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Quantitative profiling of peptides from RNAs classified as noncoding

Author

Listed:
  • Sudhakaran Prabakaran

    (Proteomics Center, Boston Children’s Hospital
    Harvard Medical School
    Present address: Tufts University Science and Technology Center Building, 4 Colby Street, Medford, Massachusetts 02155, USA)

  • Martin Hemberg

    (Boston Children’s Hospital
    Present address: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK)

  • Ruchi Chauhan

    (Proteomics Center, Boston Children’s Hospital
    F.M. Kirby Neurobiology Center, Boston Children’s Hospital)

  • Dominic Winter

    (Proteomics Center, Boston Children’s Hospital
    Present address: Institute for Biochemistry and Molecular Biology, Nussallee 11, 53115 Bonn, Germany)

  • Ry Y. Tweedie-Cullen

    (F.M. Kirby Neurobiology Center, Boston Children’s Hospital
    Present address: School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand)

  • Christian Dittrich

    (F.M. Kirby Neurobiology Center, Boston Children’s Hospital
    Present address: Merck Millipore, Im Laternenacker 5, 8200 Schaffhausen, Switzerland)

  • Elizabeth Hong

    (F.M. Kirby Neurobiology Center, Boston Children’s Hospital
    Present address: Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA)

  • Jeremy Gunawardena

    (Harvard Medical School)

  • Hanno Steen

    (Proteomics Center, Boston Children’s Hospital
    Boston Children’s Hospital and Harvard Medical School)

  • Gabriel Kreiman

    (Boston Children’s Hospital
    F.M. Kirby Neurobiology Center, Boston Children’s Hospital)

  • Judith A. Steen

    (Proteomics Center, Boston Children’s Hospital
    F.M. Kirby Neurobiology Center, Boston Children’s Hospital)

Abstract

Only a small fraction of the mammalian genome codes for messenger RNAs destined to be translated into proteins, and it is generally assumed that a large portion of transcribed sequences—including introns and several classes of noncoding RNAs (ncRNAs)—do not give rise to peptide products. A systematic examination of translation and physiological regulation of ncRNAs has not been conducted. Here we use computational methods to identify the products of non-canonical translation in mouse neurons by analysing unannotated transcripts in combination with proteomic data. This study supports the existence of non-canonical translation products from both intragenic and extragenic genomic regions, including peptides derived from antisense transcripts and introns. Moreover, the studied novel translation products exhibit temporal regulation similar to that of proteins known to be involved in neuronal activity processes. These observations highlight a potentially large and complex set of biologically regulated translational events from transcripts formerly thought to lack coding potential.

Suggested Citation

  • Sudhakaran Prabakaran & Martin Hemberg & Ruchi Chauhan & Dominic Winter & Ry Y. Tweedie-Cullen & Christian Dittrich & Elizabeth Hong & Jeremy Gunawardena & Hanno Steen & Gabriel Kreiman & Judith A. St, 2014. "Quantitative profiling of peptides from RNAs classified as noncoding," Nature Communications, Nature, vol. 5(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6429
    DOI: 10.1038/ncomms6429
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