Introduction

RNA-sequencing protocols can quantify gene expression regulation from transcription to protein synthesis. Ribosome profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. We have developed RiboTaper (available at https://ohlerlab.mdc-berlin.de/software/), a rigorous statistical approach that identifies translated regions on the basis of the characteristic three-nucleotide periodicity of Ribo-seq data. We used RiboTaper with deep Ribo-seq data from HEK293 cells to derive an extensive map of translation that covered open reading frame (ORF) annotations for more than 11,000 protein-coding genes. We also found distinct ribosomal signatures for several hundred upstream ORFs and ORFs in annotated noncoding genes (ncORFs). Mass spectrometry data confirmed that RiboTaper achieved excellent coverage of the cellular proteome. Although dozens of novel peptide products were validated in this manner, few of the currently annotated long noncoding RNAs appeared to encode stable polypeptides. RiboTaper is a powerful method for comprehensive de novo identification of actively used ORFs from Ribo-seq data.

Publications

  1. Detecting actively translated open reading frames in ribosome profiling data.
    Cite this
    Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U, 2016-02-01 - Nature methods

Credits

  1. Lorenzo Calviello
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany

  2. Neelanjan Mukherjee
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany

  3. Emanuel Wyler
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany

  4. Henrik Zauber
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany

  5. Antje Hirsekorn
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany

  6. Matthias Selbach
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany

  7. Markus Landthaler
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany

  8. Benedikt Obermayer
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany

  9. Uwe Ohler
    Investigator

    Department of Computer Science, Humboldt University, Germany

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Summary
AccessionBT006607
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByUwe Ohler