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Post-Transcriptional Gene Regulation pp 83–110Cite as

Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2404))

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.

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Author information

Author notes

  1. Alexander L. Cope and Sangeevan Vellappan contributed equally.

Authors and Affiliations

  1. Department of Genetics, Rutgers University, Piscataway, NJ, USA

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

  2. Human Genetics Institute of New Jersey, Piscataway, NJ, USA

    Alexander L. Cope, John S. Favate & Premal Shah

  3. Waksman Institute, Rutgers University, Piscataway, NJ, USA

    Sangeevan Vellappan, Kyle S. Skalenko & Srujana S. Yadavalli

Authors
  1. Alexander L. Cope
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  2. Sangeevan Vellappan
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  3. John S. Favate
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  4. Kyle S. Skalenko
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  5. Srujana S. Yadavalli
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  6. Premal Shah
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Corresponding author

Correspondence to Premal Shah .

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Editors and Affiliations

  1. Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

    Erik Dassi

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Cope, A.L., Vellappan, S., Favate, J.S., Skalenko, K.S., Yadavalli, S.S., Shah, P. (2022). Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling. In: Dassi, E. (eds) Post-Transcriptional Gene Regulation. Methods in Molecular Biology, vol 2404. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1851-6_5

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  • DOI: https://doi.org/10.1007/978-1-0716-1851-6_5

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1850-9

  • Online ISBN: 978-1-0716-1851-6

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