{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T11:31:46Z","timestamp":1790508706823,"version":"4.1.0"},"reference-count":80,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2018,6,22]],"date-time":"2018-06-22T00:00:00Z","timestamp":1529625600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2018,6,22]],"date-time":"2018-06-22T00:00:00Z","timestamp":1529625600000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2018,6,22]],"date-time":"2018-06-22T00:00:00Z","timestamp":1529625600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["12\/IA\/1335"],"award-info":[{"award-number":["12\/IA\/1335"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-1413223"],"award-info":[{"award-number":["DMS-1413223"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["RSF16-14-10065"],"award-info":[{"award-number":["RSF16-14-10065"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002081","name":"Irish Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002081","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Translation initiation is the rate-limiting step of protein synthesis that is downregulated during the Integrated Stress Response (ISR). Previously, we demonstrated that most human mRNAs that are resistant to this inhibition possess translated upstream open reading frames (uORFs), and that in some cases a single uORF is sufficient for the resistance. Here we developed a computational model of Initiation Complexes Interference with Elongating Ribosomes (ICIER) to gain insight into the mechanism. We explored the relationship between the flux of scanning ribosomes upstream and downstream of a single uORF depending on uORF features. Paradoxically, our analysis predicts that reducing ribosome flux upstream of certain uORFs increases initiation downstream. The model supports the derepression of downstream translation as a general mechanism of uORF-mediated stress resistance. It predicts that stress resistance can be achieved with long slowly decoded uORFs that do not favor translation reinitiation and that start with initiators of low leakiness.<\/jats:p>","DOI":"10.7554\/elife.32563","type":"journal-article","created":{"date-parts":[[2018,6,22]],"date-time":"2018-06-22T08:00:25Z","timestamp":1529654425000},"source":"Crossref","is-referenced-by-count":52,"title":["TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response"],"prefix":"10.7554","volume":"7","author":[{"given":"Dmitry E","family":"Andreev","sequence":"first","affiliation":[{"name":"School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland"},{"name":"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxim","family":"Arnold","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J","family":"Kiniry","sequence":"additional","affiliation":[{"name":"School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2683-5597","authenticated-orcid":true,"given":"Gary","family":"Loughran","sequence":"additional","affiliation":[{"name":"School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey M","family":"Michel","sequence":"additional","affiliation":[{"name":"School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitrii","family":"Rachinskii","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9017-0270","authenticated-orcid":true,"given":"Pavel V","family":"Baranov","sequence":"additional","affiliation":[{"name":"School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4374","published-online":{"date-parts":[[2018,6,22]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"e03971","DOI":"10.7554\/eLife.03971","article-title":"Translation of 5' leaders is pervasive in genes resistant to eIF2 repression","volume":"4","author":"Andreev","year":"2015","journal-title":"eLife"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13059-015-0651-z","article-title":"Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes","volume":"16","author":"Andreev","year":"2015","journal-title":"Genome Biology"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1038\/nature18647","article-title":"Dynamics of ribosome scanning and recycling revealed by translation complex profiling","volume":"535","author":"Archer","year":"2016","journal-title":"Nature"},{"key":"bib4","article-title":"uORF_TASEP_ICIER","volume-title":"GitHub","author":"Arnold","year":"2018","unstructured":"Arnold M. 2018. uORF_TASEP_ICIER. GitHub. 118d650. https:\/\/github.com\/maximarnold\/uORF_TASEP_ICIER."},{"key":"bib5","doi-asserted-by":"publisher","first-page":"e28387","DOI":"10.4161\/trla.28387","article-title":"Why is start codon selection so precise in eukaryotes?","volume":"2","author":"Asano","year":"2014","journal-title":"Translation"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"307","DOI":"10.3945\/an.112.002113","article-title":"Eukaryotic initiation factor 2 phosphorylation and translational control in metabolism","volume":"3","author":"Baird","year":"2012","journal-title":"Advances in Nutrition"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"e1003529","DOI":"10.1371\/journal.pgen.1003529","article-title":"Gene expression regulation by upstream open reading frames and human disease","volume":"9","author":"Barbosa","year":"2013","journal-title":"PLoS Genetics"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1046\/j.1365-2958.2003.03898.x","article-title":"Dynamics and processivity of 40S ribosome scanning on mRNA in yeast","volume":"51","author":"Berthelot","year":"2004","journal-title":"Molecular Microbiology"},{"key":"bib9","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1038\/nmeth.3688","article-title":"Detecting actively translated open reading frames in ribosome profiling data","volume":"13","author":"Calviello","year":"2016","journal-title":"Nature Methods"},{"key":"bib10","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1093\/nar\/gkp1034","article-title":"Differential regulation of CHOP translation by phosphorylated eIF4E under stress conditions","volume":"38","author":"Chen","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1002\/embj.201385651","article-title":"Translation elongation can control translation initiation on eukaryotic mRNAs","volume":"33","author":"Chu","year":"2014","journal-title":"The EMBO Journal"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"5512","DOI":"10.1093\/nar\/gki847","article-title":"Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes","volume":"33","author":"Churbanov","year":"2005","journal-title":"Nucleic Acids Research"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"051904","DOI":"10.1103\/PhysRevE.81.051904","article-title":"Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation","volume":"81","author":"Ciandrini","year":"2010","journal-title":"Physical Review E"},{"key":"bib14","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1016\/0092-8674(92)90193-G","article-title":"Phosphorylation of initiation factor 2 alpha by protein kinase GCN2 mediates gene-specific translational control of GCN4 in yeast","volume":"68","author":"Dever","year":"1992","journal-title":"Cell"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"4685","DOI":"10.1128\/MCB.02138-06","article-title":"Efficient translation initiation directed by the 900-nucleotide-long and GC-rich 5' untranslated region of the human retrotransposon LINE-1 mRNA is strictly cap dependent rather than internal ribosome entry site mediated","volume":"27","author":"Dmitriev","year":"2007","journal-title":"Molecular and Cellular Biology"},{"key":"bib16","doi-asserted-by":"publisher","first-page":"2208","DOI":"10.1101\/gr.139568.112","article-title":"Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting","volume":"22","author":"Fritsch","year":"2012","journal-title":"Genome Research"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"17394","DOI":"10.1073\/pnas.1120799109","article-title":"Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress","volume":"109","author":"Gerashchenko","year":"2012","journal-title":"PNAS"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1261\/rna.055046.115","article-title":"In-depth analysis of cis-determinants that either promote or inhibit reinitiation on GCN4 mRNA after translation of its four short uORFs","volume":"22","author":"Guni\u0161ov\u00e1","year":"2016","journal-title":"Rna"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"5880","DOI":"10.1093\/nar\/gku204","article-title":"Fail-safe mechanism of GCN4 translational control--uORF2 promotes reinitiation by analogous mechanism to uORF1 and thus secures its key role in GCN4 expression","volume":"42","author":"Guni\u0161ov\u00e1","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"bib20","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1186\/s13059-014-0409-z","article-title":"Expanded identification and characterization of mammalian circular RNAs","volume":"15","author":"Guo","year":"2014","journal-title":"Genome Biology"},{"key":"bib21","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1126\/science.aad9868","article-title":"Translational control by 5'-untranslated regions of eukaryotic mRNAs","volume":"352","author":"Hinnebusch","year":"2016","journal-title":"Science"},{"key":"bib22","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1111\/j.1365-2958.1993.tb01947.x","article-title":"Gene-specific translational control of the yeast GCN4 gene by phosphorylation of eukaryotic initiation factor 2","volume":"10","author":"Hinnebusch","year":"1993","journal-title":"Molecular Microbiology"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1146\/annurev-biochem-060713-035802","article-title":"The scanning mechanism of eukaryotic translation initiation","volume":"83","author":"Hinnebusch","year":"2014","journal-title":"Annual Review of Biochemistry"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2011.10.002","article-title":"Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes","volume":"147","author":"Ingolia","year":"2011","journal-title":"Cell"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"4220","DOI":"10.1093\/nar\/gkr007","article-title":"Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences","volume":"39","author":"Ivanov","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"bib27","doi-asserted-by":"publisher","first-page":"10079","DOI":"10.1073\/pnas.0801590105","article-title":"uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs","volume":"105","author":"Ivanov","year":"2008","journal-title":"PNAS"},{"key":"bib28","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1016\/j.molcel.2018.03.015","article-title":"Polyamine control of translation elongation regulates start site selection on antizyme inhibitor mRNA via ribosome queuing","volume":"70","author":"Ivanov","year":"2018","journal-title":"Molecular Cell"},{"key":"bib29","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/nrm2838","article-title":"The mechanism of eukaryotic translation initiation and principles of its regulation","volume":"11","author":"Jackson","year":"2010","journal-title":"Nature Reviews Molecular Cell Biology"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"706","DOI":"10.15252\/embj.201592759","article-title":"Upstream ORFs are prevalent translational repressors in vertebrates","volume":"35","author":"Johnstone","year":"2016","journal-title":"The EMBO Journal"},{"key":"bib31","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/S0378-1119(99)00210-3","article-title":"Initiation of translation in prokaryotes and eukaryotes","volume":"234","author":"Kozak","year":"1999","journal-title":"Gene"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"e01257","DOI":"10.7554\/eLife.01257","article-title":"Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments","volume":"3","author":"Lareau","year":"2014","journal-title":"eLife"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"E2424","DOI":"10.1073\/pnas.1207846109","article-title":"Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution","volume":"109","author":"Lee","year":"2012","journal-title":"PNAS"},{"key":"bib34","doi-asserted-by":"publisher","first-page":"6661","DOI":"10.1074\/jbc.M806735200","article-title":"An upstream open reading frame regulates translation of GADD34 during cellular stresses that induce eIF2alpha phosphorylation","volume":"284","author":"Lee","year":"2009","journal-title":"Journal of Biological Chemistry"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"1064","DOI":"10.1016\/j.cell.2013.04.055","article-title":"The eEF2 kinase confers resistance to nutrient deprivation by blocking translation elongation","volume":"153","author":"Leprivier","year":"2013","journal-title":"Cell"},{"key":"bib36","doi-asserted-by":"publisher","first-page":"e2001882","DOI":"10.1371\/journal.pbio.2001882","article-title":"Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain","volume":"15","author":"Lintner","year":"2017","journal-title":"PLOS Biology"},{"key":"bib37","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1109\/TCBB.2012.88","article-title":"Stability analysis of the ribosome flow model","volume":"9","author":"Margaliot","year":"2012","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1186\/s12859-014-0380-4","article-title":"Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning","volume":"15","author":"Michel","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"bib39","doi-asserted-by":"publisher","first-page":"D859","DOI":"10.1093\/nar\/gkt1035","article-title":"GWIPS-viz: development of a ribo-seq genome browser","volume":"42","author":"Michel","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"bib40","doi-asserted-by":"publisher","first-page":"D823","DOI":"10.1093\/nar\/gkx790","article-title":"GWIPS-viz: 2018 update","volume":"46","author":"Michel","year":"2018","journal-title":"Nucleic Acids Research"},{"key":"bib41","doi-asserted-by":"publisher","first-page":"2658","DOI":"10.1093\/nar\/gkx049","article-title":"In vivo evidence that eIF3 stays bound to ribosomes elongating and terminating on short upstream ORFs to promote reinitiation","volume":"45","author":"Mohammad","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"bib42","doi-asserted-by":"publisher","first-page":"12915","DOI":"10.1038\/ncomms12915","article-title":"Comparative survey of the relative impact of mRNA features on local ribosome profiling read density","volume":"7","author":"O'Connor","year":"2016","journal-title":"Nature Communications"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"1295","DOI":"10.1016\/j.cell.2011.10.044","article-title":"Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo","volume":"147","author":"Oh","year":"2011","journal-title":"Cell"},{"key":"bib44","doi-asserted-by":"publisher","first-page":"28169","DOI":"10.18632\/oncotarget.8612","article-title":"Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress","volume":"7","author":"Oh","year":"2016","journal-title":"Oncotarget"},{"key":"bib45","doi-asserted-by":"publisher","first-page":"10939","DOI":"10.1074\/jbc.M110.216093","article-title":"Phosphorylation of eIF2 facilitates ribosomal bypass of an inhibitory upstream ORF to enhance CHOP translation","volume":"286","author":"Palam","year":"2011","journal-title":"Journal of Biological Chemistry"},{"key":"bib46","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1016\/j.molcel.2016.04.007","article-title":"Regulation of poly(A) Tail and translation during the somatic cell cycle","volume":"62","author":"Park","year":"2016","journal-title":"Molecular Cell"},{"key":"bib47","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1016\/j.celrep.2017.04.042","article-title":"mTORC1 balances cellular amino acid supply with demand for protein synthesis through post-transcriptional control of ATF4","volume":"19","author":"Park","year":"2017","journal-title":"Cell Reports"},{"key":"bib48","doi-asserted-by":"crossref","first-page":"5031","DOI":"10.1016\/S0021-9258(18)83694-8","article-title":"Translation initiation at non-AUG triplets in mammalian cells","volume":"264","author":"Peabody","year":"1989","journal-title":"The Journal of Biological Chemistry"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"1609","DOI":"10.1038\/emboj.2008.90","article-title":"Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes","volume":"27","author":"Pisarev","year":"2008","journal-title":"The EMBO Journal"},{"key":"bib50","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1016\/j.tibs.2016.05.003","article-title":"New peptides under the s(ORF)ace of the genome","volume":"41","author":"Pueyo","year":"2016","journal-title":"Trends in Biochemical Sciences"},{"key":"bib51","doi-asserted-by":"publisher","first-page":"e1002127","DOI":"10.1371\/journal.pcbi.1002127","article-title":"Genome-scale analysis of translation elongation with a ribosome flow model","volume":"7","author":"Reuveni","year":"2011","journal-title":"PLoS Computational Biology"},{"key":"bib52","doi-asserted-by":"publisher","first-page":"D110","DOI":"10.1093\/nar\/gks1058","article-title":"APPRIS: annotation of principal and alternative splice isoforms","volume":"41","author":"Rodriguez","year":"2013","journal-title":"Nucleic Acids Research"},{"key":"bib53","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1016\/j.cell.2013.05.049","article-title":"Rate-limiting steps in yeast protein translation","volume":"153","author":"Shah","year":"2013","journal-title":"Cell"},{"key":"bib54","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/j.molcel.2012.11.028","article-title":"Widespread regulation of translation by elongation pausing in heat shock","volume":"49","author":"Shalgi","year":"2013","journal-title":"Molecular Cell"},{"key":"bib55","doi-asserted-by":"publisher","first-page":"e05033","DOI":"10.7554\/eLife.05033","article-title":"The small molecule ISRIB reverses the effects of eIF2\u03b1 phosphorylation on translation and stress granule assembly","volume":"4","author":"Sidrauski","year":"2015","journal-title":"eLife"},{"key":"bib56","doi-asserted-by":"publisher","first-page":"2528","DOI":"10.1093\/nar\/gkw137","article-title":"Quantitative assessment of ribosome drop-off in E. coli","volume":"44","author":"Sin","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"bib57","doi-asserted-by":"publisher","first-page":"1690","DOI":"10.1016\/j.biocel.2013.04.020","article-title":"A perspective on mammalian upstream open reading frame function","volume":"45","author":"Somers","year":"2013","journal-title":"The International Journal of Biochemistry & Cell Biology"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"aad3867","DOI":"10.1126\/science.aad3867","article-title":"Translation from the 5' untranslated region shapes the integrated stress response","volume":"351","author":"Starck","year":"2016","journal-title":"Science"},{"key":"bib59","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1038\/224957a0","article-title":"Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA","volume":"224","author":"Steitz","year":"1969","journal-title":"Nature"},{"key":"bib60","doi-asserted-by":"publisher","first-page":"e1005288","DOI":"10.1371\/journal.ppat.1005288","article-title":"The transcription and translation landscapes during human Cytomegalovirus infection reveal novel Host-Pathogen interactions","volume":"11","author":"Tirosh","year":"2015","journal-title":"PLOS Pathogens"},{"key":"bib61","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1002\/wrna.52","article-title":"Cap and cap-binding proteins in the control of gene expression","volume":"2","author":"Topisirovic","year":"2011","journal-title":"Wiley Interdisciplinary Reviews: RNA"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"3645","DOI":"10.1073\/pnas.0909910107","article-title":"Translation efficiency is determined by both codon bias and folding energy","volume":"107","author":"Tuller","year":"2010","journal-title":"PNAS"},{"key":"bib63","doi-asserted-by":"publisher","first-page":"150203","DOI":"10.1098\/rsob.150203","article-title":"Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform","volume":"6","author":"Tzani","year":"2016","journal-title":"Open Biology"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/S0076-6879(07)29008-1","article-title":"In vivo stabilization of preinitiation complexes by formaldehyde cross-linking","volume":"429","author":"Val\u00e1sek","year":"2007","journal-title":"Methods in Enzymology"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"5555","DOI":"10.1093\/nar\/gkr147","article-title":"Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation","volume":"39","author":"Vassilenko","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"bib66","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1046\/j.1365-2958.2003.03622.x","article-title":"Regulation of fungal gene expression via short open reading frames in the mRNA 5'untranslated region","volume":"49","author":"Vilela","year":"2003","journal-title":"Molecular Microbiology"},{"key":"bib67","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.plantsci.2013.09.006","article-title":"Regulation of plant translation by upstream open reading frames","volume":"214","author":"von Arnim","year":"2014","journal-title":"Plant Science"},{"key":"bib68","doi-asserted-by":"publisher","first-page":"e201204002","DOI":"10.5936\/csbj.201204002","article-title":"Mathematical and computational modelling of ribosomal movement and protein synthesis: an overview","volume":"1","author":"von der Haar","year":"2012","journal-title":"Computational and Structural Biotechnology Journal"},{"key":"bib69","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1038\/nature06716","article-title":"Following translation by single ribosomes one codon at a time","volume":"452","author":"Wen","year":"2008","journal-title":"Nature"},{"key":"bib70","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1038\/nature14978","article-title":"Cell-fate determination by ubiquitin-dependent regulation of translation","volume":"525","author":"Werner","year":"2015","journal-title":"Nature"},{"key":"bib71","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1002\/wrna.1245","article-title":"The regulatory potential of upstream open reading frames in eukaryotic gene expression","volume":"5","author":"Wethmar","year":"2014","journal-title":"Wiley Interdisciplinary Reviews: RNA"},{"key":"bib72","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1002\/j.1460-2075.1988.tb03233.x","article-title":"Ribosome pausing and stacking during translation of a eukaryotic mRNA","volume":"7","author":"Wolin","year":"1988","journal-title":"The EMBO Journal"},{"key":"bib73","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/s12864-015-2354-y","article-title":"Improved transcription and translation with L-leucine stimulation of mTORC1 in Roberts syndrome","volume":"17","author":"Xu","year":"2016","journal-title":"BMC Genomics"},{"key":"bib74","doi-asserted-by":"publisher","first-page":"6546","DOI":"10.1074\/jbc.M115.705640","article-title":"Ribosome elongation stall directs Gene-specific translation in the integrated stress response","volume":"291","author":"Young","year":"2016","journal-title":"Journal of Biological Chemistry"},{"key":"bib75","doi-asserted-by":"publisher","first-page":"16927","DOI":"10.1074\/jbc.R116.733899","article-title":"Upstream open reading frames differentially regulate Gene-specific translation in the integrated stress response","volume":"291","author":"Young","year":"2016","journal-title":"Journal of Biological Chemistry"},{"key":"bib76","doi-asserted-by":"publisher","first-page":"28257","DOI":"10.1074\/jbc.M115.693184","article-title":"Ribosome reinitiation directs Gene-specific translation and regulates the integrated stress response","volume":"290","author":"Young","year":"2015","journal-title":"Journal of Biological Chemistry"},{"key":"bib77","doi-asserted-by":"publisher","first-page":"20706","DOI":"10.1074\/jbc.M114.547828","article-title":"Stress-induced start codon fidelity regulates arsenite-inducible regulatory particle-associated protein (AIRAP) translation","volume":"289","author":"Zach","year":"2014","journal-title":"Journal of Biological Chemistry"},{"key":"bib78","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/1752-0509-8-25","article-title":"mRNA translation and protein synthesis: an analysis of different modelling methodologies and a new PBN based approach","volume":"8","author":"Zhao","year":"2014","journal-title":"BMC Systems Biology"},{"key":"bib79","article-title":"Modeling translation in protein synthesis with TASEP: a tutorial and recent developments","volume-title":"Arxiv","author":"Zia","year":"2011","unstructured":"Zia R, Dong J, Schmittmann B. 2011. Modeling translation in protein synthesis with TASEP: a tutorial and recent developments. Arxiv. https:\/\/arxiv.org\/abs\/1108.3312."},{"key":"bib80","doi-asserted-by":"publisher","first-page":"1365","DOI":"10.1261\/rna.062059.117","article-title":"Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs","volume":"23","author":"Zinshteyn","year":"2017","journal-title":"RNA"}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/32563\/elife-32563-v2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/32563\/elife-32563-v2.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/32563","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,11]],"date-time":"2023-10-11T20:49:56Z","timestamp":1697057396000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/32563"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,6,22]]},"references-count":80,"alternative-id":["10.7554\/eLife.32563"],"URL":"https:\/\/doi.org\/10.7554\/elife.32563","archive":["CLOCKSS"],"relation":{"has-review":[{"id-type":"doi","id":"10.7554\/eLife.32563.029","asserted-by":"object"},{"id-type":"doi","id":"10.7554\/eLife.32563.030","asserted-by":"object"}],"has-preprint":[{"id-type":"doi","id":"10.1101\/204784","asserted-by":"object"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,22]]},"article-number":"e32563"}}