TY - JOUR TI - 3D imaging of Sox2 enhancer clusters in embryonic stem cells AU - Liu, Zhe AU - Legant, Wesley R AU - Chen, Bi-Chang AU - Li, Li AU - Grimm, Jonathan B AU - Lavis, Luke D AU - Betzig, Eric AU - Tjian, Robert A2 - Kowalczykowski, Stephen C VL - 3 PY - 2014 DA - 2014/12/24 SP - e04236 C1 - eLife 2014;3:e04236 DO - 10.7554/eLife.04236 UR - https://doi.org/10.7554/eLife.04236 AB - Combinatorial cis-regulatory networks encoded in animal genomes represent the foundational gene expression mechanism for directing cell-fate commitment and maintenance of cell identity by transcription factors (TFs). However, the 3D spatial organization of cis-elements and how such sub-nuclear structures influence TF activity remain poorly understood. Here, we combine lattice light-sheet imaging, single-molecule tracking, numerical simulations, and ChIP-exo mapping to localize and functionally probe Sox2 enhancer-organization in living embryonic stem cells. Sox2 enhancers form 3D-clusters that are segregated from heterochromatin but overlap with a subset of Pol II enriched regions. Sox2 searches for specific binding targets via a 3D-diffusion dominant mode when shuttling long-distances between clusters while chromatin-bound states predominate within individual clusters. Thus, enhancer clustering may reduce global search efficiency but enables rapid local fine-tuning of TF search parameters. Our results suggest an integrated model linking cis-element 3D spatial distribution to local-versus-global target search modalities essential for regulating eukaryotic gene transcription. KW - embryonic stem cell KW - single-molecule imaging KW - enhancer organization JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -