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Updated: Jul 4, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
Published on: August 9, 2019
TBP recruitment to the U1 snRNA gene promoter is disrupted by substituting a U6 proximal sequence element A (PSEA)
Nermeen H Barakat1, William E Stumph
1Department of Chemistry and Biochemistry and Molecular Biology Institute, San Diego State University, San Diego, CA 92182-1030, United States.
Abstract:
Transcription of Drosophila U1 or U6 snRNAs by RNA polymerases II and III respectively requires a unique approximately 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.
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