Hinckley Will E, Jack Austen, Li Aurelia, Frangos Samantha, Pasquino Angelo, Huang Shao-Shan Carol, Coruzzi Gloria M
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.
bioRxiv. 2025 May 11:2025.05.06.652526. doi: 10.1101/2025.05.06.652526.
Transcription Factors (TFs) govern vast networks of gene regulation. However, TF-DNA binding and TF-gene regulation datasets are typically measured separately due to experimental constraints, making it challenging to disentangle true biological relationships from batch effects. To fill this gap, we developed DamID-seq Incorporating Transcriptomics (Dam-IT), which simultaneously captures TF-DNA binding, direct TF-gene regulation, and chromatin accessibility in the same batch of cells. Dam-IT uses a transient cell-based TF-target validation system that is scalable and flexible to many experimental designs. As proof of concept, we used Dam-IT to reveal that bZIP1 directly regulates genes by binding to DNA regions of relatively low chromatin accessibility, supporting a "Hit-and-Run" mechanism of transcription.
转录因子（TFs）调控着庞大的基因调控网络。然而，由于实验限制，TF-DNA结合和TF-基因调控数据集通常是分别测量的，这使得从批次效应中区分出真正的生物学关系具有挑战性。为了填补这一空白，我们开发了整合转录组学的DamID测序技术（Dam-IT），它能在同一批细胞中同时捕获TF-DNA结合、TF对基因的直接调控以及染色质可及性。Dam-IT使用了一种基于瞬时细胞的TF靶点验证系统，该系统对许多实验设计具有可扩展性和灵活性。作为概念验证，我们使用Dam-IT揭示了bZIP1通过结合染色质可及性相对较低的DNA区域直接调控基因，支持了一种“Hit-and-Run”转录机制。
