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Selective profiling of ribosomes associated with yeast Upf proteins.

ABSTRACT: Ribosomes associated with nonsense-mediated decay factors Upf1, Upf2, or Upf3 were purified by immunoprecipitation, and enrichment and stoichiometry of Upf factors and ribosomal proteins were analyzed by western blot and mass spectrometry. Using a small RNA library preparation protocol that eliminates in-gel RNA and cDNA size selection and incorporates four random nucleotides on each side of the ribosome-protected RNA fragment allowed recovery, detection, and analysis of all size classes of protected fragments from a sample simultaneously.

SUBMITTER: Ganesan R

PROVIDER: S-EPMC6387845 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Selective profiling of ribosomes associated with yeast Upf proteins.

Ganesan Robin R Leszyk John J Jacobson Allan A

Methods (San Diego, Calif.) 20181226

Ribosomes associated with nonsense-mediated decay factors Upf1, Upf2, or Upf3 were purified by immunoprecipitation, and enrichment and stoichiometry of Upf factors and ribosomal proteins were analyzed by western blot and mass spectrometry. Using a small RNA library preparation protocol that eliminates in-gel RNA and cDNA size selection and incorporates four random nucleotides on each side of the ribosome-protected RNA fragment allowed recovery, detection, and analysis of all size classes of prot ...[more]

PMID: 30593864

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