CUG-BP1/CELF1 requires UGU-rich sequences for high-affinity binding
Résumé
CUG-BP1 (CUG-binding protein 1 also called CELF1) is a human RNA-binding protein that has been implicated in the control of splicing and mRNA translation. The Xenopus homologue (EDEN-BP) is required for rapid deadenylation of certain maternal mRNAs just after fertilisation. A variety of sequence elements have been described as target sites for these two proteins but their binding specificity is still controversial. Using a SELEX procedure and recombinant CUG-BP1 we selected two families of aptamers. Surface Plasmon Resonance and Electrophoretic Mobility Shift Assays showed that these two families differed in their ability to bind CUG-BP1. Furthermore; the selected high affinity aptamers form two complexes with CUG-BP1 in electrophoretic mobility assays whereas those that bind with low affinity only form one. The validity of the distinction between the two families of aptamers was confirmed by a functional in vivo deadenylation assay. Only those aptamers that bound CUG-BP1 with high affinity conferred deadenylation on a reporter mRNA. These high affinity RNAs are characterised by a richness in UGU motifs. Using these binding site characteristics we identified the Xenopus maternal mRNA encoding the MAP kinase phosphatase (XCl100) as a substrate for EDEN-BP. In conclusion, high affinity CUG-BP1 binding sites are sequence elements at least 30 nucleotides in length that are enriched in combinations U and G nucleotides and contain at least 4 UGU trinucleotide motifs. Such sequence elements are functionally competent to target a RNA for deadenylation in vivo.
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