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- Title
Genome-wide identification and differential analysis of translational initiation.
- Authors
Peng Zhang; Dandan He; Yi Xu; Jiakai Hou; Bih-Fang Pan; Yunfei Wang; Tao Liu; Davis, Christel M.; Ehli, Erik A.; Lin Tan; Feng Zhou; Jian Hu; Yonghao Yu; Xi Chen; Nguyen, Tuan M.; Rosen, Jeffrey M.; Hawke, David H.; Zhe Ji; Yiwen Chen
- Abstract
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.
- Publication
Nature Communications, 2017, Vol 8, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-017-01981-8