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BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones

Nature Structural & Molecular Biology volume 21, pages 10471057 (2014) | Download Citation

Abstract

Small-molecule BET inhibitors interfere with the epigenetic interactions between acetylated histones and the bromodomains of the BET family proteins, including BRD4, and they potently inhibit growth of malignant cells by targeting cancer-promoting genes. BRD4 interacts with the pause-release factor P-TEFb and has been proposed to release RNA polymerase II (Pol II) from promoter-proximal pausing. We show that BRD4 occupies widespread genomic regions in mouse cells and directly stimulates elongation of both protein-coding transcripts and noncoding enhancer RNAs (eRNAs), in a manner dependent on bromodomain function. BRD4 interacts with elongating Pol II complexes and assists Pol II in progression through hyperacetylated nucleosomes by interacting with acetylated histones via bromodomains. On active enhancers, the BET inhibitor JQ1 antagonizes BRD4-associated eRNA synthesis. Thus, BRD4 is involved in multiple steps of the transcription hierarchy, primarily by facilitating transcript elongation both at enhancers and on gene bodies independently of P-TEFb.

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Acknowledgements

We thank L.J. Core and J.T. Lis (Cornell University) for the global run-on sequencing (GRO-seq) protocol, V. Sartorelli and D. Clark for critical discussion and reading of the manuscript and J. Kadonaga (University of California, San Diego) for ND423. This work was supported by the Intramural Research Programs of the US National Institutes of Health NICHD, NIAMS and NIAID.

Author information

Author notes

    • Tom D Heightman

    Present address: Astex Pharmaceuticals, Cambridge, UK.

    • Tomohiko Kanno
    • , Yuka Kanno
    •  & Gary LeRoy

    These authors contributed equally to this work.

    • Tomohiko Kanno
    • , Danny Reinberg
    • , Ulrich Siebenlist
    • , John J O'Shea
    •  & Keiko Ozato

    These authors jointly supervised this work.

Affiliations

  1. Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA.

    • Tomohiko Kanno
    •  & Ulrich Siebenlist
  2. Program in Genomics of Differentiation, National Institutes of Child Health and Human Development, Bethesda, Maryland, USA.

    • Tomohiko Kanno
    •  & Keiko Ozato
  3. Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA.

    • Yuka Kanno
    • , Golnaz Vahedi
    •  & John J O'Shea
  4. Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA.

    • Gary LeRoy
    • , Eric Campos
    •  & Danny Reinberg
  5. Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA.

    • Hong-Wei Sun
    •  & Stephen R Brooks
  6. Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK.

    • Tom D Heightman
  7. Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Benjamin A Garcia

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Contributions

T.K. conceived the study, designed experiments, performed all experiments except supercoiling assays and in vitro transcription analysis, interpreted all data and wrote and handled the manuscript as the corresponding author. Y.K. performed RNA-seq, GRO-seq and ChIP-seq, interpreted data and wrote the manuscript. G.L., E.C. and B.A.G. conceived, designed and performed in vitro transcription analysis and plasmid supercoiling assays. H.-W.S., S.R.B. and G.V. performed genome-wide data processing. T.D.H. oversaw the JQ1 experiment. D.R., U.S., J.J.O. and K.O. discussed the results and edited the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Tomohiko Kanno or John J O'Shea or Keiko Ozato.

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DOI

https://doi.org/10.1038/nsmb.2912

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