RT Journal Article
SR Electronic
T1 A spectral analysis approach to detect actively translated open reading frames in high-resolution ribosome profiling data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 031625
DO 10.1101/031625
A1 Calviello, Lorenzo
A1 Mukherjee, Neelanjan
A1 Wyler, Emanuel
A1 Zauber, Henrik
A1 Hirsekorn, Antje
A1 Selbach, Matthias
A1 Landthaler, Markus
A1 Obermayer, Benedikt
A1 Ohler, Uwe
YR 2015
UL http://biorxiv.org/content/early/2015/11/13/031625.abstract
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.