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Treffer: Start Right to End Right: Authentic Open Reading Frame Selection Matters for Nonsense-Mediated Decay Target Identification.

Title:
Start Right to End Right: Authentic Open Reading Frame Selection Matters for Nonsense-Mediated Decay Target Identification.
Authors:
Bagherian M; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley 6009, Australia., Harris G; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley 6009, Australia., Sathishkumar P; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley 6009, Australia., Lloyd JPB; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley 6009, Australia.; Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, University of Western Australia, Crawley 6009, Australia.
Source:
Genes [Genes (Basel)] 2025 Nov 01; Vol. 16 (11). Date of Electronic Publication: 2025 Nov 01.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: MDPI Country of Publication: Switzerland NLM ID: 101551097 Publication Model: Electronic Cited Medium: Internet ISSN: 2073-4425 (Electronic) Linking ISSN: 20734425 NLM ISO Abbreviation: Genes (Basel) Subsets: MEDLINE
Imprint Name(s):
Original Publication: Basel : MDPI
MeSH Terms:
Nonsense Mediated mRNA Decay*/genetics , Open Reading Frames*/genetics , Arabidopsis*/genetics , Codon, Initiator*/genetics, Molecular Sequence Annotation/methods ; Transcriptome/genetics ; Arabidopsis Proteins/genetics ; Codon, Nonsense/genetics
References:
Genes Dev. 2007 Mar 15;21(6):708-18. (PMID: 17369403)
PLoS One. 2012;7(2):e31917. (PMID: 22384098)
Nature. 2020 Sep;585(7823):79-84. (PMID: 32663838)
Nucleic Acids Res. 2024 Jan 5;52(D1):D368-D375. (PMID: 37933859)
EMBO J. 2007 Mar 21;26(6):1591-601. (PMID: 17318186)
Plant J. 2017 Feb;89(4):789-804. (PMID: 27862469)
Nature. 2004 Nov 4;432(7013):112-8. (PMID: 15525991)
Nucleic Acids Res. 2018 Jun 20;46(11):5822-5836. (PMID: 29596649)
Mol Biol Evol. 2015 Apr;32(4):1072-9. (PMID: 25576366)
Mol Cell. 2003 Apr;11(4):939-49. (PMID: 12718880)
Nucleic Acids Res. 2021 Jan 8;49(D1):D458-D460. (PMID: 33104802)
Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4118-23. (PMID: 15024115)
Nat Genet. 2016 Oct;48(10):1112-8. (PMID: 27618451)
Nat Methods. 2017 Jul;14(7):687-690. (PMID: 28581496)
Nat Biotechnol. 2010 May;28(5):511-5. (PMID: 20436464)
Cell Host Microbe. 2014 Sep 10;16(3):376-90. (PMID: 25211079)
Genes Dev. 2015 Jan 1;29(1):63-80. (PMID: 25561496)
Plant Cell. 2013 Oct;25(10):3726-42. (PMID: 24163313)
Nature. 2007 Apr 19;446(7138):926-9. (PMID: 17361132)
Genome Res. 2024 Nov 20;34(11):1919-1930. (PMID: 39505490)
Nat Commun. 2020 Apr 14;11(1):1768. (PMID: 32286305)
Mol Cell. 2019 Jul 25;75(2):324-339.e11. (PMID: 31155380)
Plant J. 2010 Oct;64(2):243-55. (PMID: 20735772)
Cell Rep. 2023 Jun 27;42(6):112642. (PMID: 37314931)
Mol Cell. 2020 Nov 19;80(4):648-665.e9. (PMID: 33176162)
Plant Cell Environ. 2022 Apr;45(4):1229-1241. (PMID: 35128674)
Nat Biotechnol. 2015 Mar;33(3):290-5. (PMID: 25690850)
Nature. 2024 Jun;630(8016):493-500. (PMID: 38718835)
Cell. 2010 Oct 29;143(3):379-89. (PMID: 21029861)
Plant Cell. 2020 Sep;32(9):2725-2741. (PMID: 32665305)
Nucleic Acids Res. 2012 Jul;40(12):5615-24. (PMID: 22379136)
Plant Cell. 2015 Aug;27(8):2083-7. (PMID: 26286536)
Nat Methods. 2025 Oct;22(10):2002-2006. (PMID: 40890551)
Nucleic Acids Res. 2012 Mar;40(6):2454-69. (PMID: 22127866)
Genome Biol. 2022 Jul 7;23(1):149. (PMID: 35799267)
F1000Res. 2018 Aug 15;7:1299. (PMID: 30345031)
Nucleic Acids Res. 2023 Apr 24;51(7):3055-3066. (PMID: 36912101)
Plant J. 2013 Dec;76(5):800-10. (PMID: 24103012)
Nat Methods. 2017 Apr;14(4):417-419. (PMID: 28263959)
Sci Rep. 2017 Nov 30;7(1):16692. (PMID: 29192227)
Elife. 2016 Jan 08;5:. (PMID: 26744779)
Plant Cell. 2014 Feb;26(2):754-64. (PMID: 24532591)
Contributed Indexing:
Keywords: NMD; ORF; alternative splicing; genome annotation; genomes; genomics
Substance Nomenclature:
0 (Codon, Initiator)
0 (Arabidopsis Proteins)
0 (Codon, Nonsense)
Entry Date(s):
Date Created: 20251127 Date Completed: 20251127 Latest Revision: 20251130
Update Code:
20251130
PubMed Central ID:
PMC12652563
DOI:
10.3390/genes16111297
PMID:
41300748
Database:
MEDLINE

Weitere Informationen

Backgrounds: Accurate annotation of open reading frames (ORFs) is fundamental for understanding gene function and post-transcriptional regulation. A critical but often overlooked aspect of transcriptome annotation is the selection of authentic translation start sites. Many genome annotation pipelines identify the longest possible ORF in alternatively spliced transcripts, using internal methionine codons as putative start sites. However, this computational approach ignores the biological reality that ribosomes select start codons based on sequence context, not ORF length.
Methods: Here, we demonstrate that this practice leads to systematic misannotation of nonsense-mediated decay (NMD) targets in the Arabidopsis thaliana Araport11 reference transcriptome. Using TranSuite software to identify authentic start codons, we reanalyzed transcriptomic data from an NMD-deficient mutant.
Results: We found that correct ORF annotation more than doubles the number of identifiable NMD targets with premature termination codons followed by downstream exon junctions, from 203 to 426 transcripts. Furthermore, we show that incorrect ORF annotations can lead to erroneous protein structure predictions, potentially introducing computational artefacts into protein databases.
Conclusions: Our findings underscore the importance of biologically informed ORF annotation for accurate assessment of post-transcriptional regulation and proteome prediction, with implications for all eukaryotic genome annotation projects.