Large-scale discovery of enhancers from human heart tissue

Journal name:
Nature Genetics
Volume:
44,
Pages:
89–93
Year published:
DOI:
doi:10.1038/ng.1006
Received
Accepted
Published online

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.

At a glance

Figures

  1. ChIP-Seq identification of candidate enhancer regions from human fetal and adult heart.
    Figure 1: ChIP-Seq identification of candidate enhancer regions from human fetal and adult heart.

    Human fetal heart was obtained at gestational week 16, and adult heart tissue was obtained from the septum of an adult failing heart. (a) Overview of strategy and results of ChIP-Seq analysis. In total, 5,047 regions from fetal heart and 2,233 from adult heart were significantly enriched in p300/CBP-binding sites and were considered as candidate human heart enhancers (distal: ≥2.5 kb from the nearest transcript start site; proximal or promoter associated: <2.5 kb from the nearest TSS). (b) Overlap of candidate enhancers identified in fetal and adult heart tissues. (c) ChIP-Seq profiles of p300/CBP in the genomic region of the tested hs1763 element (thin black bar). Thick black bars indicate two regions significantly enriched for p300/CBP binding in introns of the INPP5A gene. The thin black line represents a read depth of 10; maximum read depth shown is 50.

  2. Human p300/CBP candidate enhancers are enriched near genes expressed in human heart.
    Figure 2: Human p300/CBP candidate enhancers are enriched near genes expressed in human heart.

    (a,b) Frequency of human fetal heart candidate enhancers (red) compared to matched random regions (black) near genes that are overexpressed (a) or underexpressed (b) in fetal heart relative to other human tissues (see Online Methods). Error bars indicate 95% confidence intervals.

  3. In vivo testing of predicted human heart enhancer activities in transgenic mice.
    Figure 3: In vivo testing of predicted human heart enhancer activities in transgenic mice.

    (a) In vivo enhancer activity of the 65 tested elements. (b) Proportion of reproducible enhancers by extent of sequence constraint (+, phastCons > 350; −, phastCons ≤ 350). (c) Proportion of reproducible enhancers by binding conservation to the mouse (+, p300/CBP binding significant or subsignificant but above background; −, p300/CBP binding not above background or in non-alignable peaks). Pairwise comparison for each subcategory was calculated with two-tailed Fisher's exact test; P > 0.05 in all cases.

  4. In vivo activity of human cardiac enhancers in embryonic and 4-week-old transgenic mice.
    Figure 4: In vivo activity of human cardiac enhancers in embryonic and 4-week-old transgenic mice.

    (ad) From left to right: whole-mount stained E11.5 embryo, close-up and histological section of heart at E11.5, whole-mount stained heart at P28 and longitudinal section of heart at P28. All specimens were stained for LacZ enhancer reporter activity (dark blue). Element ID, reproducibility in E11.5 embryos and flanking genes are indicated. LV, left ventricle; RV, right ventricle; LA, left atrium; RA, right atrium; OFT, outflow tract; PA, pulmonary artery; Ao, aorta.

Accession codes

Referenced accessions

Gene Expression Omnibus

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Author information

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

    • Brian C Jensen

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.

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The authors declare no competing financial interests.

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