Genome-wide identification and differential analysis of translational initiation

Peng Zhang, Dandan He, Yi Xu, Jiakai Hou, Bih Fang Pan, Yunfei Wang, Tao Liu, Christel M. Davis, Erik A. Ehli, Lin Tan, Feng Zhou, Jian Hu, Yonghao Yu, Xi Chen, Tuan M. Nguyen, Jeffrey M. Rosen, David H. Hawke, Zhe Ji, Yiwen Chen

Research output: Contribution to journalArticle

12 Scopus citations

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.

Original languageEnglish (US)
Article number1749
JournalNature Communications
Volume8
Issue number1
DOIs
Publication statusPublished - Dec 1 2017

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ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Zhang, P., He, D., Xu, Y., Hou, J., Pan, B. F., Wang, Y., ... Chen, Y. (2017). Genome-wide identification and differential analysis of translational initiation. Nature Communications, 8(1), [1749]. https://doi.org/10.1038/s41467-017-01981-8