Arrangement of the 4.5 Myb domain repeats of SNAP190 on the U1 gene promoter

Abstract

The small nuclear RNA activating protein complex (SNAPc) is a transcription factor essential for expression of genes coding for the spliceosomal snRNAs. In D. melanogaster, DmSNAPc recognizes a 21 base‐pair DNA sequence, the PSEA, located approximately 40–60 base pairs upstream of the transcription start site. DmSNAPc is a heterotrimer of subunits named DmSNAP190, DmSNAP50, and DmSNAP43. All three subunits are required for DNA binding activity, but only DmSNAP190 contains a “canonical” DNA binding domain that consists of 4.5 Myb repeats. Myb repeats are each ~50 amino acid residues in length and were first identified in the DNA binding domain of the Myb oncoprotein. By using a site‐specific protein‐DNA photo‐cross‐linking assay combined with site‐specific protein digestion, we have been able to determine where each of the 4.5 Myb repeats of DmSNAP190 contact the DNA of the U1 PSEA. The protein is arranged with the more C‐terminal Myb repeats contacting the upstream region of the PSEA and the N‐terminal repeats contacting the PSEA closer to the start site. Moreover, the C‐terminal repeats appear to contact the 5′ half of the PSEA in a manner consistent with those observed for Myb‐DNA complexes, whereas the N‐terminal repeats appear to contact the 3′ half of the PSEA (where DmSNAP50 and DmSNAP43 also bind to the PSEA) in a non‐canonical manner. (Supported by NSF and in part by the California Metabolic Research Foundation.)