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Genome-wide localization of small molecules

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Abstract

A vast number of small-molecule ligands, including therapeutic drugs under development and in clinical use, elicit their effects by binding specific proteins associated with the genome. An ability to map the direct interactions of a chemical entity with chromatin genome-wide could provide important insights into chemical perturbation of cellular function. Here we describe a method that couples ligand-affinity capture and massively parallel DNA sequencing (Chem-seq) to identify the sites bound by small chemical molecules throughout the human genome. We show how Chem-seq can be combined with ChIP-seq to gain unique insights into the interaction of drugs with their target proteins throughout the genome of tumor cells. These methods will be broadly useful to enhance understanding of therapeutic action and to characterize the specificity of chemical entities that interact with DNA or genome-associated proteins.

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Figure 1: Chem-seq from intact cells or cellular lysates reveals genomic sites bound by the BET bromodomain-targeting drug JQ1.
Figure 2: Genome-wide drug target analysis.
Figure 3: Chem-seq reveals genomic occupancy of a protein kinase inhibitor and a DNA-intercalating drug.

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Acknowledgements

We thank T. Volkert, J. Love, J.-A. Kwon and S. Gupta at the Whitehead Genome Technology Core for Solexa sequencing, E. Cohick for help with cell culture, and A. Federation and R. St. Pierre at the Dana-Farber Cancer Institute for biochemistry support. This work was supported by US National Institutes of Health grants HG002668 (R.A.Y.), CA109901 (R.A.Y.) and CA146445 (R.A.Y., T.I.L.), Swedish Research Council Postdoctoral Fellowship VR-B0086301 (J.L.), American Cancer Society Postdoctoral Fellowship PF-11-042- 01-DMC (P.B.R.), the Leukemia & Lymphoma Society (J.Q. and J.E.B.) and the Damon-Runyon Cancer Research Foundation (J.E.B.).

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Authors and Affiliations

Authors

Contributions

J.J.M., P.B.R., J.E.B. and R.A.Y. conceived of the Chem-seq method, L.A. and M.G.G. developed the method, L.A. generated bio-JQ1 and bio-psoralen Chem-seq data, M.G.G. generated bio-AT7519 Chem-seq data, Z.P.F. developed computational methods and analyzed the data, J.Q. and J.J.M. synthesized biotinylated derivatives of chemical probes, J.Q. performed protein biochemistry, L.A. generated ChIP-seq data for BRD2, BRD3, BRD4, CDK7, CDK8, H4K20me3 and H3K27me3, P.B.R. and J.L. generated ChIP-seq data for RNA Pol II and CDK9, W.B.S. generated cellular proliferation data, A.A.S. contributed to optimize Chem-seq, T.I.L. provided advice on method development, and J.E.B. and R.A.Y. supervised the research.

Corresponding authors

Correspondence to James E Bradner or Richard A Young.

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Competing interests

J.E.B. and R.A.Y. are founders of Syros Pharmaceuticals. J.J.M., P.B.R., M.G.G. and J.L. are employees of Syros Pharmaceuticals.

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Supplementary Figures 1–6, Supplementary Methods and Supplementary Table 1 (PDF 4352 kb)

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Anders, L., Guenther, M., Qi, J. et al. Genome-wide localization of small molecules. Nat Biotechnol 32, 92–96 (2014). https://doi.org/10.1038/nbt.2776

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