terminal proteoform stability.
To understand the impact of alternative translation initiation on a proteome, we performed the first large-scale study of protein turnover rates in which we distinguish between N-terminal proteoforms pointing to translation initiation events. Using pulsed SILAC combined with N-terminal COFRADIC we m...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2019-03-13 | MSV000083565 | MassIVE
TranscriptomicsTranslational control of cell viability downstreams of eIF4E, using polyribosome RNA
Aberrant activation of the translation initiation machinery is a common property of malignant cells, and is essential for breast carcinoma cells to manifest a malignant phenotype. How does sustained activation of the rate limiting step in protein synthesis so fundamentally alter a cell? In this repo...
ORGANISM(S): Mus musculus 
2010-06-10 | E-GEOD-2094 | biostudies-arrayexpress
TranscriptomicsRibosome profiling of early zebrafish embryos -- miRNA-mediated regulation during embryogenesis causes translational repression before mRNA decay
MicroRNAs regulate gene expression through deadenylation, repression and mRNA decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature...
ORGANISM(S): Danio rerio 
2012-03-15 | E-GEOD-34743 | biostudies-arrayexpress
TranscriptomicsSilva_UMinho_Initial translational response of Saccharomyces cerevisiae to acetic acid-induced apoptosis
The initial translational response of the yeast Saccharomyces cerevisiae in response to acetic acid-induced apoptosis was investigated by microarray profiling of mRNAs contained in polysomal fractions obtained upon 0 (used as control), 15 and 30 minutes of acetic acid treatment. The mRNA fraction th...
ORGANISM(S): Saccharomyces cerevisiae 
2013-02-24 | E-MEXP-3570 | biostudies-arrayexpress
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