title: Detecting actively translated open reading frames in ribosome profiling data.
abstract: 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.
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Calviello
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Neelanjan
authors.initials: N
authors.lastname: Mukherjee
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Emanuel
authors.initials: E
authors.lastname: Wyler
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Henrik
authors.initials: H
authors.lastname: Zauber
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Antje
authors.initials: A
authors.lastname: Hirsekorn
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Selbach
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Landthaler
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Benedikt
authors.initials: B
authors.lastname: Obermayer
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.|Department of Biology, Humboldt University, Berlin, Germany.|Department of Computer Science, Humboldt University, Berlin, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
mesh_terms: D057809:HEK293 Cells; D006801:Humans; D016366:Open Reading Frames; D014176:Protein Biosynthesis / Q000235:genetics; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome