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*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

65 Scopus citations


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
Issue number1
StatePublished - Dec 1 2017

ASJC Scopus subject areas

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


Dive into the research topics of 'Genome-wide identification and differential analysis of translational initiation'. Together they form a unique fingerprint.

Cite this