The activity of the SR protein family of splicing
factors in constitutive or alternative splicing requires
direct interactions with the pre-mRNA substrate. Thus it
is important to define the high affinity targets of the
various SR species and to evaluate their ability to discriminate
between defined RNA targets. We have analyzed the binding
specificity of the 30-kDa SR protein 9G8, which contains
a zinc knuckle in addition to the RNA binding domain (RBD).
Using a SELEX approach, we demonstrate that 9G8 selects
RNA sequences formed by GAC triplets, whereas a mutated
zinc knuckle variant selects different RNA sequences, centered
around a (A/U)C(A/U)(A/U)C motif, indicating that the zinc
knuckle is involved in the RNA recognition specificity
of 9G8. In contrast, SC35 selects sequences composed of
pyrimidine or purine-rich motifs. Analyses of RNA–protein
interactions with purified recombinant 30-kDa SR proteins
or in nuclear extracts, by means of UV crosslinking and
immunoprecipitation, demonstrate that 9G8, SC35, and ASF/SF2
recognize their specific RNA targets with high specificity.
Interestingly, the RNA sequences selected by the mutated
zinc knuckle 9G8 variant are efficiently recognized by
SRp20, in agreement with the fact that the RBD of 9G8 and
SRp20 are similar. Finally, we demonstrate the ability
of 9G8 and of its zinc knuckle variant, or SRp20, to act
as efficient splicing transactivators through their specific
RNA targets. Our results provide the first evidence for
cooperation between an RBD and a zinc knuckle in defining
the specificity of an RNA binding domain.