Hunold Pascal, Pizzolato Giulia, Heramvand Nadia, Kaiser Laura, Barbiera Giulia, van Ray Olivia, Thomas Roman, George Julie, Peifer Martin, Hänsel-Hertsch Robert
Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital, Cologne, University of Cologne, Cologne, Germany.
Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
Nat Commun. 2025 Jul 28;16(1):6585. doi: 10.1038/s41467-025-61797-9.
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 uncovers 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 R248Q at enriched gene pathways (e.g. epithelial-mesenchymal transition), following chemotherapy treatment. Collectively, we believe that DynaTag represents a significant technological advancement, facilitating precise characterization of TF landscapes across diverse biological systems and complex models.
在低输入样本和单细胞水平上系统地发现转录因子（TF）图谱是分子生物学、遗传学和表观遗传学领域的一项重大挑战。在此，我们展示了动态靶点切割与转座酶标签化技术（DynaTag），该技术能够在样本制备过程中使用生理盐溶液对TF-DNA相互作用进行可靠的图谱绘制。DynaTag揭示了干细胞和癌症组织模型中15种转录因子的占位改变。我们强调了在干细胞分化过程中，NANOG、MYC和OCT4的TF-DNA结合在整体和单细胞分辨率下的变化。DynaTag在信噪比和分辨率方面优于CUT&RUN和ChIP-seq。此外，使用来自单一女性供体的小细胞肺癌模型肿瘤，DynaTag显示化疗治疗后，FOXA1、MYC和突变型p53 R248Q在富集基因通路（如上皮-间质转化）中的染色质占位增加。总体而言，我们认为DynaTag代表了一项重大的技术进步，有助于在不同生物系统和复杂模型中精确表征TF图谱。
