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Large-scale discovery of enhancers from human heart tissue

Nature Genetics volume 44, pages 89–93 (2012)Cite this article

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Abstract

Development and function of the human heart depend on the dynamic control of tissue-specific gene expression by distant-acting transcriptional enhancers. To generate an accurate genome-wide map of human heart enhancers, we used an epigenomic enhancer discovery approach and identified ∼6,200 candidate enhancer sequences directly from fetal and adult human heart tissue. Consistent with their predicted function, these elements were markedly enriched near genes implicated in heart development, function and disease. To further validate their in vivo enhancer activity, we tested 65 of these human sequences in a transgenic mouse enhancer assay and observed that 43 (66%) drove reproducible reporter gene expression in the heart. These results support the discovery of a genome-wide set of noncoding sequences highly enriched in human heart enhancers that is likely to facilitate downstream studies of the role of enhancers in development and pathological conditions of the heart.

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Figure 1: ChIP-Seq identification of candidate enhancer regions from human fetal and adult heart.
Figure 2: Human p300/CBP candidate enhancers are enriched near genes expressed in human heart.
Figure 3: In vivo testing of predicted human heart enhancer activities in transgenic mice.
Figure 4: In vivo activity of human cardiac enhancers in embryonic and 4-week-old transgenic mice.

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Gene Expression Omnibus

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Acknowledgements

The authors thank R. Hosseini and S. Phouanenavong for technical support, S. Deutsch for help in retrieving human genetic data and C. Attanasio and D. Dickel for critical comments on the manuscript. L.A.P. and A.V. were supported by a grant funded by the National Human Genome Research Institute (HG003988). B.L.B. was supported by grants from the National Heart, Lung, and Blood Institute (NHLBI, HL64658 and HL89707). D.M. and T.K. were supported by European Molecular Biology Organization (EMBO) long-term postdoctoral fellowships. B.C.J. was supported by the GlaxoSmithKline Research and Education Foundation for Cardiovascular Disease, University of California, San Francisco (UCSF) Foundation for Cardiac Research and a grant from the NHLBI (HL096836). P.C.S. was supported by the NHLBI and the Department of Veterans Affairs. Research was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute (Department of Energy Contract DE-AC02-05CH11231, University of California).

Author information

Author notes

  1. Brian C Jensen

    Present address: Current address: Division of Cardiology, University of North Carolina, Chapel Hill, North Carolina, USA.,

Affiliations

  1. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Dalit May, Matthew J Blow, Jennifer A Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Veena Afzal, Edward M Rubin, James Bristow, Len A Pennacchio & Axel Visel

  2. United States Department of Energy Joint Genome Institute, Walnut Creek, California, USA

    Matthew J Blow, Crystal Wright, Edward M Rubin, James Bristow, Len A Pennacchio & Axel Visel

  3. Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA.

    Tommy Kaplan

  4. School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel

    Tommy Kaplan

  5. Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA

    David J McCulley, Paul C Simpson & Brian L Black

  6. Division of Cardiology, University of California, San Francisco, San Francisco, California, USA.

    Brian C Jensen

  7. Cardiology Division, Virginia Medical Center, San Francisco, California, USA

    Paul C Simpson

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Contributions

D.M., E.M.R., J.B., L.A.P. and A.V. conceived of and designed the experiments. D.M., M.J.B., T.K., D.J.M., B.C.J., J.A.A., A.H., I.P.-F., M.S., C.W. and V.A. performed experiments and data analysis. P.C.S. and B.L.B. provided reagents and materials and performed data analysis. All authors contributed to the writing of the manuscript.

Corresponding authors

Correspondence to Len A Pennacchio or Axel Visel.

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The authors declare no competing financial interests.

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Supplementary Note, Supplementary Figures 1–12 and Supplementary Tables 1–12. (PDF 5528 kb)

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May, D., Blow, M., Kaplan, T. et al. Large-scale discovery of enhancers from human heart tissue. Nat Genet 44, 89–93 (2012). https://doi.org/10.1038/ng.1006

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