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ChIP-Seq identification of weakly conserved heart enhancers

Nature Genetics volume 42, pages 806–810 (2010)Cite this article

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Abstract

Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme noncoding-sequence conservation has successfully predicted enhancers that are active in many tissues but has failed to identify substantial numbers of heart-specific enhancers. Here, we used ChIP-Seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over 3,000 candidate heart enhancers genome wide. Compared to enhancers active in othertissues we studied at this time point, most candidate heart enhancers were less deeply conserved in vertebrate evolution. Nevertheless, transgenic mouse assays of 130 candidate regions revealed that most function reproducibly as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary conservation of embryonic enhancers can vary depending on tissue type.

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Figure 1: Weak evolutionary conservation of candidate heart enhancers identified by p300 binding in embryos at E11.5.
Figure 2: In vivo testing of p300 heart enhancer predictions.
Figure 3: Examples of the diverse structural and cell type specificities of p300 ChIP-Seq identified cardiac enhancers.
Figure 4: Enrichment of heart p300 ChIP-Seq peaks near genes implicated in heart development.

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Acknowledgements

The authors wish to thank R. Hosseini and S. Phouanenavong for technical support. L.A.P. and E.M.R. were supported by grant HL066681, Berkeley Program for Genomic Applications, which is funded by the National Heart, Lung, and Blood Institute. L.A.P. was also supported by grant HG003988, which is funded by the National Human Genome Research Institute. B.L.B was supported by grants HL64658 and HL89707 from the National Heart, Lung, and Blood Institute. B.R. is supported by funding from the National Human Genome Research Institute and the Ludwig Institute for Cancer Research. Research was conducted at the E.O. Lawrence Berkeley National Laboratory and was performed under the Department of Energy Contract DE-AC02-05CH11231, University of California.

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Authors and Affiliations

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

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

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

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

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

    David J McCulley & Brian L Black

  4. Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA

    David J McCulley & Brian L Black

  5. Ludwig Institute for Cancer Research, University of California San Diego (UCSD) School of Medicine, La Jolla, California, USA

    Zirong Li & Bing Ren

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Contributions

M.J.B., A.V. and L.A.P. wrote the manuscript. All authors contributed to data collection and analysis and provided comments on the manuscript.

Corresponding authors

Correspondence to Axel Visel or Len A Pennacchio.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11, Supplementary Tables 5,7,8 and Supplementary Note. (PDF 4563 kb)

Supplementary Tables 1–4

List of p300 peaks from forebrain (XLS 2109 kb)

Supplementary Table 6

Reproducibility of LacZ staining in confirmed positive heart enhancers (XLS 45 kb)

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Blow, M., McCulley, D., Li, Z. et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42, 806–810 (2010). https://doi.org/10.1038/ng.650

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