Peptidomic discovery of short open reading frame–encoded peptides in human cells

Slavoff, Sarah A.; Mitchell, Andrew J.; Schwaid, Adam G.; Cabili, Moran N.; Ma, Ji; Levin, Joshua Z.; Karger, Amir; Budnik, Bogdan; Rinn, John L.; Saghatelian, Alan

doi:10.1038/nchembio.1120

Cited by 545 publications

(770 citation statements)

References 49 publications

(76 reference statements)

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“…These ncRNAs were unstructured and encoded very short ORFs (<30 aa). They could be RNAs specifying short biologically active peptides, as recently identified in mammalian cells (53). This enigmatic cohort of ribosome-associated ncRNAs will require further study to determine whether they are translated or function in a manner that involves association with ribosomes.…”

Section: Hypoxia Reduces Ribosome Protection Associated With Initiatimentioning

confidence: 99%

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

Juntawong

Girke

Bazin

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

346

408

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Translational regulation contributes to plasticity in metabolism and growth that enables plants to survive in a dynamic environment. Here, we used the precise mapping of ribosome footprints (RFs) on mRNAs to investigate translational regulation under control and sublethal hypoxia stress conditions in seedlings of Arabidopsis thaliana. Ribosomes were obtained by differential centrifugation or immunopurification and were digested with RNase I to generate footprint fragments that were deep-sequenced. Comparison of RF number and position on genic regions with fragmented total and polysomal mRNA illuminated numerous aspects of posttranscriptional and translational control under both growth conditions. When seedlings were oxygen-deprived, the frequency of ribosomes at the start codon was reduced, consistent with a global decline in initiation of translation. Hypoxia-up-regulated gene transcripts increased in polysome complexes during the stress, but the number of ribosomes per transcript relative to normoxic conditions was not enhanced. On the other hand, many mRNAs with limited change in steady-state abundance had significantly fewer ribosomes but with an overall similar distribution under hypoxia, consistent with restriction of initiation rather than elongation of translation. RF profiling also exposed the inhibitory effect of upstream ORFs on the translation of downstream protein-coding regions under normoxia, which was further modulated by hypoxia. The data document translation of alternatively spliced mRNAs and expose ribosome association with some noncoding RNAs. Altogether, we present an experimental approach that illuminates prevalent and nuanced regulation of protein synthesis under optimal and energy-limiting conditions. ribosome profiling | uORF | alternative splicing | long intergenic noncoding RNA | translational efficiency

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Section: Hypoxia Reduces Ribosome Protection Associated With Initiatimentioning

confidence: 99%

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

Juntawong

Girke

Bazin

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

346

408

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“…Peptidomics is a modified form of proteomics that combines MS and computational prediction (Fig. 2D) (Ma et al, 2016;Matsumoto et al, 2017;Slavoff et al, 2013). Peptides are usually concentrated with the use of a molecular weight cutoff filter (MWCO) or sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in order to reduce the background signal due to larger annotated proteins.…”

Section: Identification Of Hidden Peptidesmentioning

confidence: 99%

Hidden Peptides Encoded by Putative Noncoding RNAs

Matsumoto

Nakayama

2018

Cell Struct. Funct.

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Although the definition of a noncoding RNA (ncRNA) is an RNA molecule that does not encode a protein, recent evidence has revealed that some ncRNAs are indeed translated to give rise to small polypeptides (usually containing fewer than 100 amino acids). Despite their small size, however, these peptides are often biologically relevant in that they are required for a variety of cellular processes. In this review, we summarize the production and functions of peptides that have been recently identified as translation products of putative ncRNAs.4

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“…Translational profiling and mass spectrometry (MS) studies have recently identified a large pool of noncanonical small translation products in mammalian cells initiated from non-AUG codons and from intron sequences (25,26). After insertion of the 6xHis-tag after the SL8 epitope in the Glob-exon-SL8-PTC construct (Glob-exon/intron-SL8-His-PTC) (Fig.…”

Section: Ribosomal Scanning Of Nonspliced Mrnas Gives Rise To Productmentioning

confidence: 99%

Translation of pre-spliced RNAs in the nuclear compartment generates peptides for the MHC class I pathway

Apcher

Millot

Daskalogianni

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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The scanning of maturing mRNAs by ribosomes plays a key role in the mRNA quality control process. When ribosomes first engage with the newly synthesized mRNA, and if peptides are produced, is unclear, however. Here we show that ribosomal scanning of prespliced mRNAs occurs in the nuclear compartment, and that this event produces peptide substrates for the MHC class I pathway. Inserting antigenic peptide sequences in introns that are spliced out before the mRNAs exit the nuclear compartment results in an equal amount of antigenic peptide products as when the peptides are encoded from the main open reading frame (ORF). Taken together with the detection of intron-encoded nascent peptides and RPS6/RPL7-carrying complexes in the perinucleolar compartment, these results show that peptides are produced by a translation event occurring before mRNA splicing. This suggests that ribosomes occupy and scan mRNAs early in the mRNA maturation process, and suggests a physiological role for nuclear mRNA translation, and also helps explain how the immune system tolerates peptides derived from tissue-specific mRNA splice variants.MHC class I restricted antigen presentation | mRNA maturation | nuclear translation R NAs carrying premature termination codons or are recognized as defective in other aspects are prevented from further translation and disposed of by the nonsense-mediated decay (NMD) pathway (1). The detection of premature stop codons is mediated by the scanning ribosome; however, when the ribosomes first engage with the newly synthesized mRNA, and if this event results in the production of peptides, is unclear. Two observations from the field of immunology and the presentation of peptides on MHC class I molecules have highlighted some aspects relevant to the role of the ribosomes in the mRNA maturation process. The first observation is related to the detection of antigenic peptides originating from intron sequences, and the second is related to the observation that the synthesis of antigenic peptide substrates and full-length proteins are two spatiotemporarily distinct events (2-5).The presentation of antigenic peptides on MHC class I molecules allows CD8 + T cells to detect and eliminate cells in which the repertoire of peptide substrates has been altered owing to the presence of viruses or to changes in the presentation of endogenous antigens (6, 7). However, despite the key role of antigen presentation on MHC class I molecules in immune surveillance, the source of peptides for the MHC class I pathway is not yet known. Accumulating evidence indicates that the processing of alternative peptide substrates plays a major role, and that degradation products derived from full-length proteins have limited access to the MHC class I pathway (8-10). We recently demonstrated that pioneer translation products (PTPs) that form antigenic peptide substrates for the MHC class I pathway are produced by a translation event that is distinct from the canonical event giving rise to full-length proteins and does not require the cap-binding ...

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Peptidomic discovery of short open reading frame–encoded peptides in human cells

Cited by 545 publications

References 49 publications

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

Hidden Peptides Encoded by Putative Noncoding RNAs

Translation of pre-spliced RNAs in the nuclear compartment generates peptides for the MHC class I pathway

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