Genome-wide identification and differential analysis of translational initiation.
Translation is principally regulated at the initiation stage. The development of the translation initiation (TI) sequencing (TI-seq) technique has enabled the global mapping of TIs and revealed unanticipated complex translational landscapes in metazoans. Despite the wide adoption of TI-seq, there is no computational tool currently available for analyzing TI-seq data. To fill this gap, we develop a comprehensive toolkit named Ribo-TISH, which allows for detecting and quantitatively comparing TIs across conditions from TI-seq data. Ribo-TISH can also predict novel open reading frames (ORFs) from regular ribosome profiling (rRibo-seq) data and outperform several established methods in both computational efficiency and prediction accuracy. Applied to published TI-seq/rRibo-seq data sets, Ribo-TISH uncovers a novel signature of elevated mitochondrial translation during amino-acid deprivation and predicts novel ORFs in 5'UTRs, long noncoding RNAs, and introns. These successful applications demonstrate the power of Ribo-TISH in extracting biological insights from TI-seq/rRibo-seq data.
|Year of Publication||
2017 11 23
|PubMed Central ID||
R00 CA172700 / CA / NCI NIH HHS / United States
K99 CA207865 / CA / NCI NIH HHS / United States
R00 CA175290 / CA / NCI NIH HHS / United States
R01 CA016303 / CA / NCI NIH HHS / United States
R00 CA207865 / CA / NCI NIH HHS / United States
R01 GM114160 / GM / NIGMS NIH HHS / United States