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Nanoclustering of a plant transcription factor enables strong yet specific DNA binding doi.org/10.1101/2025... Automatic identification and annotation of MYB gene family members in plants doi.org/10.1101/2021...

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Nanoclustering of a plant transcription factor enables strong yet specific DNA binding Transcription factors (TFs) are traditionally depicted as monomeric, or oligomeric, units that recognize and bind specific DNA sequences to regulate transcription. Emerging evidence suggests that many TFs can undergo liquid phase separation, resulting in condensates that bind DNA through a different mechanism. For the Auxin Response Factors (ARFs), canonical plant TFs, evidence for both scenarios exists. But which of these scenarios is operational in the plant nucleus is unclear. Here, we demonstrate using MpARF2 of Marchantia polymorpha that a third scenario is operational: MpARF2 forms nanoscopic clusters under physiological conditions. Nanoclusters combine DNA-binding features that cannot be accessed by the other two scenarios: high-affinity, switch-like, and sequence-specific. Our results suggest nanoclustering as a mechanism that equips TFs with the DNA-binding properties necessary for transcriptional regulation. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, Catch 101000981 European Research Council, DIRNDL 833867 Human Frontiers Science Program, RGP0015/2022 Marie Skłodowska-Curie Individual Fellowship 2020, REOX 101026004 NWO, 184.036.012 https://doi.org/10.1101/2025.11.05.686732