Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):10010-5. doi: 10.1073/pnas.1017386108. Epub 2011 May 24.

Abstract

Many protein-protein and protein-nucleic acid interactions have been experimentally characterized, whereas RNA-RNA interactions have generally only been predicted computationally. Here, we describe a high-throughput method to identify intramolecular and intermolecular RNA-RNA interactions experimentally by cross-linking, ligation, and sequencing of hybrids (CLASH). As validation, we identified 39 known target sites for box C/D modification-guide small nucleolar RNAs (snoRNAs) on the yeast pre-rRNA. Novel snoRNA-rRNA hybrids were recovered between snR4-5S and U14-25S. These are supported by native electrophoresis and consistent with previously unexplained data. The U3 snoRNA was found to be associated with sequences close to the 3' side of the central pseudoknot in 18S rRNA, supporting a role in formation of this structure. Applying CLASH to the yeast U2 spliceosomal snRNA led to a revised predicted secondary structure, featuring alternative folding of the 3' domain and long-range contacts between the 3' and 5' domains. CLASH should allow transcriptome-wide analyses of RNA-RNA interactions in many organisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Blotting, Northern
  • DNA, Complementary / chemistry
  • DNA, Complementary / genetics
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • RNA, Fungal / chemistry
  • RNA, Fungal / genetics*
  • RNA, Fungal / metabolism
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / genetics*
  • RNA, Ribosomal / metabolism
  • RNA, Ribosomal, 18S / chemistry
  • RNA, Ribosomal, 18S / genetics
  • RNA, Ribosomal, 18S / metabolism
  • RNA, Small Nuclear / chemistry
  • RNA, Small Nuclear / genetics
  • RNA, Small Nuclear / metabolism
  • RNA, Small Nucleolar / chemistry
  • RNA, Small Nucleolar / genetics*
  • RNA, Small Nucleolar / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Sequence Analysis, DNA
  • Spliceosomes / genetics
  • Spliceosomes / metabolism

Substances

  • DNA, Complementary
  • RNA, Fungal
  • RNA, Ribosomal
  • RNA, Ribosomal, 18S
  • RNA, Small Nuclear
  • RNA, Small Nucleolar
  • RNA, U3 small nucleolar
  • U2 small nuclear RNA