End-to-end pipeline for differential analysis of pausing in ribosome profiling data

Keegan Flanagan; Wanxin Li; Ethan J Greenblatt; Khanh Dao Duc

doi:10.1016/j.xpro.2022.101605

End-to-end pipeline for differential analysis of pausing in ribosome profiling data

STAR Protoc. 2022 Aug 18;3(3):101605. doi: 10.1016/j.xpro.2022.101605. eCollection 2022 Sep 16.

Authors

Keegan Flanagan¹, Wanxin Li², Ethan J Greenblatt³, Khanh Dao Duc⁴

Affiliations

¹ Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada; Department of Mathematics, University of British Columbia, Vancouver, BC, Canada.
² School of Computer Science, University of Waterloo, Waterloo, ON, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada.
³ Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada. Electronic address: ethan.greenblatt@ubc.ca.
⁴ Department of Mathematics, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada. Electronic address: kdd@math.ubc.ca.

Abstract

Ribosome profiling is a powerful technique which maps the distribution of ribosomes along mRNAs to analyze translation genome-wide. Ribosome density can be affected by multiple factors, such as changes to translation initiation or elongation rates. We describe the application of a metric for identifying genes rate-limited by these rates by analyzing the relative distribution of ribosome footprints along transcripts. This protocol also details two sample analyses comparing gene translation efficiencies and the distribution of ribosome densities on downloadable datasets. For complete details on the use and execution of this protocol, please refer to Flanagan et al. (2022).

Keywords: Bioinformatics; Genomics; Sequence analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Protein Biosynthesis*
RNA, Messenger
Ribosomes*

Substances

RNA, Messenger