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TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin

Nature Structural & Molecular Biology volume 24, pages 344352 (2017) | Download Citation

Abstract

The resolution and formation of facultative heterochromatin are essential for development, reprogramming, and oncogenesis. The mechanisms underlying these changes are poorly understood owing to the difficulty of studying heterochromatin dynamics and structure in vivo. We devised an in vivo approach to investigate these mechanisms and found that topoisomerase II (TOP2), but not TOP1, synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin independent of transcription. This indicates that changes in DNA topology that take place through (de-)catenation rather than the release of torsional stress through swiveling are necessary for heterochromatin resolution. TOP2 and BAF cooperate to recruit pluripotency factors, which explains some of the instructive roles of BAF complexes. Unexpectedly, we found that TOP2 also plays a role in the re-formation of facultative heterochromatin; this finding suggests that facultative heterochromatin and accessible chromatin exist at different states of catenation or other topologies, which might be critical to their structures.

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Acknowledgements

This work was supported by funds awarded to G.R.C. from the Howard Hughes Medical Institute, the Simons Foundation Autism Research Initiative, and the NIH (grants NS046789 and CA163915). E.L.M. was supported by the Lucille P. Markey Stanford Graduate Fellowship in Biomedical Research and by the Stanford University Genetics & Developmental Biology Training Program (NIH-NIGMS T32 GM007790). D.C.H. was supported by NCI career transition award K99CA184043. C.H. is supported by NCI career transition award K99CA187565. ATAC-seq libraries were prepared with advice from B. Wu. We used the BioX3 cluster, which is supported by NIH S10 Shared Instrumentation Grant 1S10RR02664701, for sequencing analysis. Many thanks to A. Koh and C. Weber for technical advice and support.

Author information

Author notes

    • Diana C Hargreaves

    Present address: Salk Institute for Biological Studies, San Diego, California, USA.

Affiliations

  1. Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.

    • Erik L Miller
    • , Diana C Hargreaves
    • , Chiung-Ying Chang
    • , Joseph P Calarco
    • , Courtney Hodges
    •  & Gerald R Crabtree
  2. Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA.

    • Erik L Miller
    • , Diana C Hargreaves
    • , Chiung-Ying Chang
    • , Joseph P Calarco
    • , Courtney Hodges
    •  & Gerald R Crabtree
  3. Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

    • Erik L Miller
    •  & William J Greenleaf
  4. Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.

    • Cigall Kadoch
  5. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Cigall Kadoch
    •  & Jason D Buenrostro
  6. Harvard Society of Fellows, Harvard University, Cambridge, Massachusetts, USA.

    • Jason D Buenrostro
  7. Systems Biology Center, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA.

    • Kairong Cui
    •  & Keji Zhao
  8. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

    • Gerald R Crabtree

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Contributions

The studies of TOP2/BAF function were designed and conducted by E.L.M., G.R.C., and D.C.H. The CiA system was conceived by G.R.C., adapted for analysis of BAF mechanisms by C.K., and adapted for analysis of LSH and INO80 mechanisms by J.P.C. ATAC-seq experiments were conceived by W.J.G. and J.D.B., performed by E.L.M. and C.-Y.C., and analyzed by E.L.M. MNase assays and sequencing were performed by E.L.M., K.Z., and K.C. and analyzed by E.L.M. Binding kinetics were calculated by C.H. E.L.M. and G.R.C. wrote the manuscript, with input from the other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Gerald R Crabtree.

Integrated supplementary information

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–6

  2. 2.

    Supplementary Data Set 1

    Uncropped gels

Excel files

  1. 1.

    Supplementary Table 1

    ATAC-seq peaks with decreased, unchanged, or increased accessibility after 24 h of ICRF-193 treatment or conditional knockout of Brg1 or Baf53a

  2. 2.

    Supplementary Table 2

    List of public ChIP-seq data sets used

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https://doi.org/10.1038/nsmb.3384