Article | Published:

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

Nature Biotechnology volume 33, pages 11651172 (2015) | Download Citation

Abstract

Chromatin profiling provides a versatile means to investigate functional genomic elements and their regulation. However, current methods yield ensemble profiles that are insensitive to cell-to-cell variation. Here we combine microfluidics, DNA barcoding and sequencing to collect chromatin data at single-cell resolution. We demonstrate the utility of the technology by assaying thousands of individual cells and using the data to deconvolute a mixture of ES cells, fibroblasts and hematopoietic progenitors into high-quality chromatin state maps for each cell type. The data from each single cell are sparse, comprising on the order of 1,000 unique reads. However, by assaying thousands of ES cells, we identify a spectrum of subpopulations defined by differences in chromatin signatures of pluripotency and differentiation priming. We corroborate these findings by comparison to orthogonal single-cell gene expression data. Our method for single-cell analysis reveals aspects of epigenetic heterogeneity not captured by transcriptional analysis alone.

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Author information

Author notes

    • Ralph A Sperling

    Current address: Fraunhofer ICT-IMM, Mainz, Germany.

    • Assaf Rotem
    • , Oren Ram
    •  & Noam Shoresh

    These authors contributed equally to this work.

Affiliations

  1. Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.

    • Assaf Rotem
    • , Ralph A Sperling
    •  & David A Weitz
  2. Epigenomics Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Assaf Rotem
    • , Oren Ram
    • , Noam Shoresh
    •  & Bradley E Bernstein
  3. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

    • Oren Ram
    •  & Bradley E Bernstein
  4. Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Oren Ram
    •  & Bradley E Bernstein
  5. Broad Technology Labs, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Alon Goren

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Competing interests

D.A.W. and B.E.B. are both founders and consultants for HiFiBio.

Corresponding authors

Correspondence to David A Weitz or Bradley E Bernstein.

We thank A. Regev, N. Yosef, E. Shema, I. Tirosh, H. Zhang, S. Gillespie and J. Xing for their valuable comments and critiques of this work. We also thank G. Kelsey for sharing single-cell data for comparisons. This research was supported by funds from Howard Hughes Medical Institute, the National Human Genome Research Institute's Centers of Excellence in Genome Sciences (P50HG006193), ENCODE Project (U54HG006991), the National Heart, Lung, and Blood Institute (U01HL100395), the National Science Foundation (DMR-1310266), the Harvard Materials Research Science and Engineering Center (DMR-1420570) and the Defense Advanced Research Projects Agency (HR0011-11-C-0093).

Integrated supplementary information

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–10, Supplementary Tables 1 and 3, and Supplementary Notes 1–3

Excel files

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    Supplementary Table 2

    Barcodes design

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    Supplementary Table 4

    Signatures data set sources

Zip files

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    Supplementary Design Files

    Design of microfluidic devices. This compressed folder includes 3 ACAD designs, one for the 96 parallel drop makers, one for the co-flow drop maker and one for the 3 point merger.

Videos

  1. 1.

    Cell encapsulation.

    A slowed down movie showing barcode drops (small) and drops containing cellular chromatin (large) merge together with labeling buffer flowing into the T-junction.

  2. 2.

    Drop labeling.

    A slowed down movie showing barcode drops (small) and drops containing cellular chromatin (large) merge together with labeling buffer flowing into the T-junction.

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DOI

https://doi.org/10.1038/nbt.3383

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