In both the literal and figurative sense, building bridges can really get you places! Knowing this, genome engineers and epigenetic architects recently created a blueprint demonstrating how a pioneer transcription factor – NANOG – uses prion-like behavior to form gel-like protein condensates that create interstrand DNA “bridges” to reorganize chromatin and clear a rapid path towards pluripotency.
NANOG expression has a dose-dependent effect, with increased expression (with the help of OCT4) tightly correlated with pluripotency induction and chromatin reorganization. Additionally, research describing how KLF4 liquid-like condensates (with the help of DNA methylation) facilitate NANOG expression suggests that chromatin reorganization occurs through liquid-liquid phase separation. This research prompted a construction team led by Wenbo Li (UT Health Houston, Texas), Allan Chris M. Ferreon, and Josephine C. Ferreon (Baylor College of Medicine, Texas) to characterize NANOG’s unique features to explore its pluripotency activating activity. Their study now demonstrates how prion-like behavior induces NANOG oligomerization into gel-like condensates that bridge DNA to reorganize chromatin and activate pluripotency.
Let’s don our hard hats and heavy boots and pour our eyes over this new blueprint from Choi, Quan, Qi, and colleagues:
- A C-terminal prion-like domain of NANOG displays high aggregation potential and drives phase transitions to form gel-like condensates in a manner distinct from KLF4
- NANOG quickly forms higher-order oligomers in embryonic stem cells (ESCs) and NANOG-transfected HEK 293T cells (the two cell models employed throughout)
- Full-length NANOG readily undergoes higher-order oligomerization at nanomolar concentrations at least three orders of magnitude lower for protein assemblies such as amyloids, signalosomes, and multivalent complexes
- Oligomerization at ultra-low concentrations may underlie the dose-sensitive activity of NANOG and explain why NANOG levels represent a critical parameter controlling the activation of pluripotency
- Analysis with single-molecule Förster resonance energy transfer and fluorescence cross-correlation techniques demonstrate the ability of oligomerized NANOG to bridge DNA strands in vitro
- ESCs expressing NANOG with a mutated prion-like domain that fails to form oligomers and does not bridge DNA soon undergo differentiation
- ChIP-seq, Hi-C 3.0, and paired-end spatial chromatin analysis demonstrate that NANOG oligomerization through its prion-like domain supports the recognition of specific DNA sequences, bridging multiple distant DNA strands, and the formation of distant chromatin interactions, respectively
These findings build bridges between published research and exciting hypotheses to describe how NANOG condensates formed through prion-like behavior support DNA bridging, which induces the subsequent chromatin reorganization required to shape the path towards pluripotency; however, there may be a few side roads to explore before reaching our desired destination.
“In the future, we hope to understand more about the role of NANOG and its prion-like region in recruiting or cooperating with important transcription factors, coactivators and epigenetic modulators to reshape the genomic landscape,” concludes co-senior author Josephine C. Ferreon.
To see the complete blueprints for these architecturally breathtaking bridges, make your own way to Nature Cell Biology, April 2022.