Antibody-Free and Rapid Profiling of Transcription Factor Binding Sites by Aptamer-Guided Chromatin Cleavage and Sequencing (AptaChC-Seq)

Mapping transcription factor (TF) binding sites is crucial for understanding the regulatory mechanisms by which TFs and associated proteins control biological processes. Existing methods rely on antibodies as protein-binding reagents, making them highly dependent on the availability and quality of commercial antibodies. Here, we present Aptamer-Guided Chromatin Cleavage with Sequencing (AptaChC-seq), an antibody-free approach for rapid profiling of TF binding sites that leverages aptamer-directed Tn5 transposome tagmentation. We demonstrate the efficacy of AptaChC-seq through successful application to three TFs, including FOXM1, RELA, and RBPJ, yielding high-quality mapping data. Our results show that aptamers exhibit high stability and reproducibility in this context. Furthermore, the AptaChC-seq workflow can be completed in approximately 4 h, making it the fastest currently available method for TF binding site profiling. This approach provides a robust complementary tool for TF studies, facilitating mechanistic investigations and advancing biomedical applications.