SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Transcription factors (TFs) regulate gene expression via sequence-specific DNA binding.
• Existing methods for studying TF binding preferences have limitations in dynamic range, specificity, and throughput.
• Understanding TF binding landscapes is crucial for deciphering gene regulation.

Purpose of the Study:

• To develop a high-throughput microfluidic device for comprehensive mapping of transcription factor binding affinities.
• To overcome limitations of current methods for studying sequence-specific TF-DNA interactions.
• To generate detailed landscapes of TF binding affinities for multiple proteins in parallel.

Main Methods:

• Development of a microfluidic device for SELEX Affinity Landscape MAPping (SELMAP).
• High-throughput measurement of TF binding affinities for 16 proteins in parallel.
• Equilibrium-based detection of both high and low-affinity TF-DNA interactions across millions of binding sites.

Main Results:

• SELMAP successfully generated comprehensive landscapes of relative TF affinities to DNA 6-mers and 10-mers.
• The method detected both high and low-affinity interactions for Pho4, AtERF2, and Btd proteins.
• High-quality results were obtained using low quantities of TFs and DNA, reducing experimental costs.

Conclusions:

• SELMAP provides a powerful, high-throughput tool for in-depth screening of hundreds of TFs.
• The technology enables a more thorough understanding of TF binding landscapes and their role in gene regulation.
• SELMAP significantly advances the study of sequence-specific TF-DNA interactions.