The RNA binding protein YB-1 binds A/C-rich exon enhancers and stimulates splicing of the CD44 alternative exon v4

Exon enhancers are accessory pre-mRNA splicing signals that stimulate exon splicing. One class of proteins, the serine-arginine-rich (SR) proteins, ha ve been demonstrated to bind enhancers and activate splicing. Here we repor t that A/C-rich exon enhancers (ACE elements) are recognized by the human Y B-1 protein, a non-SR protein. Sequence-specific binding of YB-1 was observ ed both to an ACE derived from an in vivo iterative selection protocol and to ACE elements in an alternative exon (v4) from the human CD44 gene. The A CE element that was the predominant YB-1 binding site in CD44 exon v4 was r equired for maximal in vivo splicing and in vitro spliceosome assembly. Exp ression of wild-type YB-1 increased inclusion of exon v4, whereas a truncat ed form of YB-1 did not. Stimulation of exon v4 inclusion by wild-type YB-1 required the ACE necessary for YB-1 binding in vitro, suggesting that YB-1 stimulated exon inclusion in vivo by binding to an exonic ACE element. The se observations identify a protein in addition to SR proteins that particip ates in the recognition of exon enhancers.