Nanoclustering of a plant transcription factor enables strong yet specific DNA binding

Abstract 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. Teaser Transcription factor nanoclusters balance the DNA-binding trade-off between weakly binding oligomers and nonspecific condensates.

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Publication Details

Journal
Science Advances
Published
2026-07-24
DOI
https://doi.org/10.1126/sciadv.aed7904
Citations
2
Primary Topic
Plant Molecular Biology Research
Type
article
Field-Weighted Citation Impact
12.95

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article

Nanoclustering of a plant transcription factor enables strong yet specific DNA binding

Boudewijn Janssen, Joris Sprakel, Johannes Hohlbein, Jan Willem Borst et al.
2 citations
Science Advances
Plant Molecular Biology Research
12.95
article

Nanoclustering of a plant transcription factor enables strong yet specific DNA binding

Boudewijn Janssen, Joris Sprakel, Johannes Hohlbein, Jan Willem Borst, Martijn de Roij, Jorge Hernández‐García, Carlo P. M. van Mierlo, João J. Ramalho, Melissa Dipp-Álvarez, Dolf Weijers, Jasper Lamers, Maartje van der Woude, Kasper Arfman, Robin Romein, Sophie van den Boom, Maartje Rademaker, Lucas Jansen
article en
2 citations

Abstract

Abstract 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. Teaser Transcription factor nanoclusters balance the DNA-binding trade-off between weakly binding oligomers and nonspecific condensates.

Science AdvancesVol. 12(30)
Utrecht University (NL), Wageningen University & Research (NL)
Nederlandse Organisatie voor Wetenschappelijk Onderzoek, H2020 European Research Council
Openalex Percentile: Top 3%
Plant Molecular Biology Research
12.95
DOIOpen Access PDFOpenAlex
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