DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution
Systematic discovery of transcription factor (TF) landscapes in low-input samples and at single cell level is a major challenge in the fields of molecular biology, genetics, and epigenetics. Here, we present cleavage under Dynamic targets and Tagmentation (DynaTag), enabling robust mapping of TF-DNA interactions using a physiological salt solution during sample preparation. DynaTag uncovered occupancy alterations for 15 TFs in stem cell and cancer tissue models. We highlight changes in TF-DNA binding for NANOG, MYC, and OCT4, during stem-cell differentiation, at both bulk and single-cell resolutions. DynaTag surpasses CUT&RUN and ChIP-seq in signal-to-background ratio and resolution. Furthermore, using tumours of a small cell lung cancer model derived from a single female donor, DynaTag reveals increased chromatin occupancy of FOXA1, MYC, and the mutant P53 (p.R248Q) at enriched gene pathways (e.g. epithelial-mesenchymal transition), following chemotherapy treatment. Collectively, DynaTag represents a significant technological advancement, facilitating precise characterization of TF landscapes across diverse biological systems and complex models. Overall design: DynaTag of various TFs in murine embryonic stem cells, differentiated epiblast like cells.