An mRNA-derived noncoding RNA targets and regulates the ribosome

Mol Cell. 2014 Apr 10;54(1):147-155. doi: 10.1016/j.molcel.2014.02.024. Epub 2014 Mar 27.


The structural and functional repertoire of small non-protein-coding RNAs (ncRNAs) is central for establishing gene regulation networks in cells and organisms. Here, we show that an mRNA-derived 18-nucleotide-long ncRNA is capable of downregulating translation in Saccharomyces cerevisiae by targeting the ribosome. This 18-mer ncRNA binds to polysomes upon salt stress and is crucial for efficient growth under hyperosmotic conditions. Although the 18-mer RNA originates from the TRM10 locus, which encodes a tRNA methyltransferase, genetic analyses revealed the 18-mer RNA nucleotide sequence, rather than the mRNA-encoded enzyme, as the translation regulator. Our data reveal the ribosome as a target for a small regulatory ncRNA and demonstrate the existence of a yet unkown mechanism of translation regulation. Ribosome-targeted small ncRNAs are found in all domains of life and represent a prevalent but so far largely unexplored class of regulatory molecules.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological
  • Binding Sites
  • Exons
  • Gene Expression Regulation, Fungal
  • Osmotic Pressure
  • Polyribosomes / genetics
  • Polyribosomes / metabolism*
  • Protein Biosynthesis
  • RNA, Fungal / metabolism*
  • RNA, Messenger / metabolism*
  • RNA, Small Untranslated / metabolism*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / growth & development
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Stress, Physiological
  • Time Factors
  • tRNA Methyltransferases / genetics
  • tRNA Methyltransferases / metabolism


  • RNA, Fungal
  • RNA, Messenger
  • RNA, Small Untranslated
  • Saccharomyces cerevisiae Proteins
  • TRM10 protein, S cerevisiae
  • tRNA Methyltransferases