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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References
Bulger, M. & Groudine, M. Functional and mechanistic diversity of distal transcription enhancers. Cell 144, 327–339 (2011).
Visel, A., Rubin, E.M. & Pennacchio, L.A. Genomic views of distant-acting enhancers. Nature 461, 199–205 (2009).
Noonan, J.P. & McCallion, A.S. Genomics of long-range regulatory elements. Annu. Rev. Genomics Hum. Genet. 11, 1–23 (2010).
Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).
Boyle, A.P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).
Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43–49 (2011).
Encode Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Maurano, M.T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012).
Calo, E. & Wysocka, J. Modification of enhancer chromatin: what, how, and why? Mol. Cell 49, 825–837 (2013).
Stadler, M.B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011).
Ng, J.-H. et al. In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures. Dev. Cell 24, 324–333 (2013).
Creyghton, M.P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. USA 107, 21931–21936 (2010).
Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011).
Shi, Y. et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941–953 (2004).
Boch, J. et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509–1512 (2009).
Moscou, M.J. & Bogdanove, A.J. A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501 (2009).
Mussolino, C. & Cathomen, T. TALE nucleases: tailored genome engineering made easy. Curr. Opin. Biotechnol. 23, 644–650 (2012).
Joung, J.K. & Sander, J.D. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 14, 49–55 (2013).
Dhami, P. et al. Genomic approaches uncover increasing complexities in the regulatory landscape at the human SCL (TAL1) locus. PLoS ONE 5, e9059 (2010).
Zhang, F. et al. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat. Biotechnol. 29, 149–153 (2011).
Lee, M.G. et al. Functional interplay between histone demethylase and deacetylase enzymes. Mol. Cell. Biol. 26, 6395–6402 (2006).
Lee, M.G., Wynder, C., Cooch, N. & Shiekhattar, R. An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 10.1038/nature04021 (2005).
Whyte, W.A. et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482, 221–225 (2012).
Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. Nat. Biotechnol. 30, 460–465 (2012).
Yoon, O.K. & Brem, R.B. Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA 16, 1256–1267 (2010).
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
Konermann, S. et al. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472–476 (2013).
Maeder, M.L. et al. Robust, synergistic regulation of human gene expression using TALE activators. Nat. Methods 10, 243–245 (2013).
Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008).
Pickrell, J.K., Gaffney, D.J., Gilad, Y. & Pritchard, J.K. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics 27, 2144–2146 (2011).
Ram, O. et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 147, 1628–1639 (2011).
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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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.
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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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DOI: https://doi.org/10.1038/nbt.2701
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