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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.

SUBMITTER: Erhard F 

PROVIDER: S-EPMC6152898 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Improved Ribo-seq enables identification of cryptic translation events.

Erhard Florian F   Halenius Anne A   Zimmermann Cosima C   L'Hernault Anne A   Kowalewski Daniel J DJ   Weekes Michael P MP   Stevanovic Stefan S   Zimmer Ralf R   Dölken Lars L  

Nature methods 20180312 5

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-deriv  ...[more]

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