PT  - JOURNAL ARTICLE
AU  - Lorenzo Calviello
AU  - Neelanjan Mukherjee
AU  - Emanuel Wyler
AU  - Henrik Zauber
AU  - Antje Hirsekorn
AU  - Matthias Selbach
AU  - Markus Landthaler
AU  - Benedikt Obermayer
AU  - Uwe Ohler
TI  - A spectral analysis approach to detect actively translated open reading frames in high-resolution ribosome profiling data
AID  - 10.1101/031625
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 031625
4099  - http://biorxiv.org/content/early/2015/11/13/031625.short
4100  - http://biorxiv.org/content/early/2015/11/13/031625.full
AB  - RNA sequencing protocols allow for quantifying gene expression regulation at each individual step, from transcription to protein synthesis. Ribosome Profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. Despite its great potential, a rigorous statistical approach to identify translated regions by means of the characteristic three-nucleotide periodicity of Ribo-seq data is not yet available. To fill this gap, we developed RiboTaper, which quantifies the significance of periodic Ribo-seq reads via spectral analysis methods.We applied RiboTaper on newly generated, deep Ribo-seq data in HEK293 cells, to derive an extensive map of translation that covers Open Reading Frame (ORF) annotations for more than 11,000 protein-coding genes. We also find distinct ribosomal signatures for several hundred detected upstream ORFs and ORFs in annotated non-coding genes (ncORFs). Mass spectrometry data confirms that RiboTaper achieves excellent coverage of the cellular proteome and validates dozens of novel peptide products. Collectively, RiboTaper (available at https://ohlerlab.mdc-berlin.de/software/) is a powerful method for comprehensive de novo identification of actively used ORFs in the human genome.