Letter | Published:

Single-cell chromatin accessibility reveals principles of regulatory variation

Nature volume 523, pages 486490 (23 July 2015) | Download Citation


Cell-to-cell variation is a universal feature of life that affects a wide range of biological phenomena, from developmental plasticity1,2 to tumour heterogeneity3. Although recent advances have improved our ability to document cellular phenotypic variation4,5,6,7,8, the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of mammalian DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells by assay for transposase-accessible chromatin using sequencing (ATAC-seq)9 integrated into a programmable microfluidics platform. Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provide insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type-specific accessibility variance across eight cell types. Targeted perturbations of cell cycle or transcription factor signalling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome compartments10 de novo, linking single-cell accessibility variation to three-dimensional genome organization. Single-cell analysis of DNA accessibility provides new insight into cellular variation of the ‘regulome’.

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Data deposits

All data has been deposited in GEO under the accession number GSE65360. Fluidigm C1 scripts for performing scATAC-seq are available at https://www.fluidigm.com/c1openapp/scripthub/script/2015-06/single-cell-chromatin-accessib-1433443631246-1.


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This work was supported by National Institutes of Health (NIH) P50HG007735 (to H.Y.C. and W.J.G.), UH2 AR067676 and Lifespan Extension Foundation (H.Y.C.), U19AI057266 (to W.J.G.) and the Rita Allen Foundation (to W.J.G.) and the Baxter Foundation Faculty Scholar Grant (to W.J.G); H.Y.C. is an Early Career Scientist of the Howard Hughes Medical Institute. J.D.B. acknowledges support from the National Science Foundation Graduate Research Fellowships and NIH training grant T32HG000044 for support. M.P.S. acknowledges the NIH and the National Human Genome Research Institute (NHGRI) for funding through 5U54HG00455805. We thank members of Greenleaf and Chang laboratories, as well as the Fluidigm team, including L. Xi for discussions. We acknowledge the S. Kim laboratory for assistance with FACS sorting and the C. Bustamante laboratory for help with sequencing. We also thank R. Nichols, C. Mazumdar, V. Sebastiano and V. Risca for cells.

Author information

Author notes

    • Beijing Wu
    •  & Ulrike M. Litzenburger

    These authors contributed equally to this work.


  1. Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

    • Jason D. Buenrostro
    • , Beijing Wu
    • , Michael P. Snyder
    •  & William J. Greenleaf
  2. Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA

    • Jason D. Buenrostro
    • , Ulrike M. Litzenburger
    •  & Howard Y. Chang
  3. Fluidigm Corporation, South San Francisco, California 94080, USA

    • Dave Ruff
    •  & Michael L. Gonzales
  4. Department of Applied Physics, Stanford University, Stanford, California 94025, USA

    • William J. Greenleaf


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J.D.B., H.Y.C. and W.J.G. conceived of the method. J.D.B., B.W., M.G. and D.R. developed the Fluidigm C1 microfluidic protocols. B.W. performed all scATAC-seq experiments with supervision from J.D.B. U.M.L. conducted the flow analysis, immunostains and drug treatments. J.D.B. developed and implemented the analysis infrastructure with input from W.J.G. All authors interpreted the data and wrote the manuscript. W.J.G. and H.Y.C. supervised all aspects of this work.

Competing interests

Stanford University has filed a provisional patent application on the methods described, and J.D.B., H.Y.C. and W.J.G. are named as inventors. D.R. and M.L.G. declare competing financial interests as employees of Fluidigm Corp.

Corresponding authors

Correspondence to Howard Y. Chang or William J. Greenleaf.

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