YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts

Nucleic Acids Res. 2012 Sep 1;40(17):8622-36. doi: 10.1093/nar/gks579. Epub 2012 Jun 22.


The human Y box-binding protein-1 (YB-1) is a deoxyribonucleic acid (DNA)/ribonucleic acid (RNA)-binding protein with pleiotropic functions. Besides its roles in the regulation of transcription and translation, several recent studies indicate that YB-1 is a spliceosome-associated protein and is involved in alternative splicing, but the underlying mechanism has remained elusive. Here, we define both CAUC and CACC as high-affinity binding motifs for YB-1 by systematic evolution of ligands by exponential enrichment (SELEX) and demonstrate that these newly defined motifs function as splicing enhancers. Interestingly, on the endogenous CD44 gene, YB-1 appears to mediate a network interaction to activate exon v5 inclusion via multiple CAUC motifs in both the alternative exon and its upstream polypyrimidine tract. We provide evidence that YB-1 activates splicing by facilitating the recruitment of U2AF65 to weak polypyrimidine tracts through direct protein-protein interactions. Together, these findings suggest a vital role of YB-1 in activating a subset of weak 3' splice sites in mammalian cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Binding Sites
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism
  • Exons*
  • HEK293 Cells
  • Humans
  • Hyaluronan Receptors / genetics
  • Hyaluronan Receptors / metabolism
  • Introns*
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / metabolism*
  • Nucleotide Motifs
  • Protein Interaction Domains and Motifs
  • RNA / chemistry
  • RNA / metabolism
  • RNA Precursors / metabolism
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism*
  • Ribonucleoproteins / chemistry
  • Ribonucleoproteins / metabolism*
  • SELEX Aptamer Technique
  • Splicing Factor U2AF
  • Y-Box-Binding Protein 1 / chemistry
  • Y-Box-Binding Protein 1 / metabolism*


  • DNA-Binding Proteins
  • DSX protein, Drosophila
  • Drosophila Proteins
  • Hyaluronan Receptors
  • Nuclear Proteins
  • RNA Precursors
  • RNA, Messenger
  • RNA-Binding Proteins
  • Ribonucleoproteins
  • Splicing Factor U2AF
  • U2AF2 protein, human
  • Y-Box-Binding Protein 1
  • YBX1 protein, human
  • RNA