Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9.
Article
CAS
PubMed
Google Scholar
Andreev DE, O’Connor PB, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, et al. Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression. Elife. 2015;4:303971.
Article
Google Scholar
Barbosa C, Peixeiro I, Romão L. Gene expression regulation by upstream open Reading frames and human disease. PLoS Genet. 2013;9(8):e1003529.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J. Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci U S A. 2017;114(46):E10018–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, et al. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J. 2014;33(9):981–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Blevins WR, Tavella T, Moro SG, Blasco-Moreno B, Closa-Mosquera A, Díez J, et al. Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker’s yeast. Sci Rep. 2019;9(1):11005.
Article
PubMed
PubMed Central
CAS
Google Scholar
Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science. 2012;335:552–7.
Article
CAS
PubMed
Google Scholar
Brar GA, Weissman JS. Ribosome profiling reveals the what, when, where and how of protein synthesis. Nat Rev Mol Cell Biol. 2015;16(11):651–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vilela C, Linz B, Rodrigues-Pousada C, McCarthy JE. The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability. Nucleic Acids Res. 1998;26(5):1150–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Calvo SE, Pagliarini DJ, Mootha VK. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci. 2009;106(18):7507–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen J, Brunner A-D, Cogan JZ, Nuñez JK, Fields AP, Adamson B, et al. Pervasive functional translation of noncanonical human open reading frames. Science (80-). 2020;367:1140–6.
Article
CAS
Google Scholar
Chew G-L, Pauli A, Schier AF. Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun. 2016;7(1):11663.
Article
CAS
PubMed
PubMed Central
Google Scholar
Clemens MJ. Initiation factor eIF2α phosphorylation in stress responses and apoptosis. In: Progress in molecular and subcellular biology, vol. 27; 2001. p. 57–89.
Google Scholar
Clements JM, Laz TM, Sherman F. Efficiency of translation initiation by non-AUG codons in Saccharomyces cerevisiae. Mol Cell Biol. 1988;8(10):4533–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Couso J-P, Patraquim P. Classification and function of small open reading frames. Nat Rev Mol Cell Biol. 2017;18(9):575–89.
Article
CAS
PubMed
Google Scholar
Duncan CDS, Mata J. Effects of cycloheximide on the interpretation of ribosome profiling experiments in Schizosaccharomyces pombe. Sci Rep. 2017;7(1):10331.
Article
PubMed
PubMed Central
CAS
Google Scholar
Duncan CDS, Rodríguez-López M, Ruis P, Bähler J, Mata J. General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4. Proc Natl Acad Sci. 2018;115(8):E1829–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Finley D, Özkaynak E, Varshavsky A. The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses. Cell. 1987;48(6):1035–46.
Article
CAS
PubMed
Google Scholar
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, et al. Genomic expression programs in the response of yeast cells to environmental changes ed. P.A. Silver. Mol Biol Cell. 2000;11(12):4241–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gerashchenko MV, Gladyshev VN. Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic Acids Res. 2014;42(17):e134.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gerashchenko MV, Lobanov AV, Gladyshev VN. Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress. Proc Natl Acad Sci. 2012;109(43):17394–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grant CM, Miller PF, Hinnebusch AG. Sequences 5′ of the first upstream open reading frame in GCN4 mRNA are required for efficient translational reinitiation. Nucleic Acids Res. 1995;23(19):3980–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
van Heesch S, Witte F, Schneider-Lunitz V, Schulz JF, Adami E, Faber AB, et al. The translational landscape of the human heart. Cell. 2019;178:242–260.e29.
Article
PubMed
CAS
Google Scholar
Hinnebusch AG. Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol. 2005;59(1):407–50.
Article
CAS
PubMed
Google Scholar
Hinnebusch AG, Ivanov IP, Sonenberg N. Translational control by 5′-untranslated regions of eukaryotic mRNAs. Science. 2016;352(6292):1413–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ingolia NT. Ribosome footprint profiling of translation throughout the genome. Cell. 2016;165(1):22–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324(5924):218–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell. 2011;147(4):789–802.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ji Z, Song R, Regev A, Struhl K. Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins ed. N Sonenberg. Elife. 2015;4:e08890.
Article
PubMed
PubMed Central
Google Scholar
Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J. 2016;35(7):706–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jungfleisch J, Nedialkova DD, Dotu I, Sloan KE, Martinez-Bosch N, Brüning L, et al. A novel translational control mechanism involving RNA structures within coding sequences. Genome Res. 2017;27(1):95–106.
Article
CAS
PubMed
PubMed Central
Google Scholar
Juntawong P, Girke T, Bazin J, Bailey-Serres J. Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc Natl Acad Sci U S A. 2014;111(1):E203–12.
Article
CAS
PubMed
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Law CW, Chen Y, Shi W, Smyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15:R29.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lei L, Shi J, Chen J, Zhang M, Sun S, Xie S, et al. Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress. Plant J. 2015;84(6):1206–18.
Article
CAS
PubMed
Google Scholar
Llácer JL, Hussain T, Saini AK, Nanda JS, Kaur S, Gordiyenko Y, et al. Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition. Elife. 2018;7:e39273.
Article
PubMed
PubMed Central
Google Scholar
Maiti T, Maitra U. Characterization of translation initiation factor 5 (eIF5) from Saccharomyces cerevisiae. J Biol Chem. 1997;272(29):18333–40.
Article
CAS
PubMed
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17:10.
Article
Google Scholar
Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, et al. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A. 2006;103(47):17846–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morano KA, Grant CM, Moye-Rowley WS. The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics. 2012;190(4):1157–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008;320(5881):1344–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patraquim P, Mumtaz MAS, Pueyo JI, Aspden JL, Couso J-P. Developmental regulation of canonical and small ORF translation from mRNAs. Genome Biol. 2020;21(1):128.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Article
CAS
PubMed
Google Scholar
Ruiz-Orera J, Albà MM. Translation of small open Reading frames: roles in regulation and evolutionary innovation. Trends Genet. 2019;35(3):186–98.
Article
CAS
PubMed
Google Scholar
Ruiz-Orera J, Messeguer X, Subirana JA, Alba MM. Long non-coding RNAs as a source of new peptides. Elife. 2014;3:e03523.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ruiz-Orera J, Verdaguer-Grau P, Villanueva-Cañas JL, Messeguer X, Albà MM. Translation of neutrally evolving peptides provides a basis for de novo gene evolution. Nat Ecol Evol. 2018;2(5):890–6.
Article
PubMed
Google Scholar
Gusinova S, Valasek LS. Fail-safe mechanism of GCN4 translational control--uORF2 promotes Reinitiation by analogous mechanism to uORF1 and thus secures its key role in GCN4 expression. Nucleic Acids Res. 2014;42:5880–93.
Article
CAS
Google Scholar
Schulz J, Mah N, Neuenschwander M, Kischka T, Ratei R, Schlag PM, et al. Loss-of-function uORF mutations in human malignancies. Sci Rep. 2018;8(1):2395.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shenton D, Smirnova JB, Selley JN, Carroll K, Hubbard SJ, Pavitt GD, et al. Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J Biol Chem. 2006;281(39):29011–21.
Article
CAS
PubMed
Google Scholar
Sundaram A, Grant CM. A single inhibitory upstream open reading frame (uORF) is sufficient to regulate Candida albicans GCN4 translation in response to amino acid starvation conditions. RNA. 2014;20(4):559–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vattem KM, Wek RC. Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc Natl Acad Sci. 2004;101(31):11269–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vogel C, Silva GM, Marcotte EM. Protein expression regulation under oxidative stress. Mol Cell Proteomics. 2011;10(12):M111.009217.
Article
PubMed
PubMed Central
CAS
Google Scholar
Werner M, Feller A, Messenguy F, Piérard A. The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression. Cell. 1987;49(6):805–13.
Article
CAS
PubMed
Google Scholar
Wethmar K, Schulz J, Muro EM, Talyan S, Andrade-Navarro MA, Leutz A. Comprehensive translational control of tyrosine kinase expression by upstream open reading frames. Oncogene. 2016;35(13):1736–42.
Article
CAS
PubMed
Google Scholar
Whiffin N, Karczewski KJ, Zhang X, Chothani S, Smith MJ, Evans DG, et al. Characterising the loss-of-function impact of 5′ untranslated region variants in 15,708 individuals. Nat Commun. 2020;11(1):2523.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu G, Greene GH, Yoo H, Liu L, Marqués J, Motley J, et al. Global translational reprogramming is a fundamental layer of immune regulation in plants. Nature. 2017;545(7655):487–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, et al. Bidirectional promoters generate pervasive transcription in yeast. Nature. 2009;457(7232):1033–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, et al. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A. 2009;106(9):3264–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang H, Dou S, He F, Luo J, Wei L, Lu J. Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development. PLoS Biol. 2018;16(7):e2003903.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang Z, Dietrich FS. Identification and characterization of upstream open reading frames (uORF) in the 5′ untranslated regions (UTR) of genes in Saccharomyces cerevisiae. Curr Genet. 2005;48(2):77–87.
Article
CAS
PubMed
Google Scholar
Zhao W, Zhou T, Zheng H-Z, Qiu K-P, Cui H-J, Yu H, et al. Yeast polyubiquitin gene UBI4 deficiency leads to early induction of apoptosis and shortened replicative lifespan. Cell Stress Chaperones. 2018;23(4):527–37.
Article
PubMed
CAS
Google Scholar
Zhong Y, Karaletsos T, Drewe P, Sreedharan VT, Kuo D, Singh K, et al. RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints. Bioinformatics. 2017;33(1):139–41.
Article
CAS
PubMed
Google Scholar
Zhou F, Zhang H, Kulkarni SD, Lorsch JR, Hinnebusch AG. eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide. RNA. 2020;26(4):419–38.
Article
PubMed
PubMed Central
Google Scholar
Zitomer RS, Walthall DA, Rymond BC, Hollenberg CP. Saccharomyces cerevisiae ribosomes recognize non-AUG initiation codons. Mol Cell Biol. 1984;4(7):1191–7.
Article
CAS
PubMed
PubMed Central
Google Scholar