title: 3D imaging of Sox2 enhancer clusters in embryonic stem cells.
abstract: 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.
authors.affiliation: Junior Fellow Program, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States.
authors.forename: Wesley R
authors.initials: WR
authors.lastname: Legant
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States.
authors.forename: Bi-Chang
authors.initials: BC
authors.lastname: Chen
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States.
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States.
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: Grimm
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States.
authors.forename: Luke D
authors.initials: LD
authors.lastname: Lavis
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States.
authors.forename: Eric
authors.initials: E
authors.lastname: Betzig
authors.affiliation: Transcription Imaging Consortium, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States.
authors.forename: Robert
authors.initials: R
authors.lastname: Tjian
mesh_terms: D000818:Animals; D001665:Binding Sites; D002467:Cell Nucleus / Q000378:metabolism; D002470:Cell Survival; D016000:Cluster Analysis; D003198:Computer Simulation; D004058:Diffusion; D053595:Embryonic Stem Cells / Q000378:metabolism*; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D044127:Epigenesis, Genetic; D016678:Genome; D049452:Green Fluorescent Proteins / Q000378:metabolism; D006570:Heterochromatin / Q000378:metabolism; D021621:Imaging, Three-Dimensional; D051379:Mice; D021381:Protein Transport; D012319:RNA Polymerase II / Q000378:metabolism; D055748:SOXB1 Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D006570:Heterochromatin; D055748:SOXB1 Transcription Factors; D049452:Green Fluorescent Proteins; D012319:RNA Polymerase II
keywords: biophysics; chromosomes; embryonic stem cells; enhancer organization; genes; mouse; single-molecule imaging; structural biology