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bioRxiv · 10.1101/2025.05.06.652526

Transcription Factor (TF) validation using Dam-IT simultaneously captures genome-wide TF-DNA binding, direct gene regulation, and chromatin accessibility in plant cells

Hinckley, W. E.·Jack, A.·Li, A.·Frangos, S.·Pasquino, A.·Huang, S.-s. C.·Coruzzi, G. M.
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Abstract

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.

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Hinckley, W. E., Jack, A., Li, A., Frangos, S., Pasquino, A., Huang, S.-s. C., Coruzzi, G. M.. 2025-05-11. Transcription Factor (TF) validation using Dam-IT simultaneously captures genome-wide TF-DNA binding, direct gene regulation, and chromatin accessibility in plant cells. https://doi.org/10.1101/2025.05.06.652526

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