SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters

  • Nat Genet. 2017 Nov;49(11):1613-1623. doi: 10.1038/ng.3958.
Robert T Nakayama  1  2 ,  John L Pulice  1  3 ,  Alfredo M Valencia  1  4 ,  Matthew J McBride  1  4 ,  Zachary M McKenzie  1 ,  Mark A Gillespie  5 ,  Wai Lim Ku  6 ,  Mingxiang Teng  7 ,  Kairong Cui  6 ,  Robert T Williams  1 ,  Seth H Cassel  1  8 ,  He Qing  1 ,  Christian J Widmer  1 ,  George D Demetri  2 ,  Rafael A Irizarry  7 ,  Keji Zhao  6 ,  Jeffrey A Ranish  5 ,  Cigall Kadoch  1  3
Affiliations
  • 1. Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
  • 2. Ludwig Center at Dana-Farber/Harvard and Center for Sarcoma and Bone Oncology, Department of Medical Oncology, Harvard Medical School, Boston, Massachusetts, USA.
  • 3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
  • 4. Program in Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.
  • 5. Institute for Systems Biology, Seattle, Washington, USA.
  • 6. Systems Biology Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA.
  • 7. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
  • 8. Medical Scientist Training Program, Harvard Medical School, Boston, Massachusetts, USA.
PMID: 28945250 DOI: 10.1038/ng.3958
Abstract

Perturbations to mammalian SWI/SNF (mSWI/SNF or BAF) complexes contribute to more than 20% of human cancers, with driving roles first identified in malignant rhabdoid tumor, an aggressive pediatric Cancer characterized by biallelic inactivation of the core BAF complex subunit SMARCB1 (BAF47). However, the mechanism by which this alteration contributes to tumorigenesis remains poorly understood. We find that BAF47 loss destabilizes BAF complexes on chromatin, absent significant changes in complex assembly or integrity. Rescue of BAF47 in BAF47-deficient sarcoma cell lines results in increased genome-wide BAF complex occupancy, facilitating widespread enhancer activation and opposition of Polycomb-mediated repression at bivalent promoters. We demonstrate differential regulation by two distinct mSWI/SNF assemblies, BAF and PBAF complexes, enhancers and promoters, respectively, suggesting that each complex has distinct functions that are perturbed upon BAF47 loss. Our results demonstrate collaborative mechanisms of mSWI/SNF-mediated gene activation, identifying functions that are co-opted or abated to drive human cancers and developmental disorders.