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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
ProteomicsGonatopoulos-Pournatzis _eIF4Gmicroexon_P105_Lumos
A This dataset consists of 24 raw MS files, acquired on Orbitrap Fusion Lumos Tribrid mass spectrometer operated in Data Dependent Acquisition mode. B Mouse samples were generated by Thomas Gonatopoulos-Pournatzis. Proteomics sample preparation and mass spectrometric acquisition was performed by Sh...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2019-12-04 | MSV000084658 | MassIVE
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
ProteomicsSystemic remodeling of translation efficiencies on oxygen stimulus.
Protein concentrations evolve under greater evolutionary constraint than mRNA levels. In addition, translation efficiency of mRNA populations represents the chief determinant of basal protein concentrations. This raises a fundamental question as to how mRNA and protein levels are actively coordina...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-07-20 | MSV000079962 | MassIVE
UnknownMammalian Alternative Translation Initiation Is Mostly Nonadaptive.
Not available
S-EPMC7828576 | biostudies-literature
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
TranscriptomicsRibosome profiling of HeLa cells infected with Enterovirus coxsackiepol (strain CVA-13/Flores)
Ribosome profiling of enterovirus infected cells was used to investigate expression of the virus polyprotein and upstream open reading frames. Samples were either pretreated with initiation inhibitor lactimidomycin (LTM) to cause ribosomes to accumulate at initiation sites, or were flash frozen with...
ORGANISM(S): Homo sapiens 
2025-11-26 | E-MTAB-14994 | biostudies-arrayexpress
GenomicsProgrammable mRNA translation initiation by trans-RNA
Programmable mRNA translation initiation by trans-RNA
PRJNA1163724 | ENA
TranscriptomicsTime resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells
Oxygen and glucose metabolism plays a pivotal role in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) occurs during ischemia and stroke, resulting in extensive tissue injury and cell death. We applied time-resolved ribosome profiling technique to assess earl...
ORGANISM(S): Rattus norvegicus 
2015-04-10 | E-GEOD-60752 | biostudies-arrayexpress
ProteomicseIF1 modulates the recognition of sub-optimal translation start sites and steers gene expression control mediated by uORFs.
Alternative translation initiation mechanisms such as leaky scanning and re-initiation potentiate the polycistronic nature of transcripts. By allowing for reprogrammed translation, these mechanisms can mediate biological responses to stress stimuli. We combined proteomics with ribosome profiling and...
ORGANISM(S): Homo sapiens (Human) 
2017-09-13 | PXD004980 | Pride
Q-exactive hf Alternative translation initiation Human Label-free shotgun proteomics Eif1 Eif1b 
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