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.
Keywords:
NMD; Selective ribosome profiling; Upf proteins.
Copyright © 2018 Elsevier Inc. All rights reserved.
Publication types
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Research Support, N.I.H., Extramural
MeSH terms
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Codon, Nonsense
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Gene Expression Regulation, Fungal*
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Immunoprecipitation / methods
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Nonsense Mediated mRNA Decay
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Protein Binding
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Protein Isoforms / genetics
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Protein Isoforms / metabolism
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RNA Helicases / genetics*
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RNA Helicases / metabolism
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RNA Stability
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RNA, Fungal / genetics*
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RNA, Fungal / metabolism
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RNA, Messenger / genetics*
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RNA, Messenger / metabolism
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Ribosomal Proteins / genetics
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Ribosomal Proteins / metabolism
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Ribosomes / classification
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Ribosomes / genetics*
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Ribosomes / metabolism
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Saccharomyces cerevisiae / genetics*
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Saccharomyces cerevisiae / growth & development
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Saccharomyces cerevisiae / metabolism
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Saccharomyces cerevisiae Proteins / genetics*
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Saccharomyces cerevisiae Proteins / metabolism
Substances
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Codon, Nonsense
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Protein Isoforms
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RNA, Fungal
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RNA, Messenger
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Ribosomal Proteins
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Saccharomyces cerevisiae Proteins
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NAM7 protein, S cerevisiae
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RNA Helicases