Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Michel, Audrey M ^a   Andreev, Dmitry E ^b   Baranov, Pavel V ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

5' leader; 5' UTR TISs; Kozak context; Leaky scanning; Non AUG initiation; Ribosome profiling; Translation initiation; uORF

Indexed keywords

ARTIFICIAL INTELLIGENCE; COMPUTATIONAL METHODS; MACROMOLECULES; MAMMALS; PROBABILITY;

5' LEADER; 5' UTR TISS; KOZAK CONTEXT; NON-AUG INITIATION; RIBOSOME PROFILING; UORF;

SCANNING;

EUKARYOTA; MAMMALIA;

MESSENGER RNA; START CODON;

ANIMAL; BIOLOGY; CELL CULTURE; GENETIC PROCEDURES; GENETICS; METABOLISM; PROBABILITY; PROCEDURES; PROTEIN SYNTHESIS; RIBOSOME; RNA TRANSLATION; START CODON;

ANIMALS; CELLS, CULTURED; CODON, INITIATOR; COMPUTATIONAL BIOLOGY; GENETIC TECHNIQUES; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PROBABILITY; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, MESSENGER;

EID: 84923927316     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-014-0380-4     Document Type: Article

References (33)

1. Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS: Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324(80):218-223.
2. Michel AM, Baranov PV: Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale. Wiley Interdiscip Rev RNA 2013, 4:473-490.
3. 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.
4. Lee S, Liu B, Lee S, Huang S-X, Shen B, Qian S-B: Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. ProcNatlAcad Sci U S A 2012, 109:E2424-E2432.
5. Fritsch C, Herrmann A, Nothnagel M, Szafranski K, Huse K, Schumann F, Schreiber S, Platzer M, Krawczak M, Hampe J, Brosch M: Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res 2012, 22:2208-2218.
6. Anderson CW, Buzash-Pollert E: Can ACG serve as an initiation codon for protein synthesis in eucaryoticcells? Mol Cell Biol 1985, 5:3621-3624.
7. Hann SR, King MW, Bentley DL, Anderson CW, Eisenman RN: A non-AUG translational initiation in c-myc exon 1 generates an N-terminally distinct protein whose synthesis is disrupted in Burkitt'slymphomas. Cell 1988, 52:185-195.
8. Peabody DS: Translation initiation at non-AUG triplets in mammalian cells. J Biol Chem 1989, 264:5031-5035.
9. Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV: Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res 2011, 39:4220-4234.
10. Kozak M: Context effects and inefficient initiation at non-AUG codons in eucaryotic cell-free translation systems. Mol Cell Biol 1989, 9:5073-5080.
11. Clements JM, Laz TM, Sherman F: Efficiency of translation initiation by non-AUG codons in saccharomyces cerevisiae. Mol Cell Biol 1988, 8:4533-4536.
12. Kozak M: Pushing the limits of the scanning mechanism for initiation of translation. Gene 2002, 299:1-34.
13. Dmitriev SE, Akulich KA, Andreev DE, Terenin IM, Shastky IN: The peculiar mode of translation elongation inhibition by antitumor drug harringtonin. FEBS J 2013, 280:51.
14. Kozak M: Effects of intercistronic length on the efficiency of reinitiation by eucaryoticribosomes. Mol Cell Biol 1987, 7:3438-3445.
15. Pöyry TAA, Kaminski A, Jackson RJ: What determines whether mammalian ribosomes resume scanning after translation of a short upstream open reading frame? Genes Dev 2004, 18:62-75.
16. Hinnebusch A: Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 2005, 59:407-450.
17. Kozak M: Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 1986, 44:283-292.
18. Kozak M: An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 1987, 15:8125-8148.
19. Kozak M: Recognition of AUG and alternative initiator codons is augmented by G in position +4 but is not generally affected by the nucleotides in positions +5 and +6. EMBO J 1997, 16:2482-2492.
20. Rogozin IB, Kochetov AV, Kondrashov A, Koonin EV, Milanesi L: Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a "weak" context of the start codon. Bioinformatics 2001, 17:890-900.
21. Nakagawa S, Niimura Y, Gojobori T, Tanaka H, Miura K: Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nucleic Acids Res 2008, 36:861-871.
22. Kozak M: Adherence to the first-AUG rule when a second AUG codon follows closely upon the first. Proc Natl Acad Sci U S A 1995, 92:7134.
23. Kozak M: Constraints on reinitiation of translation in mammals. Nucleic Acids Res 2001, 29:5226-5232.
24. Vassilenko KS, Alekhina OM, Dmitriev SE, Shatsky IN, Spirin AS: Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation. Nucleic Acids Res 2011, 39:5555-5567.
25. Zur H, Tuller T: New universal rules of eukaryotic translation initiation fidelity. PLoS Comput Biol 2013, 9:e1003136.
26. Liu B, Qian S-B: Translational reprogramming in cellular stress response. Wiley Interdiscip Rev RNA 2013, 5:301-315.
27. Hopkins BD, Fine B, Steinbach N, Dendy M, Rapp Z, Shaw J, Pappas K, Yu JS, Hodakoski C, Mense S, Klein J, Pegno S, Sulis M-L, Goldstein H, Amendolara B, Lei L, Maurer M, Bruce J, Canoll P, Hibshoosh H, Parsons R: A secreted PTEN phosphatase that enters cells to alter signaling and survival. Science 2013, 341:399-402.
28. Wan J, Qian S-B: TISdb: a database for alternative translation initiation in mammalian cells. Nucleic Acids Res 2014, 42:D845-D850.
29. Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A: Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol 2013, 9:59-64.
30. Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A: Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. J Proteome Res 2014, 13:1757-1765.
31. Menschaert G, Van Criekinge W, Notelaers T, Koch A, Crappé J, Gevaert K, Van Damme P: Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events. Mol Cell Proteomics 2013, 12:1780-1790.
32. Van Damme P, Gawron D, Van Criekinge W, Menschaert G: N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol Cell Proteomics 2014, 5(3):301-315.
33. Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PBF, Heaphy SM, Mullan JPA, Donohue CA, Higgins DG, Baranov PV: GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res 2014, 42:D859-D864.