Article | Published:

7SK-BAF axis controls pervasive transcription at enhancers

Nature Structural & Molecular Biology volume 23, pages 231238 (2016) | Download Citation

Abstract

RNA functions at enhancers remain mysterious. Here we show that the 7SK small nuclear RNA (snRNA) inhibits enhancer transcription by modulating nucleosome position. 7SK occupies enhancers and super enhancers genome wide in mouse and human cells, and it is required to limit enhancer-RNA initiation and synthesis in a manner distinct from promoter pausing. Clustered elements at super enhancers uniquely require 7SK to prevent convergent transcription and DNA-damage signaling. 7SK physically interacts with the BAF chromatin-remodeling complex, recruits BAF to enhancers and inhibits enhancer transcription by modulating chromatin structure. In turn, 7SK occupancy at enhancers coincides with that of Brd4 and is exquisitely sensitive to the bromodomain inhibitor JQ1. Thus, 7SK uses distinct mechanisms to counteract the diverse consequences of pervasive transcription that distinguish super enhancers, enhancers and promoters.

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Acknowledgements

We thank members of the Chang laboratories for discussion and the following individuals for reagents and advice. BAF, D. Hargreaves and G. Crabtree (Stanford University); GRO-seq, I. Jonkers and J. Lis (Cornell University); JQ1, J. Bradner (Dana Farber Cancer Institute); human ES-cell culture, V. Sebastiano (Stanford University); mouse ES cells, P.A. Sharp (Massachusetts Institute of Technology); traveling ratio, P. Rahl (Syros Pharmaceutical) and C. Lin (Baylor College of Medicine); critical reading of the manuscript, P. Batista and R.C. Spitale (Stanford University). This work was supported by the Stanford Medical Scientist Program and US National Institutes of Health (NIH) grants 1F30CA189514-01 (R.A.F.); NIH grants GM068122 and GM110050 (E.T.K.); the Helen Hay Whitney Foundation (E.C.); and NIH grants P50-HG007735 and R01-HG004361, the California Institutes for Regenerative Medicine and the Howard Hughes Medical Institute (H.Y.C.).

Author information

Affiliations

  1. Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.

    • Ryan A Flynn
    • , Brian T Do
    • , Byron Lee
    • , Ci Chu
    •  & Howard Y Chang
  2. Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.

    • Ryan A Flynn
    • , Brian T Do
    • , Adam J Rubin
    • , Byron Lee
    • , Ci Chu
    • , Paul A Khavari
    •  & Howard Y Chang
  3. Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA.

    • Eliezer Calo
    •  & Joanna Wysocka
  4. Department of Chemistry, Stanford University, Stanford, California, USA.

    • Hannes Kuchelmeister
    •  & Eric T Kool
  5. The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA.

    • Michael Rale

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Contributions

R.A.F. and H.Y.C. conceived and designed the study. R.A.F. carried out the majority of the experiments and analysis. R.A.F. and M.R. performed ChIRP-seq, and R.A.F. and B.T.D. analyzed ChIRP-seq data. R.A.F. and C.C. analyzed ChIRP-MS data. R.A.F., E.C. and B.L. performed ChIP-seq and analyzed the data. R.A.F., H.K. and E.T.K. synthesized icSHAPE reagents and performed icSHAPE experiments. R.A.F. performed GRO-seq, and R.A.F., B.T.D., E.C. and J.W. analyzed GRO-seq data. R.A.F. performed ATAC-seq, and R.A.F., B.T.D., B.L., P.A.K. and A.J.R. analyzed the data. R.A.F. and H.Y.C. wrote the manuscript with input from all coauthors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Howard Y Chang.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8

  2. 2.

    Supplementary Data Set 1

    Western blots supporting Figure 6c

Excel files

  1. 1.

    Supplementary Table 1

    BED6 formatted coordinates for SE (individual peaks), TE, and promoters used for all analysis

  2. 2.

    Supplementary Table 2

    ChIRP-seq (7SK) and ChIP-seq (Baf155 and Hexim1) peaks called using MACS2

  3. 3.

    Supplementary Table 3

    IP-MS of Arid1a from mouse ES cells

  4. 4.

    Supplementary Table 4

    icSHAPE reactivity scores of 7SK snRNA from Hexim1- or BAF-coIP experiments

  5. 5.

    Supplementary Table 5

    Oligonucleotides used in experimental assays

  6. 6.

    Supplementary Table 6

    Read number and mapping rate for all sequencing experiments

  7. 7.

    Supplementary Table 7

    Matrix of every Enhancer (sheet 1) and Promoter (sheet 2) analyzed in the study with the corresponding values for GRO-seq, ChIP-seq, and ConvT changes observed after 7SK depletion

  8. 8.

    Supplementary Table 8

    List of all used publically available ChIP-seq datasets obtained from GEO

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DOI

https://doi.org/10.1038/nsmb.3176

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