Paper List

Journal: ArXiv Preprint
Published: Unknown
BiophysicsStem Cell Biology

Modulation of DNA rheology by a transcription factor that forms aging microgels

University of Edinburgh | University of Glasgow | MRC Human Genetics Unit | WPI-SKCM2, Hiroshima University

Amandine Hong-Minh, Yair Augusto Gutiérrez Fosado, Abbie Guild, Nicholas Mullin, Laura Spagnolo, Ian Chambers, Davide Michieletto
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The 30-Second View

IN SHORT: This work addresses the fundamental question of how the transcription factor NANOG, essential for embryonic stem cell pluripotency, physically regulates gene expression beyond simple DNA binding, by revealing its ability to form self-limiting, aging microgels that modulate DNA rheology.

Innovation (TL;DR)

  • Methodology First demonstration that a transcription factor (NANOG) forms self-limiting micelle-like clusters (~22-25 monomers) with exposed DNA-binding domains, acting as transient cross-linkers for DNA molecules.
  • Biology Discovery of an aging microgel formation by NANOG, where viscoelasticity increases over time (10,000-fold viscosity increase over 12h), driven by its intrinsically disordered tryptophan-rich (WR) domain.
  • Theory Proposes a novel 'rheological gene regulation' paradigm: NANOG may regulate gene expression not by large-scale chromatin reorganization, but by stabilizing and restricting the *dynamics* of key regulatory sites via aging condensates, potentially ingraining mechanical memory.

Key conclusions

  • Wild-type NANOG forms macroscopic aging gels (10,000-fold viscosity increase over 12h at 37°C) and self-limiting micelle-like clusters (~22-25 proteins), while the oligomerization-deficient mutant (W10A) does not.
  • Both clustering (via WR domain) and DNA binding (via homeodomain) are required for NANOG to act as an effective DNA cross-linker, significantly enhancing the viscoelasticity of entangled DNA solutions (observed in WT but not in W10A or DNA-binding-deficient N51A mutants).
  • Aging (increasing viscoelasticity over time) occurs in NANOG-DNA solutions for both WT and the DNA-binding-deficient N51A mutant, indicating that oligomerization alone is sufficient to drive this slow restructuring toward gel-like states.
Background and Gap： While NANOG is known to be essential for pluripotency and can undergo phase separation, the precise physical mechanism linking its oligomerization domain (WR) to its function, and the lack of observed large-scale chromatin reorganization upon its overexpression, remained unexplained.

Abstract: Proteins and nucleic acids form non-Newtonian liquids with complex rheological properties that contribute to their function in vivo. Here we investigate the rheology of the transcription factor NANOG, a key protein in sustaining embryonic stem cell self-renewal. We discover that at high concentrations NANOG forms macroscopic aging gels through its intrinsically disordered tryptophan-rich domain. By combining molecular dynamics simulations, mass photometry and Cryo-EM, we also discover that NANOG forms self-limiting micelle-like clusters which expose their DNA-binding domains. In dense solutions of DNA, NANOG micelle-like structures stabilize inter-molecular entanglements and crosslinks, forming microgel-like structures. Our findings suggest that NANOG may contribute to regulate gene expression in a unconventional way: by restricting and stabilizing genome dynamics at key transcriptional sites through the formation of an aging microgel-like structure, potentially enabling mechanical memory in the gene network.