3D imaging of Sox2 enhancer clusters in embryonic stem cells

• DOI: 10.7554/elife.04236
• Publication Date: 2014-12-24T07:02:38Z
• Authors: Zhe Liu; Wesley R Legant; Bi-Chang Chen; Li Li; Jonathan B Grimm; Luke D Lavis; Eric Betzig; Robert Tjian
• Keywords: Chromosome conformation capture

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, 3D spatial organization cis-elements how such sub-nuclear structures influence TF activity remain poorly understood. Here, we combine lattice light-sheet imaging, single-molecule tracking, numerical simulations, ChIP-exo mapping to localize functionally probe Sox2 enhancer-organization living embryonic stem cells. enhancers form 3D-clusters that are segregated from heterochromatin but overlap with a subset Pol II enriched regions. searches specific binding targets via 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 enables rapid local fine-tuning parameters. Our results suggest an integrated model linking cis-element distribution local-versus-global target modalities essential regulating eukaryotic transcription.