Results 51 to 60 of about 16,252 (205)

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana [PDF]

, 2017
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in ...
Gevaert, Kris, Jonckheere, Veronique, Martens, Lennart, Ndah, Elvis, Stael, Simon, Sticker, Adriaan, Van Breusegem, Frank, Van Damme, Petra, Willems, Patrick   +8 more
core   +1 more source

Extensive translation of small ORFs revealed by polysomal ribo-Seq [PDF]

, 2014
ABSTRACTThousands of small Open Reading Frames (smORFs) encoding small peptides of fewer than 100 amino acids exist in our genomes. Examples of functional smORFs have been characterised in a few species but the actual number of translated smORFs, and their molecular, functional and evolutionary features are not known.
Aspden, Julie L, Eyre-Walker, Ying Chen, Phillips, Rose J., Brocard, Michele, Amin, Unum, Couso, Juan   +5 more
openaire   +1 more source

Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.

PLoS Computational Biology, 2023
Gene expression is the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids.
Carole Chevalier, Jérôme Dorignac, Yahaya Ibrahim, Armelle Choquet, Alexandre David, Julie Ripoll, Eric Rivals, Frédéric Geniet, Nils-Ole Walliser, John Palmeri, Andrea Parmeggiani, Jean-Charles Walter   +11 more
doaj   +1 more source

Positional proteomics reveals differences in N-terminal proteoform stability [PDF]

, 2016
To understand the impact of alternative translation initiation on a proteome, we performed a proteome-wide study on protein turnover using positional proteomics and ribosome profiling to distinguish between N-terminal proteoforms of individual genes.
Brown JL, Daria Gawron, Elvis Ndah, Kris Gevaert, Petra Van Damme   +4 more
core   +2 more sources

A novel class of microRNA-recognition elements that function only within open reading frames. [PDF]

, 2018
MicroRNAs (miRNAs) are well known to target 3' untranslated regions (3' UTRs) in mRNAs, thereby silencing gene expression at the post-transcriptional level.
A Aizer, A Helwak, A Jakymiw, A Lal, AE Pasquinelli, AJ Giraldez, Alexander Dobin, AM Duursma, AR Buskirk, AR Quinlan, B Langmead, Bing Zhou, CJ Decker, CJ Shoemaker, CJ Woolstenhulme, CP Petersen, Dehe Wang, DP Bartel, DT Humphreys, E Huntzinger, EL Nostrand Van, GB Loeb, Guangqiao Liu, H Guo, HA Meijer, HO Iwakawa, I Behm-Ansmant, I Elcheva, J Hausser, J Liu, J Liu, JH Kim, Jie Zhou, JJ Forman, JP Broughton, K Seggerson, KA O’Donnell, Kai Zhang, L Wu, Ligang Wu, M Hafner, M Kouwenhove van, M Rehmsmeier, MD Robinson, MK Doma, ML Donnelly, N Rajewsky, NT Schirle, PA Maroney, Qian Zhao, R Ishimura, R Ishimura, R Parker, Ran Cao, RS Pillai, S Bagga, S Djuranovic, S Grosswendt, S Gu, S Jonas, S Nottrott, S Takagi, SN Bhattacharyya, SW Chi, SW Eichhorn, Timothy Nilsen, TT Tat, V Presnyak, W Filipowicz, Wen Ruan, X Adiconis, Xiang-Dong Fu, Xiaorong Zhang, Y Ishigaki, Y Liao, Y Tay, Y Wang, Y Xue, Y Zhao, Ya Zhao, Yan Qin, Yu Zhou, Yuanchao Xue, Z Cai, Zhiqiang Cai, Zonggui Chen   +85 more
core   +2 more sources

Discovering microproteins: making the most of ribosome profiling data

RNA Biology, 2023
Building a reference set of protein-coding open reading frames (ORFs) has revolutionized biological process discovery and understanding. Traditionally, gene models have been confirmed using cDNA sequencing and encoded translated regions inferred using ...
Sonia Chothani, Lena Ho, Sebastian Schafer, Owen Rackham   +3 more
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, McGeachy, Anna M, Sidrauski, Carmela, Walter, Peter   +3 more
core   +2 more sources

Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling [PDF]

, 2013
Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. The anticodon modification mcm[superscript 5]s[superscript 2]U[superscript 34] is required for normal growth and stress resistance in ...
Gilbert, Wendy, Zinshteyn, Boris
core   +7 more sources

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration [PDF]

, 2014
An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. However, several factors, including extensive regulation of mRNA translation and the need for three- or six-frame ...
Crappé, Jeroen, De Keulenaer, Sarah, De Meester, Ellen, De Meyer, Tim, Fijalkowska, Daria, Koch, Alexander, Menschaert, Gerben, Ndah, Elvis, Steyaert, Sandra, Van Criekinge, Wim, Van Damme, Petra   +10 more
core   +1 more source

sORFs.org : a repository of small ORFs identified by ribosome profiling [PDF]

, 2015
With the advent of ribosome profiling, a next generation sequencing technique providing a ‘snap-shot’ of translated mRNA in a cell, many short open reading frames (sORFs) with were identified.
Crappé, Jeroen, Martens, Lennart, Menschaert, Gerben, Olexiouk, Volodimir, Verbruggen, Steven, Verheggen, Kenneth   +5 more
core   +3 more sources