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Cai D, Feliciano D, Dong P, Flores E, Gruebele M, Porat-Shliom N, Sukenik S, Liu Z, Lippincott-Schwartz J. Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression. Nat Cell Biol 2019; 21:1578-1589. [PMID: 31792379 PMCID: PMC8259329 DOI: 10.1038/s41556-019-0433-z] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 10/30/2019] [Indexed: 12/21/2022]
Abstract
Yes-associated Protein (YAP) is a transcriptional co-activator that regulates cell proliferation and survival by binding to a select set of enhancers for target gene activation. How YAP coordinates these transcriptional responses is unknown. Here, we demonstrate that YAP forms liquid-like condensates in the nucleus. Formed within seconds of hyperosmotic stress, YAP condensates compartmentalized YAP’s transcription factor TEAD1 and other YAP-related co-activators, including TAZ, and subsequently induced transcription of YAP-specific proliferation genes. Super-resolution imaging using Assay for Transposase Accessible Chromatin with photoactivated localization microscopy (ATAC-PALM) revealed that YAP nuclear condensates were areas enriched in accessible chromatin domains organized as super-enhancers. Initially devoid of RNA Polymerase II (RNAPII), the accessible chromatin domains later acquired RNAPII, transcribing RNA. Removal of YAP’s intrinsically-disordered transcription activation domain (TAD) prevented YAP condensate formation and diminished downstream YAP signaling. Thus, dynamic changes in genome organization and gene activation during YAP reprogramming is mediated by liquid-liquid phase separation.
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Affiliation(s)
- Danfeng Cai
- Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Daniel Feliciano
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.,Thoracic and Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Eduardo Flores
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Natalie Porat-Shliom
- Thoracic and Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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