Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity.

Area of Science:

• Developmental Biology
• Evolutionary Genetics
• Molecular Biology

Background:

• Sequence variation in enhancers is crucial for evolution and disease.
• The functional consequences of this variation on transcription factor (TF) binding and enhancer activity are not well understood.

Purpose of the Study:

• To investigate how sequence variation affects TF binding and enhancer activity in Drosophila.
• To understand the interplay between TF cooperativity, binding, and in vivo enhancer function.

Main Methods:

• Assayed binding of five essential TFs across embryogenesis in two distant Drosophila species.
• Identified thousands of orthologous enhancers with conserved or diverged TF occupancy.
• Analyzed TF binding signatures to assess cooperativity and enhancer activity.

Main Results:

• Discovered conserved combinatorial TF binding at orthologous enhancers despite sequence divergence, suggesting protein interactions maintain collective occupancy.
• Found conserved in vivo enhancer activity even when TF occupancy diverged.
• Identified enhancers with divergent motifs but conserved occupancy, and vice versa.

Conclusions:

• Conserved TF binding and enhancer activity can persist despite sequence and occupancy divergence.
• Protein-protein interactions may stabilize conserved TF binding patterns.
• Functional assays are essential to fully understand the impact of sequence divergence on enhancer function.