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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.<\/jats:p>","DOI":"10.7554\/elife.04236","type":"journal-article","created":{"date-parts":[[2014,12,24]],"date-time":"2014-12-24T02:02:38Z","timestamp":1419386558000},"source":"Crossref","is-referenced-by-count":230,"title":["3D imaging of Sox2 enhancer clusters in embryonic stem cells"],"prefix":"10.7554","volume":"3","author":[{"given":"Zhe","family":"Liu","sequence":"first","affiliation":[{"name":"Junior Fellow Program, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States"},{"name":"Transcription Imaging Consortium, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States"}]},{"given":"Wesley R","family":"Legant","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United 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