Letter | Published:

Locus-specific editing of histone modifications at endogenous enhancers

Nature Biotechnology volume 31, pages 11331136 (2013) | Download Citation

Abstract

Mammalian gene regulation is dependent on tissue-specific enhancers that can act across large distances to influence transcriptional activity1,2,3. Mapping experiments have identified hundreds of thousands of putative enhancers whose functionality is supported by cell type–specific chromatin signatures and striking enrichments for disease-associated sequence variants4,5,6,7,8,9,10,11. However, these studies did not address the in vivo functions of the putative elements or their chromatin states and did not determine which genes, if any, a given enhancer regulates. Here we present a strategy to investigate endogenous regulatory elements by selectively altering their chromatin state using programmable reagents. Transcription activator–like (TAL) effector repeat domains fused to the LSD1 histone demethylase efficiently remove enhancer-associated chromatin modifications from target loci, without affecting control regions. We find that inactivation of enhancer chromatin by these fusion proteins frequently causes downregulation of proximal genes, revealing enhancer target genes. Our study demonstrates the potential of epigenome editing tools to characterize an important class of functional genomic elements.

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Acknowledgements

We thank members of the Bernstein laboratory and the Broad Institute's Epigenomics Program and for constructive comments and criticisms. We thank N. Shoresh, S. Kadri, M. Guttman and M. Garber for assistance with analysis. This research was supported by the Howard Hughes Medical Institute (to B.E.B.), the National Human Genome Research Institute's ENCODE Project U54 HG004570, U54 HG006991 (to B.E.B.), US National Institutes of Health Common Fund for Epigenomics U01 ES017155 (to B.E.B.), NIH Director's Pioneer Award DP1 GM105378 (to J.K.J.), NIH P50 HG005550 (to J.K.J.), and the Jim and Ann Orr MGH Research Scholar Award (to J.K.J.).

Author information

Author notes

    • Eric M Mendenhall

    Current address: Department of Biological Sciences, University of Alabama Huntsville, Huntsville, Alabama, USA.

Affiliations

  1. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

    • Eric M Mendenhall
    • , Kaylyn E Williamson
    • , James Y Zou
    • , Oren Ram
    •  & Bradley E Bernstein
  2. Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Eric M Mendenhall
    • , Kaylyn E Williamson
    • , Deepak Reyon
    • , James Y Zou
    • , Oren Ram
    • , J Keith Joung
    •  & Bradley E Bernstein
  3. Broad Institute of Harvard and MIT, Cambridge Massachusetts, USA.

    • Eric M Mendenhall
    • , Kaylyn E Williamson
    • , James Y Zou
    • , Oren Ram
    •  & Bradley E Bernstein
  4. Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.

    • Eric M Mendenhall
    • , Kaylyn E Williamson
    • , Oren Ram
    •  & Bradley E Bernstein
  5. School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.

    • James Y Zou

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Contributions

E.M.M., K.E.W., J.K.J. and B.E.B. designed experiments. E.M.M., K.E.W., D.R., J.Y.Z. and O.R. performed experiments. E.M.M., J.Y.Z., J.K.J. and B.E.B. wrote the paper.

Competing interests

J.K.J. has a financial interest in Transposagen Biopharmaceuticals. J.K.J.'s interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies.

Corresponding author

Correspondence to Bradley E Bernstein.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8

Excel files

  1. 1.

    Supplementary Table 1

    TALE array target sequences

  2. 2.

    Supplementary Table 2

    Primer sequences used

About this article

Publication history

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DOI

https://doi.org/10.1038/nbt.2701

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