REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes [PDF]
, 2017 Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes.
Giess, Adam +5 more
core +1 more source
Genome-wide Translation Profiling by Ribosome-Bound tRNA Capture
Cell Reports, 2018 Summary: In the ribosome complex, tRNA is a critical element of mRNA translation. A rich repertoire of cell regulation is hypothesized to occur during the recruitment of specific tRNAs in polypeptide formation.
Chien-Wen Chen, Motomasa Tanaka
doaj +1 more source
The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly. [PDF]
, 2015 Previously, we identified ISRIB as a potent inhibitor of the integrated stress response (ISR) and showed that ISRIB makes cells resistant to the effects of eIF2α phosphorylation and enhances long-term memory in rodents (Sidrauski et al., 2013).
Ingolia, Nicholas T +3 more
core +2 more sources
In Vitro Analysis of Stalled Ribosomes using Puromycin Incorporation
Bio-Protocol, 2023 Ribosome footprint profiling has demonstrated that ribosomes can be slowed or stalled on select mRNAs, often due to the presence of rare codons, stalling motifs, or via a ribosome-binding protein (e.g., FMRP).
MaKenzie Scarpitti, Michael Kearse
doaj +1 more source
Ribosome Profiling: Global Views of Translation [PDF]
Cold Spring Harbor Perspectives in Biology, 2018 The translation of messenger RNA (mRNA) into protein and the folding of the resulting protein into an active form are prerequisites for virtually every cellular process and represent the single largest investment of energy by cells. Ribosome profiling-based approaches have revolutionized our ability to monitor every step of protein synthesis in vivo ...
Nicholas T, Ingolia +2 more
openaire +2 more sources
High-Precision Analysis of Translational Pausing by Ribosome Profiling in Bacteria Lacking EFP
Cell Reports, 2015 Ribosome profiling is a powerful method for globally assessing the activity of ribosomes in a cell. Despite its application in many organisms, ribosome profiling studies in bacteria have struggled to obtain the resolution necessary to precisely define ...
Christopher J. Woolstenhulme +3 more
doaj +1 more source
Protocol for Disome Profiling to Survey Ribosome Collision in Humans and Zebrafish
STAR Protocols, 2020 Summary: Ribosomes often encounter obstacles during translation elongation and thus collide with each other. Disome profiling, an optimized ribosome profiling method, specifically sequences the long ribosome footprints generated from collided ribosomes ...
Mari Mito +2 more
doaj +1 more source
Normalized Ribo-Seq for Quantifying Absolute Global and Specific Changes in Translation
Bio-Protocol, 2022 Ribosome profiling (Ribo-Seq) is a highly sensitive method to quantify ribosome occupancies along individual mRNAs on a genome-wide scale. Hereby, ribosome-protected fragments (= footprints) are generated by nuclease digestion, isolated, and sequenced ...
Katharina Hoerth +2 more
doaj +1 more source
The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs. [PDF]
, 2018 The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian orthologue DDX3 are critical for the initiation of translation1.
Bartel, David P +10 more
core +1 more source
Characterizing inactive ribosomes in translational profiling [PDF]
Translation, 2016 The broad impact of translational regulation has emerged explosively in the last few years in part due to the technological advance in genome-wide interrogation of gene expression. During mRNA translation, the majority of actively translating ribosomes exist as polysomes in cells with multiple ribosomes loaded on a single transcript.
Botao, Liu, Shu-Bing, Qian
openaire +2 more sources