TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences

Area of Science:

• Molecular Biology
• Biochemistry
• Genetics

Background:

• The TATA-box binding protein (TBP) is crucial for transcription initiation in eukaryotes.
• The influence of DNA sequences flanking the core TATA box on TBP binding is not fully understood.
• Previous hypotheses suggested flanking sequences play a significant role, particularly with specific DNA structures.

Purpose of the Study:

• To systematically investigate the impact of TATA-box flanking sequences on TBP interaction.
• To validate the hypothesis that flanking sequences are more critical for TBP/TATA-box interactions in context-dependent DNA structures.
• To explore the general implications for protein-DNA interactions.

Main Methods:

• In vitro selection experiments were employed to probe TBP/TATA-box interactions.
• Systematic analysis of flanking sequence effects on TATA-box binding stability.
• Comparison of binding stabilities across various TATA-box and flanking sequence combinations.

Main Results:

• Selected sequences demonstrated specificity dependent on the selection method and TATA-box context.
• For (T-A)4 TATA boxes, flanking sequences exhibited variability in binding stability comparable to the core TATA box itself, indicating dominance.
• Binding stabilities of most selected (T-A)4 sequences surpassed their mononucleotide consensus sequence.
• An asymmetric flanking sequence pattern was observed despite the symmetric (T-A)4 core sequence.

Conclusions:

• Flanking sequences play a dominant role in determining TBP binding stability for (T-A)4 TATA boxes.
• The plasticity of (T-A)n sequences allows for diverse conformational TATA boxes without altering the TBP contact region.
• These findings offer insights into the broader principles of protein-DNA interactions and gene regulation.