Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling

Alexander L. Cope, Sangeevan Vellappan, John S. Favate, Kyle S. Skalenko, Srujana S. Yadavalli, Premal Shah

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The emergence of ribosome profiling as a tool for measuring the translatome has provided researchers with valuable insights into the post-transcriptional regulation of gene expression. Despite the biological insights and technical improvements made since the technique was initially described by Ingolia et al. (Science 324(5924):218–223, 2009), ribosome profiling measurements and subsequent data analysis remain challenging. Here, we describe our lab’s protocol for performing ribosome profiling in bacteria, yeast, and mammalian cells. This protocol has integrated elements from three published ribosome profiling methods. In addition, we describe a tool called RiboViz (Carja et al., BMC Bioinformatics 18:461, 2017) (https://github.com/riboviz/riboviz ) for the analysis and visualization of ribosome profiling data. Given raw sequencing reads and transcriptome information (e.g., FASTA, GFF) for a species, RiboViz performs the necessary pre-processing and mapping of the raw sequencing reads. RiboViz also provides the user with various quality control visualizations.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages83-110
Number of pages28
DOIs
StatePublished - 2022

Publication series

NameMethods in Molecular Biology
Volume2404
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Keywords

  • Antibiotic inhibitors
  • Footprinting
  • RNA
  • Ribo-seq
  • Ribosome profiling
  • Translation initiation

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