Integrated workflow for discovery of microprotein-coding small open reading frames.
Bioinformatics
Cell Biology
Cell Culture
Gene Expression
Genomics
Molecular Biology
RNAseq
Sequence Analysis
Sequencing
Journal
STAR protocols
ISSN: 2666-1667
Titre abrégé: STAR Protoc
Pays: United States
ID NLM: 101769501
Informations de publication
Date de publication:
23 Oct 2023
23 Oct 2023
Historique:
received:
08
08
2023
revised:
11
09
2023
accepted:
26
09
2023
medline:
24
10
2023
pubmed:
24
10
2023
entrez:
24
10
2023
Statut:
aheadofprint
Résumé
Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100-150 amino acids, are an emerging class of functional biomolecules. Here, we present a protocol for identifying translated smORFs in mammalian systems genome wide. We describe steps for generation of ribosome profiling (Ribo-seq) data, in silico translation of a transcriptome assembly to create an ORF database, and computational analysis of Ribo-seq to score individual smORFs for translation. Identification of translated smORFs is the first step to studying the functions of microproteins. For complete details on the use and execution of this protocol, please refer to Martinez et al.
Identifiants
pubmed: 37874679
pii: S2666-1667(23)00616-0
doi: 10.1016/j.xpro.2023.102649
pmc: PMC10618807
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
102649Informations de copyright
Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests T.F.M. is a paid consultant and shareholder of Velia Therapeutics.
Références
Cell Metab. 2023 Jan 3;35(1):166-183.e11
pubmed: 36599300
Nat Methods. 2016 Feb;13(2):165-70
pubmed: 26657557
Methods. 2017 Aug 15;126:112-129
pubmed: 28579404
Science. 2009 Apr 10;324(5924):218-23
pubmed: 19213877
Elife. 2015 Dec 19;4:e08890
pubmed: 26687005
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nat Chem Biol. 2020 Apr;16(4):458-468
pubmed: 31819274