Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq

  1. Pingzhu Zhou
  2. Fei Gu
  3. Lina Zhang
  4. Brynn N Akerberg
  5. Qing Ma
  6. Kai Li
  7. Aibin He
  8. Zhiqiang Lin
  9. Sean M Stevens
  10. Bin Zhou
  11. William T Pu  Is a corresponding author
  1. Boston Children's Hospital, United States
  2. Shanghai University of Traditional Chinese Medicine, China
  3. Chinese Academy of Sciences, China

Abstract

Understanding the mechanisms that regulate cell type-specific transcriptional programs requires developing a lexicon of their genomic regulatory elements. We developed a lineage-selective method to map transcriptional enhancers, regulatory genomic regions that activate transcription, in mice. Since most tissue-specific enhancers are bound by the transcriptional co-activator Ep300, we used Cre-directed, lineage-specific Ep300 biotinylation and pulldown on immobilized streptavidin followed by next generation sequencing of co-precipitated DNA to indentify lineage-specific enhancers. By driving this system with lineage-specific Cre transgenes, we mapped enhancers active in embryonic endothelial cells/blood or skeletal muscle. Analysis of these enhancers identified new transcription factor heterodimer motifs that likely regulate transcription in these lineages. Furthermore, we identified candidate enhancers that regulate adult heart- or lung- specific endothelial cell specialization. Our strategy for tissue-specific protein biotinylation opens new avenues for studying lineage-specific protein-DNA and protein-protein interactions.

Data availability

The following data sets were generated
The following previously published data sets were used
    1. Ren B
    2. Shen Y
    (2012) Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR
    Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE36027).
    1. Ren B
    (2016) ChIP-seq from heart (ENCSR646GHA)
    Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE82850).
    1. Len Pennacchio
    (2016) ChIP-seq from heart (ENCSR123MLY)
    Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM2191196).

Article and author information

Author details

  1. Pingzhu Zhou

    Department of Cardiology, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Fei Gu

    Department of Cardiology, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Lina Zhang

    Department of Biochemistry, Shanghai University of Traditional Chinese Medicine, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Brynn N Akerberg

    Department of Cardiology, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6470-6588
  5. Qing Ma

    Department of Cardiology, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Kai Li

    Department of Cardiology, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Aibin He

    Department of Cardiology, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3489-2305
  8. Zhiqiang Lin

    Department of Cardiology, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Sean M Stevens

    Department of Cardiology, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Bin Zhou

    State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  11. William T Pu

    Department of Cardiology, Boston Children's Hospital, Cambridge, United States
    For correspondence
    wpu@pulab.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4551-8079

Funding

National Institutes of Health (U01HL098166; HL095712)

  • William T Pu

American Heart Association (12EIA8440003)

  • William T Pu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: Animal experiments were performed under protocols approved by the Boston Children's Hospital Animal Care and Use Committee (protocols 13-08-2460R and 13-12-2601).

Reviewing Editor

  1. Deepak Srivastava, Gladstone Institutes, United States

Publication history

  1. Received: October 2, 2016
  2. Accepted: January 23, 2017
  3. Accepted Manuscript published: January 25, 2017 (version 1)
  4. Version of Record published: February 7, 2017 (version 2)
  5. Version of Record updated: April 11, 2017 (version 3)

Copyright

© 2017, Zhou et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Pingzhu Zhou
  2. Fei Gu
  3. Lina Zhang
  4. Brynn N Akerberg
  5. Qing Ma
  6. Kai Li
  7. Aibin He
  8. Zhiqiang Lin
  9. Sean M Stevens
  10. Bin Zhou
  11. William T Pu
(2017)
Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq
eLife 6:e22039.
https://doi.org/10.7554/eLife.22039
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