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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
GenomicsAnalysis of HIF and mTOR dependent translational regulation of mRNAs resolved by their transcription start sites, using HP5 technology
Analysis of HIF and mTOR dependent translational regulation of mRNAs resolved by their transcription start sites, using HP5 technology
PRJEB46188 | ENA
UnknownReannotation of translational start sites in the genome of Mycobacterium tuberculosis.
Not available
S-EPMC3582765 | biostudies-literature
UnknownPervasive isoform-specific translational regulation via alternative transcription start sites in mammals.
Not available
S-EPMC4965872 | biostudies-literature
TranscriptomicsIn vivo and transcriptome-wide identification of RNA-binding protein target sites [RNA-Seq]
Animal mRNAs are regulated by hundreds of RNA binding proteins (RBPs). The identification of RBP targets is crucial for understanding their function. A recent method, PAR-CLIP, uses photoreactive nucleosides to crosslink RBPs to target RNAs in cells prior to immunoprecipitation. Here, we establish i...
ORGANISM(S): Caenorhabditis elegans 
2011-12-09 | E-GEOD-33573 | biostudies-arrayexpress
ProteomicsNuclear release of eIF1 globally increases stringency of start codon selection to preserve mitotic arrest physiology
Regulated start codon selection has the potential to reshape the proteome through the differential production of uORFs, canonical proteins, and alternative translational isoforms. However, conditions under which start codon selection is altered remain poorly defined. Here, using transcriptome-wide t...
ORGANISM(S): Homo sapiens (Human) 
2024-10-07 | PXD054183 | Pride
Translation Ribosomes Mitosis Cell cycle 
ProteomicsNuclear release of eIF1 globally increases stringency of start codon selection to preserve mitotic arrest physiology
Regulated start codon selection has the potential to reshape the proteome through the differential production of uORFs, canonical proteins, and alternative translational isoforms. However, conditions under which start codon selection is altered remain poorly defined. Here, using transcriptome-wide t...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD054179 | Pride
Translation Ribosomes Mitosis Cell cycle 
UnknownExperimental determination of translational start sites resolves uncertainties in genomic open reading frame predictions - application to Mycobacterium tuberculosis.
Not available
S-EPMC2897130 | biostudies-literature
TranscriptomicsThe effect of Heterogeneous Transcription Start Sites (TSS) on the Translatome: Implications for the Mammalian Cellular Phenotype.
Sequencing of total RNA and polysomal RNA of two cell lines, MCF7 (tumoral) and MCF10A (non-tumoral) Polysomal and total RNA was prepared from biological triplicates from the two cell lines. For each biological triplicate sub-confluent cell monolyers were lysed to produce cytoplasmic extracts. Half...
ORGANISM(S): Homo sapiens 
2015-11-24 | E-GEOD-74232 | biostudies-arrayexpress
TranscriptomicsAnalysis of HIF and mTOR dependent translational regulation of mRNAs resolved by their transcription start sites, using HP5 technology
Changes in translational efficiency of mRNAs consequent on alteration of HIF and/or mTOR pathway activity in VHL-defective kidney cancer cell were analysed. High-resolution polysome profiling followed by sequencing of the 5′ ends of mRNAs (HP5) was used to measure translational efficiency of mRNAs r...
ORGANISM(S): Homo sapiens 
2022-05-14 | E-MTAB-10689 | biostudies-arrayexpress
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