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Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

Abstract

Chromatin immunoprecipitation (ChIP) combined with high-throughput sequencing (ChIP-seq) has become the gold standard for whole-genome mapping of protein-DNA interactions. However, conventional ChIP protocols necessitate the use of large numbers of cells, and library preparation steps associated with current high-throughput sequencing platforms require substantial amounts of DNA; both of these factors preclude the application of ChIP-seq technology to many biologically important but rare cell types. Here we describe a nano-ChIP-seq protocol that combines a high-sensitivity small-scale ChIP assay and a tailored procedure for generating high-throughput sequencing libraries from scarce amounts of ChIP DNA. In terms of the numbers of cells required, the method provides two to three orders of magnitude of improvement over the conventional ChIP-seq method and the entire procedure can be completed within 4 d.

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Figure 1: Schematic of nano-ChIP-seq library preparation method.
Figure 2: The sonication setup with the Branson 250.

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Acknowledgements

We acknowledge all the members of the Bernstein Lab for constructive discussions during the method development. We thank M. Coyne, S. Furuyama, S. Gillespie and N.A. Okan for their critical reading of the manuscript and J. Zhu, N. Shoresh and T. Mikkelsen for computational assistance. This research was supported by funds from the Starr Cancer Consortium, a Charles E. Culpeper Scholarship, the US National Human Genome Research Institute, the National Institutes of Health Roadmap for Epigenomics and the National Heart, Lung and Blood Institute.

AUTHOR CONTRIBUTIONS

M.A. and B.E.B. designed the method and analyzed the data. M.A. performed the experiments and wrote the manuscript.

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Correspondence to Mazhar Adli or Bradley E Bernstein.

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M.A. and B.E.B. have filed a patent application describing the methods presented here. Patent application #: 12 / 699508 (USA)

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Adli, M., Bernstein, B. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc 6, 1656–1668 (2011). https://doi.org/10.1038/nprot.2011.402

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