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Locus-specific editing of histone modifications at endogenous enhancers

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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Figure 1: Programmable TALE-LSD1 fusion modulates chromatin at an endogenous enhancer.
Figure 2: TALE-LSD1 fusions targeting 40 candidate enhancers in K562 cells.
Figure 3: TALE-LSD1 fusions to endogenous enhancers affect proximal gene expression.

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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.).

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Authors and Affiliations

Authors

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.

Corresponding author

Correspondence to Bradley E Bernstein.

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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.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8 (PDF 954 kb)

Supplementary Table 1

TALE array target sequences (XLSX 10 kb)

Supplementary Table 2

Primer sequences used (XLSX 13 kb)

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Mendenhall, E., Williamson, K., Reyon, D. et al. Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol 31, 1133–1136 (2013). https://doi.org/10.1038/nbt.2701

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