Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
21 07 2021
21 07 2021
Historique:
accepted:
11
06
2021
revised:
08
06
2021
received:
08
04
2021
pubmed:
7
7
2021
medline:
10
8
2021
entrez:
6
7
2021
Statut:
ppublish
Résumé
Although ribosome-profiling and translation initiation sequencing (TI-seq) analyses have identified many noncanonical initiation codons, the precise detection of translation initiation sites (TISs) remains a challenge, mainly because of experimental artifacts of such analyses. Here, we describe a new method, TISCA (TIS detection by translation Complex Analysis), for the accurate identification of TISs. TISCA proved to be more reliable for TIS detection compared with existing tools, and it identified a substantial number of near-cognate codons in Kozak-like sequence contexts. Analysis of proteomics data revealed the presence of methionine at the NH2-terminus of most proteins derived from near-cognate initiation codons. Although eukaryotic initiation factor 2 (eIF2), eIF2A and eIF2D have previously been shown to contribute to translation initiation at near-cognate codons, we found that most noncanonical initiation events are most probably dependent on eIF2, consistent with the initial amino acid being methionine. Comprehensive identification of TISs by TISCA should facilitate characterization of the mechanism of noncanonical initiation.
Identifiants
pubmed: 34226921
pii: 6312751
doi: 10.1093/nar/gkab549
pmc: PMC8287933
doi:
Substances chimiques
Codon, Initiator
0
Eukaryotic Initiation Factor-2
0
Eukaryotic Initiation Factor-3
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7298-7317Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Science. 2012 Feb 3;335(6068):552-7
pubmed: 22194413
J Proteome Res. 2014 Apr 4;13(4):2028-44
pubmed: 24555563
Cell Rep. 2020 Apr 21;31(3):107534
pubmed: 32320657
Trends Genet. 2017 Oct;33(10):728-744
pubmed: 28887026
Nat Rev Mol Cell Biol. 2010 Feb;11(2):113-27
pubmed: 20094052
Mol Cell. 2020 Aug 20;79(4):546-560.e7
pubmed: 32589964
Annu Rev Biochem. 2019 Jun 20;88:307-335
pubmed: 31220979
J Biol Chem. 2005 Apr 29;280(17):16925-33
pubmed: 15684421
Nucleic Acids Res. 2018 Jun 1;46(10):e61
pubmed: 29538776
BMC Bioinformatics. 2014 Nov 21;15:380
pubmed: 25413677
Bioinformatics. 2017 Jul 15;33(14):i234-i242
pubmed: 28881981
Nat Rev Genet. 2014 Mar;15(3):205-13
pubmed: 24468696
Nucleic Acids Res. 2017 Mar 17;45(5):2658-2674
pubmed: 28119417
Genome Biol. 2014;15(12):550
pubmed: 25516281
Science. 2020 Nov 13;370(6518):853-856
pubmed: 33184215
Nucleic Acids Res. 2018 Jan 25;46(2):985-994
pubmed: 29228265
Mol Cell Proteomics. 2020 Nov 24;20:100003
pubmed: 33517145
Cell Rep. 2020 Dec 22;33(12):108534
pubmed: 33357443
Cell. 2011 Nov 11;147(4):789-802
pubmed: 22056041
Cell Cycle. 2016 Nov 16;15(22):3115-3120
pubmed: 27686860
Mol Cell. 2020 Aug 20;79(4):575-587.e7
pubmed: 32589965
Science. 2020 Sep 4;369(6508):1220-1227
pubmed: 32883864
Cell. 1988 Jan 29;52(2):185-95
pubmed: 3277717
Nat Methods. 2015 Feb;12(2):147-53
pubmed: 25486063
Proteomics. 2015 Jul;15(14):2385-401
pubmed: 25914051
J Cell Biol. 2004 Oct 11;167(1):27-33
pubmed: 15479734
Methods. 2017 Aug 15;126:112-129
pubmed: 28579404
Nat Commun. 2017 Nov 23;8(1):1749
pubmed: 29170441
Cell. 1991 May 17;65(4):551-68
pubmed: 1851669
Nature. 2017 Jan 26;541(7638):494-499
pubmed: 28077873
Cell Rep. 2020 Apr 7;31(1):107497
pubmed: 32268096
Science. 2009 Apr 10;324(5924):218-23
pubmed: 19213877
Nature. 2016 Jul 28;535(7613):570-4
pubmed: 27437580
Elife. 2014 May 09;3:e01257
pubmed: 24842990
Elife. 2015 Dec 19;4:e08890
pubmed: 26687005
Curr Protoc Mol Biol. 2018 Oct;124(1):e67
pubmed: 30178897
Cell. 2009 Feb 20;136(4):731-45
pubmed: 19239892
J Biol Chem. 2013 Mar 29;288(13):9549-62
pubmed: 23396971
Nucleic Acids Res. 2011 May;39(10):4220-34
pubmed: 21266472
Science. 2012 Jun 29;336(6089):1719-23
pubmed: 22745432
Science. 2020 Mar 6;367(6482):1140-1146
pubmed: 32139545
Cell. 1986 Jan 31;44(2):283-92
pubmed: 3943125
Gene. 1999 Jul 8;234(2):187-208
pubmed: 10395892
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
Genome Res. 2020 Jul;30(7):974-984
pubmed: 32669370
Mol Cell. 2019 Mar 7;73(5):959-970.e5
pubmed: 30686592
Genome Res. 2004 Jun;14(6):1188-90
pubmed: 15173120
Sci Rep. 2017 Jul 26;7(1):6599
pubmed: 28747677
Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):E2424-32
pubmed: 22927429
RNA Biol. 2017 Dec 2;14(12):1660-1667
pubmed: 28745933
J Proteome Res. 2008 Jan;7(1):40-4
pubmed: 18052118
J Biol Chem. 2010 Aug 27;285(35):26779-26787
pubmed: 20566627
Structure. 2016 Jun 7;24(6):886-96
pubmed: 27210288
Mol Cell. 2018 Sep 6;71(5):761-774.e5
pubmed: 30146315
Genome Res. 2018 Jan;28(1):25-36
pubmed: 29162641
Science. 2012 Nov 23;338(6110):1088-93
pubmed: 23180859
Mol Cell. 2020 Aug 20;79(4):561-574.e5
pubmed: 32589966
FEBS Lett. 2006 Nov 13;580(26):6211-6
pubmed: 17070523
Genes Dev. 2017 Sep 1;31(17):1717-1731
pubmed: 28982758
Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):18056-60
pubmed: 20921384
Nucleic Acids Res. 2012 Apr;40(7):2898-906
pubmed: 22156057
Cell Syst. 2020 Aug 26;11(2):145-160.e5
pubmed: 32710835
Wiley Interdiscip Rev RNA. 2018 Jul;9(4):e1473
pubmed: 29624880
Nature. 2016 Aug 4;536(7614):96-9
pubmed: 27462815
Bioinformatics. 2017 Jan 1;33(1):139-141
pubmed: 27634950
Trends Biochem Sci. 2017 Aug;42(8):589-611
pubmed: 28442192
Nucleic Acids Res. 2017 Nov 2;45(19):10948-10968
pubmed: 28981723
Nat Commun. 2017 Mar 23;8:14771
pubmed: 28332494
Genomics. 2005 Mar;85(3):360-71
pubmed: 15718103
Genes Dev. 2010 Aug 15;24(16):1787-801
pubmed: 20713520