Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures.
Mass spectrometry
Microproteins
Proteogenomics
Ribosome profiling (RIBO-Seq)
Short open reading frame (sORF)
Small open reading frame (smORF)
Journal
Journal of biomedical science
ISSN: 1423-0127
Titre abrégé: J Biomed Sci
Pays: England
ID NLM: 9421567
Informations de publication
Date de publication:
17 Mar 2022
17 Mar 2022
Historique:
received:
31
12
2021
accepted:
09
03
2022
entrez:
18
3
2022
pubmed:
19
3
2022
medline:
22
3
2022
Statut:
epublish
Résumé
A short open reading frame (sORFs) constitutes ≤ 300 bases, encoding a microprotein or sORF-encoded protein (SEP) which comprises ≤ 100 amino acids. Traditionally dismissed by genome annotation pipelines as meaningless noise, sORFs were found to possess coding potential with ribosome profiling (RIBO-Seq), which unveiled sORF-based transcripts at various genome locations. Nonetheless, the existence of corresponding microproteins that are stable and functional was little substantiated by experimental evidence initially. With recent advancements in multi-omics, the identification, validation, and functional characterisation of sORFs and microproteins have become feasible. In this review, we discuss the history and development of an emerging research field of sORFs and microproteins. In particular, we focus on an array of bioinformatics and OMICS approaches used for predicting, sequencing, validating, and characterizing these recently discovered entities. These strategies include RIBO-Seq which detects sORF transcripts via ribosome footprints, and mass spectrometry (MS)-based proteomics for sequencing the resultant microproteins. Subsequently, our discussion extends to the functional characterisation of microproteins by incorporating CRISPR/Cas9 screen and protein-protein interaction (PPI) studies. Our review discusses not only detection methodologies, but we also highlight on the challenges and potential solutions in identifying and validating sORFs and their microproteins. The novelty of this review lies within its validation for the functional role of microproteins, which could contribute towards the future landscape of microproteomics.
Identifiants
pubmed: 35300685
doi: 10.1186/s12929-022-00802-5
pii: 10.1186/s12929-022-00802-5
pmc: PMC8928697
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
19Subventions
Organisme : Universiti Kebangsaan Malaysia
ID : GUP-2020-078
Informations de copyright
© 2022. The Author(s).
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