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GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms

The boundaries of protein coding sequences are more difficult to define at the 5′ end than at the 3′ end due to potential multiple translation initiation sites (TISs). Even in the presence of phylogenetic data, the use of sequence information only may not be sufficient for the accurate identificatio...

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Autores principales: Michel, Audrey M., Ahern, Anna M., Donohue, Claire A., Baranov, Pavel V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832365/
https://www.ncbi.nlm.nih.gov/pubmed/25736862
http://dx.doi.org/10.1002/pmic.201400603
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author Michel, Audrey M.
Ahern, Anna M.
Donohue, Claire A.
Baranov, Pavel V.
author_facet Michel, Audrey M.
Ahern, Anna M.
Donohue, Claire A.
Baranov, Pavel V.
author_sort Michel, Audrey M.
collection PubMed
description The boundaries of protein coding sequences are more difficult to define at the 5′ end than at the 3′ end due to potential multiple translation initiation sites (TISs). Even in the presence of phylogenetic data, the use of sequence information only may not be sufficient for the accurate identification of TISs. Traditional proteomics approaches may also fail because the N‐termini of newly synthesized proteins are often processed. Thus ribosome profiling (ribo‐seq), producing a snapshot of the ribosome distribution across the entire transcriptome, is an attractive experimental technique for the purpose of TIS location exploration. The GWIPS‐viz (Genome Wide Information on Protein Synthesis visualized) browser (http://gwips.ucc.ie) provides free access to the genomic alignments of ribo‐seq data and corresponding mRNA‐seq data along with relevant annotation tracks. In this brief, we illustrate how GWIPS‐viz can be used to explore the ribosome occupancy at the 5′ ends of protein coding genes to assess the activity of AUG and non‐AUG TISs responsible for the synthesis of proteoforms with alternative or heterogeneous N‐termini. The presence of ribo‐seq tracks for various organisms allows for cross‐species comparison of orthologous genes and the availability of datasets from multiple laboratories permits the assessment of the technical reproducibility of the ribosome densities.
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spelling pubmed-48323652016-04-20 GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms Michel, Audrey M. Ahern, Anna M. Donohue, Claire A. Baranov, Pavel V. Proteomics Technical Brief The boundaries of protein coding sequences are more difficult to define at the 5′ end than at the 3′ end due to potential multiple translation initiation sites (TISs). Even in the presence of phylogenetic data, the use of sequence information only may not be sufficient for the accurate identification of TISs. Traditional proteomics approaches may also fail because the N‐termini of newly synthesized proteins are often processed. Thus ribosome profiling (ribo‐seq), producing a snapshot of the ribosome distribution across the entire transcriptome, is an attractive experimental technique for the purpose of TIS location exploration. The GWIPS‐viz (Genome Wide Information on Protein Synthesis visualized) browser (http://gwips.ucc.ie) provides free access to the genomic alignments of ribo‐seq data and corresponding mRNA‐seq data along with relevant annotation tracks. In this brief, we illustrate how GWIPS‐viz can be used to explore the ribosome occupancy at the 5′ ends of protein coding genes to assess the activity of AUG and non‐AUG TISs responsible for the synthesis of proteoforms with alternative or heterogeneous N‐termini. The presence of ribo‐seq tracks for various organisms allows for cross‐species comparison of orthologous genes and the availability of datasets from multiple laboratories permits the assessment of the technical reproducibility of the ribosome densities. John Wiley and Sons Inc. 2015-04-23 2015-07 /pmc/articles/PMC4832365/ /pubmed/25736862 http://dx.doi.org/10.1002/pmic.201400603 Text en © 2015 The Authors. PROTEOMICS published by Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Brief
Michel, Audrey M.
Ahern, Anna M.
Donohue, Claire A.
Baranov, Pavel V.
GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms
title GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms
title_full GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms
title_fullStr GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms
title_full_unstemmed GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms
title_short GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms
title_sort gwips‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms
topic Technical Brief
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832365/
https://www.ncbi.nlm.nih.gov/pubmed/25736862
http://dx.doi.org/10.1002/pmic.201400603
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