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Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol
Ribosome profiling has revealed translation outside canonical coding sequences, including translation of short upstream ORFs, long noncoding RNAs, overlapping ORFs, ORFs in UTRs, or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling, and CRISPR-based screens...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Biochemistry and Molecular Biology
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9396073/ https://www.ncbi.nlm.nih.gov/pubmed/35788065 http://dx.doi.org/10.1016/j.mcpro.2022.100264 |
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author | Bogaert, Annelies Fijalkowska, Daria Staes, An Van de Steene, Tessa Demol, Hans Gevaert, Kris |
author_facet | Bogaert, Annelies Fijalkowska, Daria Staes, An Van de Steene, Tessa Demol, Hans Gevaert, Kris |
author_sort | Bogaert, Annelies |
collection | PubMed |
description | Ribosome profiling has revealed translation outside canonical coding sequences, including translation of short upstream ORFs, long noncoding RNAs, overlapping ORFs, ORFs in UTRs, or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling, and CRISPR-based screens showed that hundreds of ORFs derived from noncoding transcripts produce (micro)proteins, whereas other studies failed to find evidence for such types of noncanonical translation products. Here, we attempted to discover translation products from noncoding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from noncoding regions but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap-based interactome analysis of two N-terminal proteoforms originating from noncoding regions showed the functional potential of these novel proteins. |
format | Online Article Text |
id | pubmed-9396073 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Society for Biochemistry and Molecular Biology |
record_format | MEDLINE/PubMed |
spelling | pubmed-93960732022-08-25 Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol Bogaert, Annelies Fijalkowska, Daria Staes, An Van de Steene, Tessa Demol, Hans Gevaert, Kris Mol Cell Proteomics Research Ribosome profiling has revealed translation outside canonical coding sequences, including translation of short upstream ORFs, long noncoding RNAs, overlapping ORFs, ORFs in UTRs, or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling, and CRISPR-based screens showed that hundreds of ORFs derived from noncoding transcripts produce (micro)proteins, whereas other studies failed to find evidence for such types of noncanonical translation products. Here, we attempted to discover translation products from noncoding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from noncoding regions but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap-based interactome analysis of two N-terminal proteoforms originating from noncoding regions showed the functional potential of these novel proteins. American Society for Biochemistry and Molecular Biology 2022-07-02 /pmc/articles/PMC9396073/ /pubmed/35788065 http://dx.doi.org/10.1016/j.mcpro.2022.100264 Text en © 2022 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Research Bogaert, Annelies Fijalkowska, Daria Staes, An Van de Steene, Tessa Demol, Hans Gevaert, Kris Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol |
title | Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol |
title_full | Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol |
title_fullStr | Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol |
title_full_unstemmed | Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol |
title_short | Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol |
title_sort | limited evidence for protein products of noncoding transcripts in the hek293t cellular cytosol |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9396073/ https://www.ncbi.nlm.nih.gov/pubmed/35788065 http://dx.doi.org/10.1016/j.mcpro.2022.100264 |
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