3D imaging of Sox2 enhancer clusters in embryonic stem cells

• Published in: eLife Vol. 3; p. e04236
• Main Authors: Liu, Zhe, Legant, Wesley R, Chen, Bi-Chang, Li, Li, Grimm, Jonathan B, Lavis, Luke D, Betzig, Eric, Tjian, Robert
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 24.12.2014; eLife Sciences Publications, Ltd
• Subjects: Animals; Binding Sites; Biophysics and Structural Biology; Cell Nucleus - metabolism; Cell Survival; Chromatin; Cluster Analysis; Computer Simulation; Deoxyribonucleic acid; Diffusion; DNA; Embryo cells; embryonic stem cell; Embryonic Stem Cells - metabolism; Enhancer Elements, Genetic - genetics; enhancer organization; Enhancers; Epigenesis, Genetic; Gene expression; Gene mapping; Genes and Chromosomes; Genome; Genomes; Green Fluorescent Proteins - metabolism; Heterochromatin; Heterochromatin - metabolism; Imaging, Three-Dimensional; Medical research; Mice; Microscopy; Protein Transport; Proteins; RNA Polymerase II - metabolism; single-molecule imaging; SOXB1 Transcription Factors - genetics; SOXB1 Transcription Factors - metabolism; Spatial distribution; Stem cell transplantation; Stem cells; Transcription factors; United States > US; California; mouse; genes; embryonic stem cells; chromosomes; single-molecule imaging; structural biology; biophysics; enhancer organization
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.04236

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.