Nuclease-mediated depletion biases in ribosome footprint profiling libraries

Boris Zinshteyn, Jamie R. Wangen, H. U.A. Boyang, Rachel Green

Research output: Contribution to journalArticlepeer-review

Abstract

Ribosome footprint profiling is a high-throughput sequencing-based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally very abundant, ribosomal RNA sequences that dominate libraries and increase sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued as a standalone product and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them generally unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments.

Original languageEnglish (US)
Pages (from-to)1481-1488
Number of pages8
JournalRNA
Volume26
Issue number10
DOIs
StatePublished - Oct 2020

Keywords

  • RNA-seq
  • RRNA depletion
  • Ribo-Zero
  • Ribo-seq
  • Ribosome profiling

ASJC Scopus subject areas

  • Molecular Biology

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