TBP recruitment to the U1 snRNA gene promoter is disrupted by substituting a U6 proximal sequence element A (PSEA) for the U1 PSEA

Transcription of Drosophila U1 or U6 snRNAs by RNA polymerases II and III respectively requires a unique ∼21 base-pair promoter element termed the proximal sequence element A (PSEA) recognized by the snRNA activating protein complex (DmSNAPc). A five-nucleotide substitution that changed the U1 PSEA to a U6 PSEA inactivated the U1 promoter. Chromatin immunoprecipitation assays indicated this substitution did not affect DmSNAPc DNA binding but instead interfered with SNAPc recruitment of TBP to the TATA-less U1 promoter. These findings support a model wherein sequence differences between the U1 and U6 PSEAs induce distinct DmSNAPc conformational states involved in RNA polymerase selectivity.