A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency
- Liangqi Xie1,
- Sharon E. Torigoe1,5,
- Jifang Xiao2,
- Daniel H. Mai2,
- Li Li3,
- Fred P. Davis4,
- Peng Dong3,
- Herve Marie-Nelly2,
- Jonathan Grimm3,
- Luke Lavis3,
- Xavier Darzacq1,
- Claudia Cattoglio1,
- Zhe Liu3 and
- Robert Tjian1,2
- 1Howard Hughes Medical Institute, Berkeley, California 94720, USA;
- 2Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA;
- 3Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA;
- 4Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- Corresponding authors: jmlim{at}berkeley.edu, liuz11{at}janelia.hhmi.org
Abstract
Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during animal development. Despite decades of study, we know little about the dynamics or order of events animating TF assembly at cis-regulatory elements in living cells and the long-range molecular “dialog” between enhancers and promoters. Here, combining genetic, genomic, and imaging approaches, we characterize a complex long-range enhancer cluster governing Krüppel-like factor 4 (Klf4) expression in naïve pluripotency. Genome editing by CRISPR/Cas9 revealed that OCT4 and SOX2 safeguard an accessible chromatin neighborhood to assist the binding of other TFs/cofactors to the enhancer. Single-molecule live-cell imaging uncovered that two naïve pluripotency TFs, STAT3 and ESRRB, interrogate chromatin in a highly dynamic manner, in which SOX2 promotes ESRRB target search and chromatin-binding dynamics through a direct protein-tethering mechanism. Together, our results support a highly dynamic yet intrinsically ordered enhanceosome assembly to maintain the finely balanced transcription program underlying naïve pluripotency.
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Footnotes
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Supplemental material is available for this article.
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Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.303321.117.
- Received June 12, 2017.
- Accepted August 28, 2017.
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