Improved Ribo-seq enables identification of cryptic translation events

Florian Erhard; Anne Halenius; Cosima Zimmermann; Anne L'Hernault; Daniel J. Kowalewski; Michael P. Weekes; Stefan Stevanovic; Ralf Zimmer; Lars Dölken

doi:10.1038/nmeth.4631

Improved Ribo-seq enables identification of cryptic translation events

Florian Erhard^*, Anne Halenius, Cosima Zimmermann, Anne L'Hernault, Daniel J. Kowalewski, Michael P. Weekes, Stefan Stevanovic, Ralf Zimmer, Lars Dölken

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

156 Scopus citations

Abstract

Ribosome profiling has been used to predict thousands of short open reading frames (sORFs) in eukaryotic cells, but it suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method that models experimental noise to enable researchers to accurately resolve overlapping sORFs and noncanonical translation initiation. We experimentally validated translation using major histocompatibility complex class I (MHC I) peptidomics and observed that sORF-derived peptides efficiently enter the MHC I presentation pathway and thus constitute a substantial fraction of the antigen repertoire.

Original language	English
Pages (from-to)	363-366
Number of pages	4
Journal	Nature Methods
Volume	15
Issue number	5
DOIs	https://doi.org/10.1038/nmeth.4631
State	Published - 27 Apr 2018
Externally published	Yes

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title = "Improved Ribo-seq enables identification of cryptic translation events",

abstract = "Ribosome profiling has been used to predict thousands of short open reading frames (sORFs) in eukaryotic cells, but it suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method that models experimental noise to enable researchers to accurately resolve overlapping sORFs and noncanonical translation initiation. We experimentally validated translation using major histocompatibility complex class I (MHC I) peptidomics and observed that sORF-derived peptides efficiently enter the MHC I presentation pathway and thus constitute a substantial fraction of the antigen repertoire.",

author = "Florian Erhard and Anne Halenius and Cosima Zimmermann and Anne L'Hernault and Kowalewski, \{Daniel J.\} and Weekes, \{Michael P.\} and Stefan Stevanovic and Ralf Zimmer and Lars D{\"o}lken",

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day = "27",

doi = "10.1038/nmeth.4631",

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journal = "Nature Methods",

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T1 - Improved Ribo-seq enables identification of cryptic translation events

AU - Erhard, Florian

AU - Halenius, Anne

AU - Zimmermann, Cosima

AU - L'Hernault, Anne

AU - Kowalewski, Daniel J.

AU - Weekes, Michael P.

AU - Stevanovic, Stefan

AU - Zimmer, Ralf

AU - Dölken, Lars

PY - 2018/4/27

Y1 - 2018/4/27

N2 - Ribosome profiling has been used to predict thousands of short open reading frames (sORFs) in eukaryotic cells, but it suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method that models experimental noise to enable researchers to accurately resolve overlapping sORFs and noncanonical translation initiation. We experimentally validated translation using major histocompatibility complex class I (MHC I) peptidomics and observed that sORF-derived peptides efficiently enter the MHC I presentation pathway and thus constitute a substantial fraction of the antigen repertoire.

AB - Ribosome profiling has been used to predict thousands of short open reading frames (sORFs) in eukaryotic cells, but it suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method that models experimental noise to enable researchers to accurately resolve overlapping sORFs and noncanonical translation initiation. We experimentally validated translation using major histocompatibility complex class I (MHC I) peptidomics and observed that sORF-derived peptides efficiently enter the MHC I presentation pathway and thus constitute a substantial fraction of the antigen repertoire.

UR - https://www.scopus.com/pages/publications/85046262804

U2 - 10.1038/nmeth.4631

DO - 10.1038/nmeth.4631

M3 - Article

C2 - 29529017

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SN - 1548-7091

VL - 15

SP - 363

EP - 366

JO - Nature Methods

JF - Nature Methods

IS - 5

ER -

Improved Ribo-seq enables identification of cryptic translation events

Abstract

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