Invariant U2 snRNA nucleotides form a stem loop to recognize the intron early in splicing

Mol Cell. 2010 May 14;38(3):416-27. doi: 10.1016/j.molcel.2010.02.036.


U2 snRNA-intron branchpoint pairing is a critical step in pre-mRNA recognition by the splicing apparatus, but the mechanism by which these two RNAs engage each other is unknown. Here, we identify a U2 snRNA structure, the branchpoint-interacting stem loop (BSL), which presents the U2 nucleotides that will contact the intron. We provide evidence that the BSL forms prior to interaction with the intron and is disrupted by the DExD/H protein Prp5p during engagement of the snRNA with the intron. In vitro splicing complex assembly in a BSL-destabilized mutant extract suggests that the BSL is required at a previously unrecognized step between commitment complex and prespliceosome formation. The extreme evolutionary conservation of the BSL suggests that it represents an ancient structural solution to the problem of intron branchpoint recognition by dynamic RNA elements that must serve multiple functions at other times during splicing.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Base Sequence
  • Binding Sites
  • DEAD-box RNA Helicases / metabolism
  • Evolution, Molecular
  • Fungal Proteins / metabolism
  • Gene Expression Regulation, Fungal*
  • Genotype
  • Introns*
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation
  • Phenotype
  • RNA Precursors / metabolism
  • RNA Splicing*
  • RNA, Fungal / chemistry
  • RNA, Fungal / metabolism*
  • RNA, Messenger / metabolism
  • RNA, Small Nuclear / chemistry
  • RNA, Small Nuclear / metabolism*
  • Spliceosomes / metabolism*
  • Structure-Activity Relationship
  • Yeasts / genetics*
  • Yeasts / metabolism


  • Fungal Proteins
  • RNA Precursors
  • RNA, Fungal
  • RNA, Messenger
  • RNA, Small Nuclear
  • U2 small nuclear RNA
  • Adenosine Triphosphate
  • DEAD-box RNA Helicases