NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency
Kyoung‐Jae Choi, My Diem Quan, Chuangye Qi, Joo‐Hyung Lee, Phoebe S. Tsoi, Mahla Zahabiyon, Aleksandar Bajić, Liya Hu, B. V. Venkataram Prasad, Shih‐Chu Liao, Wenbo Li, Allan Chris M. Ferreon, Josephine C. Ferreon
Abstract
Human NANOG expression resets stem cells to ground-state pluripotency. Here we identify the unique features of human NANOG that relate to its dose-sensitive function as a master transcription factor. NANOG is largely disordered, with a C-terminal prion-like domain that phase-transitions to gel-like condensates. Full-length NANOG readily forms higher-order oligomers at low nanomolar concentrations, orders of magnitude lower than typical amyloids. Using single-molecule Förster resonance energy transfer and fluorescence cross-correlation techniques, we show that NANOG oligomerization is essential for bridging DNA elements in vitro. Using chromatin immunoprecipitation sequencing and Hi-C 3.0 in cells, we validate that NANOG prion-like domain assembly is essential for specific DNA recognition and distant chromatin interactions. Our results provide a physical basis for the indispensable role of NANOG in shaping the pluripotent genome. NANOG's unique ability to form prion-like assemblies could provide a cooperative and concerted DNA bridging mechanism that is essential for chromatin reorganization and dose-sensitive activation of ground-state pluripotency.