Improved Ribo-seq enables identification of cryptic translation events

Ribosome profiling has predicted thousands of short open reading frames (sORFs) in eukaryotic cells, but still suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method modeling the experimental noise to accurately resolve overlapping sORFs and n...

Descripción completa

Detalles Bibliográficos
Autores principales: Erhard, Florian, Halenius, Anne, Zimmermann, Cosima, L’Hernault, Anne, Kowalewski, Daniel J., Weekes, Michael P., Stevanovic, Stefan, Zimmer, Ralf, Dölken, Lars
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2018
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6152898/
https://www.ncbi.nlm.nih.gov/pubmed/29529017
http://dx.doi.org/10.1038/nmeth.4631
_version_ 1783357443990880256
author Erhard, Florian
Halenius, Anne
Zimmermann, Cosima
L’Hernault, Anne
Kowalewski, Daniel J.
Weekes, Michael P.
Stevanovic, Stefan
Zimmer, Ralf
Dölken, Lars
author_facet Erhard, Florian
Halenius, Anne
Zimmermann, Cosima
L’Hernault, Anne
Kowalewski, Daniel J.
Weekes, Michael P.
Stevanovic, Stefan
Zimmer, Ralf
Dölken, Lars
author_sort Erhard, Florian
collection PubMed
description Ribosome profiling has predicted thousands of short open reading frames (sORFs) in eukaryotic cells, but still suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method modeling the experimental noise to accurately resolve overlapping sORFs and non-canonical translation initiation. We experimentally validated translation using MHC-I peptidomics and saw that sORF-derived peptides efficiently enter the MHC-I presentation pathway and thus constitute a substantial fraction of the antigen repertoire.
format Online
Article
Text
id pubmed-6152898
institution National Center for Biotechnology Information
language English
publishDate 2018
record_format MEDLINE/PubMed
spelling pubmed-61528982018-09-25 Improved Ribo-seq enables identification of cryptic translation events Erhard, Florian Halenius, Anne Zimmermann, Cosima L’Hernault, Anne Kowalewski, Daniel J. Weekes, Michael P. Stevanovic, Stefan Zimmer, Ralf Dölken, Lars Nat Methods Article Ribosome profiling has predicted thousands of short open reading frames (sORFs) in eukaryotic cells, but still suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method modeling the experimental noise to accurately resolve overlapping sORFs and non-canonical translation initiation. We experimentally validated translation using MHC-I peptidomics and saw that sORF-derived peptides efficiently enter the MHC-I presentation pathway and thus constitute a substantial fraction of the antigen repertoire. 2018-03-12 2018-05 /pmc/articles/PMC6152898/ /pubmed/29529017 http://dx.doi.org/10.1038/nmeth.4631 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Erhard, Florian
Halenius, Anne
Zimmermann, Cosima
L’Hernault, Anne
Kowalewski, Daniel J.
Weekes, Michael P.
Stevanovic, Stefan
Zimmer, Ralf
Dölken, Lars
Improved Ribo-seq enables identification of cryptic translation events
title Improved Ribo-seq enables identification of cryptic translation events
title_full Improved Ribo-seq enables identification of cryptic translation events
title_fullStr Improved Ribo-seq enables identification of cryptic translation events
title_full_unstemmed Improved Ribo-seq enables identification of cryptic translation events
title_short Improved Ribo-seq enables identification of cryptic translation events
title_sort improved ribo-seq enables identification of cryptic translation events
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6152898/
https://www.ncbi.nlm.nih.gov/pubmed/29529017
http://dx.doi.org/10.1038/nmeth.4631
work_keys_str_mv AT erhardflorian improvedriboseqenablesidentificationofcryptictranslationevents
AT haleniusanne improvedriboseqenablesidentificationofcryptictranslationevents
AT zimmermanncosima improvedriboseqenablesidentificationofcryptictranslationevents
AT lhernaultanne improvedriboseqenablesidentificationofcryptictranslationevents
AT kowalewskidanielj improvedriboseqenablesidentificationofcryptictranslationevents
AT weekesmichaelp improvedriboseqenablesidentificationofcryptictranslationevents
AT stevanovicstefan improvedriboseqenablesidentificationofcryptictranslationevents
AT zimmerralf improvedriboseqenablesidentificationofcryptictranslationevents
AT dolkenlars improvedriboseqenablesidentificationofcryptictranslationevents

Ejemplares similares