Heterozygous Mutations in SMARCA2 Reprogram the Enhancer Landscape by Global Retargeting of SMARCA4

Mol Cell. 2019 Sep 5;75(5):891-904.e7. doi: 10.1016/j.molcel.2019.06.024. Epub 2019 Jul 30.


Mammalian SWI/SNF complexes are multi-subunit chromatin remodeling complexes associated with an ATPase (either SMARCA4 or SMARCA2). Heterozygous mutations in the SMARCA2 ATPase cause Nicolaides-Baraitser syndrome (NCBRS), an intellectual disability syndrome associated with delayed speech onset. We engineered human embryonic stem cells (hESCs) to carry NCBRS-associated heterozygous SMARCA2 K755R or R1159Q mutations. While SMARCA2 mutant hESCs were phenotypically normal, differentiation to neural progenitors cells (NPCs) was severely impaired. We find that SMARCA2 mutations cause enhancer reorganization with loss of SOX3-dependent neural enhancers and prominent emergence of astrocyte-specific de novo enhancers. Changes in chromatin accessibility at enhancers were associated with an increase in SMARCA2 binding and retargeting of SMARCA4. We show that the AP-1 family member FRA2 is aberrantly overexpressed in SMARCA2 mutant NPCs, where it functions as a pioneer factor at de novo enhancers. Together, our results demonstrate that SMARCA2 mutations cause impaired differentiation through enhancer reprogramming via inappropriate targeting of SMARCA4.

Keywords: AP-1; SMARCA2; SWI/SNF complex; chromatin remodeling; neural differentiation; neural progenitor cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution
  • Cell Differentiation / genetics
  • Chromatin / genetics
  • Chromatin / metabolism
  • DNA Helicases / genetics
  • DNA Helicases / metabolism*
  • Enhancer Elements, Genetic*
  • Facies
  • Foot Deformities, Congenital / genetics
  • Foot Deformities, Congenital / metabolism
  • Foot Deformities, Congenital / pathology
  • Fos-Related Antigen-2 / biosynthesis
  • Fos-Related Antigen-2 / genetics
  • HEK293 Cells
  • Heterozygote*
  • Human Embryonic Stem Cells / metabolism*
  • Human Embryonic Stem Cells / pathology
  • Humans
  • Hypotrichosis / genetics
  • Hypotrichosis / metabolism
  • Hypotrichosis / pathology
  • Intellectual Disability / genetics
  • Intellectual Disability / metabolism
  • Intellectual Disability / pathology
  • Mutation, Missense*
  • Neural Stem Cells / metabolism
  • Neural Stem Cells / pathology
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism*
  • SOXB1 Transcription Factors / genetics
  • SOXB1 Transcription Factors / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*


  • Chromatin
  • FOSL2 protein, human
  • Fos-Related Antigen-2
  • Nuclear Proteins
  • SMARCA2 protein, human
  • SOX3 protein, human
  • SOXB1 Transcription Factors
  • Transcription Factors
  • SMARCA4 protein, human
  • DNA Helicases

Supplementary concepts

  • Nicolaides Baraitser syndrome