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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Nature Methods volume 10, pages 1213–1218 (2013)Cite this article

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Abstract

We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with nucleosomes. Using ATAC-seq maps of human CD4+ T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual's epigenome on a timescale compatible with clinical decision-making.

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Figure 1: ATAC-seq probes open-chromatin state.
Figure 2: ATAC-seq provides genome-wide information on chromatin compaction.
Figure 3: ATAC-seq provides genome-wide information on nucleosome positioning in regulatory regions.
Figure 4: ATAC-seq assays genome-wide factor occupancy.
Figure 5: ATAC-seq enables real-time personal epigenomics.

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Acknowledgements

We thank members of Greenleaf and Chang labs for discussion, A. Burnet and S. Kim lab and the Stanford flow-cytometry core facility for assistance with FACS sorting, A. Schep for modeling Tn5 insertion preference, and V. Risca for graphics. This work was supported by the US National Institutes of Health (H.Y.C., W.J.G. and J.D.B.), including RC4NS073015, U01DK089532 and U19AI057229; Scleroderma Research Foundation (H.Y.C.); and California Institute for Regenerative Medicine (H.Y.C.). H.Y.C. acknowledges support as an Early Career Scientist of the Howard Hughes Medical Institute. GM12878 cells were a gift from the Snyder laboratory (Stanford University).

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Authors and Affiliations

  1. Department of Genetics, Stanford University School of Medicine, Stanford, California, USA

    Jason D Buenrostro & William J Greenleaf

  2. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA

    Jason D Buenrostro, Paul G Giresi, Lisa C Zaba & Howard Y Chang

  3. Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA

    Jason D Buenrostro, Paul G Giresi, Lisa C Zaba & Howard Y Chang

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  1. Jason D Buenrostro
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Contributions

J.D.B., P.G.G. and L.C.Z. performed the research. All authors designed experiments and interpreted the data. H.Y.C. and W.J.G. wrote the paper.

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Correspondence to Howard Y Chang or William J Greenleaf.

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Competing interests

Stanford University has filed a provisional patent application on the methods described, and J.D.B., P.G.G., H.Y.C. and W.J.G. are named as inventors.

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Supplementary Figures 1–12 and Supplementary Tables 1 and 2 (PDF 3902 kb)

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Buenrostro, J., Giresi, P., Zaba, L. et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10, 1213–1218 (2013). https://doi.org/10.1038/nmeth.2688

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