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

Nature Chemical Biology volume 9, pages 59–64 (2013)Cite this article

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Abstract

The complete extent to which the human genome is translated into polypeptides is of fundamental importance. We report a peptidomic strategy to detect short open reading frame (sORF)-encoded polypeptides (SEPs) in human cells. We identify 90 SEPs, 86 of which are previously uncharacterized, which is the largest number of human SEPs ever reported. SEP abundances range from 10–1,000 molecules per cell, identical to abundances of known proteins. SEPs arise from sORFs in noncoding RNAs as well as multicistronic mRNAs, and many SEPs initiate with non-AUG start codons, indicating that noncanonical translation may be more widespread in mammals than previously thought. In addition, coding sORFs are present in a small fraction (8 out of 1,866) of long intergenic noncoding RNAs. Together, these results provide strong evidence that the human proteome is more complex than previously appreciated.

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Figure 1: Discovering SEPs.
Figure 2: Overview of SEPs.
Figure 3: SEP quantification.
Figure 4: Expression of SEPs.
Figure 5: Characterization of the non-AUG initiation codon of the FRAT2 sORF.

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Acknowledgements

We thank X. Adiconis and L. Fan for constructing the cDNA libraries used in this study. M.N.C. is supported by a Howard Hughes Medical Institute International Student Research Fellowship, and S.A.S. is supported by an National Research Service Award postdoctoral fellowship (1F32GM099408-01). J.L.R. is supported by a Damon Runyon-Rachleff Innovator Award, a Searle Scholars Award and a Richard and Susan Smith Family Foundation Fellowship. A.S. is supported by a Burroughs Wellcome Fund Career Award in Biomedical Sciences, a Searle Scholars Award and an Alfred P. Sloan Fellowship. This work was also supported by the US National Institutes of Health training grant T32GM007598 (A.J.M.), the US National Human Genome Research Institute grant 3U54HG003067 (J.Z.L.), Director's New Innovator Awards DP2OD00667 (J.L.R.) and DP2OD002374 (A.S.), National Institute of General Medical Sciences grant R01GM102491 (A.S.) and support from Harvard University (A.S.).

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Author notes

  1. Andrew J Mitchell and Adam G Schwaid: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA

    Sarah A Slavoff, Adam G Schwaid, Jiao Ma & Alan Saghatelian

  2. Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA

    Andrew J Mitchell

  3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA

    Moran N Cabili & John L Rinn

  4. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA

    Moran N Cabili

  5. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA

    Moran N Cabili & John L Rinn

  6. Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA

    Joshua Z Levin

  7. Division of Science, Research Computing, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA

    Amir D Karger

  8. Center of Systems Biology, Mass Spectrometry and Proteomics Laboratory, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA

    Bogdan A Budnik

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Contributions

A.J.M. and A.G.S. contributed equally to this work. A.J.M., S.A.S., A.G.S., M.N.C., J.M., J.Z.L., A.D.K., B.A.B., J.L.R. and A.S. designed the experiments. A.J.M., S.A.S., A.G.S., M.N.C., A.D.K. and B.A.B. performed the experiments. A.J.M., S.A.S., J.M., A.G.S. and B.A.B. collected the peptidomics data and with A.D.K. searched this against the RefSeq database. J.Z.L. provided the RNA-seq data. M.N.C., A.J.M. and J.L.R. performed the lincRNA analysis. S.A.S. performed all cell imaging studies, cloning and FRAT2 experiments. A.J.M., S.A.S., A.G.S., M.N.C., J.L.R. and A.S. discussed the results and implications and wrote the manuscript together.

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Correspondence to Alan Saghatelian.

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Supplementary information

Supplementary Text and Figures

Supplementary Results (PDF 820 kb)

Supplementary Data Set 1

Full-list of identified SEPS (XLS 38 kb)

Supplementary Data Set 2

AAPGALPEAAVGPR Sf: .81 (PDF 5180 kb)

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Slavoff, S., Mitchell, A., Schwaid, A. et al. Peptidomic discovery of short open reading frame–encoded peptides in human cells. Nat Chem Biol 9, 59–64 (2013). https://doi.org/10.1038/nchembio.1120

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