Abstract

We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

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Acknowledgements

We thank S. Fisher, M. Kellis, B. Birren and M. Zody for technical assistance and constructive discussions. We acknowledge L. Zagachin in the MGH Nucleic Acid Quantitation core for assistance with real-time PCR. E.M. was supported by an institutional training grant from NIH. M.W. was supported by fellowships from the Human Frontiers Science Organization Program and the Ellison Foundation. This research was supported by funds from the National Human Genome Research Institute, the National Cancer Institute, the Burroughs Wellcome Fund, Massachusetts General Hospital, and the Broad Institute of MIT and Harvard.

All analysed data sets can be obtained from http://www.broad.mit.edu/seq_platform/chip/. Microarray data have been submitted to the GEO repository under accession number GSE8024.

Author information

Author notes

    • Eric S. Lander
    •  & Bradley E. Bernstein

    These authors contributed equally to this work.

Affiliations

  1. Broad Institute of Harvard and MIT,

    • Tarjei S. Mikkelsen
    • , Manching Ku
    • , David B. Jaffe
    • , Biju Issac
    • , Erez Lieberman
    • , Georgia Giannoukos
    • , Pablo Alvarez
    • , William Brockman
    • , Richard P. Koche
    • , William Lee
    • , Eric Mendenhall
    • , Aviva Presser
    • , Carsten Russ
    • , Xiaohui Xie
    • , Chad Nusbaum
    • , Eric S. Lander
    •  & Bradley E. Bernstein
  2. Division of Health Sciences and Technology, MIT, and

    • Tarjei S. Mikkelsen
    • , Erez Lieberman
    •  & Richard P. Koche
  3. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA

    • Alexander Meissner
    • , Marius Wernig
    • , Rudolf Jaenisch
    •  & Eric S. Lander
  4. Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA

    • Manching Ku
    • , Biju Issac
    • , Richard P. Koche
    • , Eric Mendenhall
    • , Aisling O’Donovan
    •  & Bradley E. Bernstein
  5. Department of Neurology, Children’s Hospital, and

    • Tae-Kyung Kim
  6. Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Bradley E. Bernstein

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Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Corresponding authors

Correspondence to Eric S. Lander or Bradley E. Bernstein.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Notes which includes the ChIP-Seq read requirement, genome coverage and accuracy and Supplementary Figures 1-10 with Legends

Excel files

  1. 1.

    Supplementary Table 1

    This file contains Supplementary Table 1 which includes the list of datasets analyzed.

  2. 2.

    Supplementary Table 2

    This file contains Supplementary Table 2 which includes the primers for RT-PCR validation of ChIP-Seq.

  3. 3.

    Supplementary Table 3

    This file contains Supplementary Table 3 which includes the list of analyzed promoters and their chromatin state in ES cells, neural progenitors and embryonic fibroblasts.

  4. 4.

    Supplementary Table 4

    This file contains Supplementary Table 4 which includes the expression levels for analyzed genes in ES cells, neural progenitors and embryonic fibroblasts.

  5. 5.

    Supplementary Table 5

    This file contains Supplementary Table 5 which includes the Gene Ontology categories associated with monovalent and bivalent promoters in ES cells.

  6. 6.

    Supplementary Table 6

    This file contains Supplementary Table 6 which includes the chromatin state of promoters associated with known regulators or markers of differentiated cell types

  7. 7.

    Supplementary Table 7

    This file contains Supplementary Table 7 which includes the allelic bias observed at verified or putative imprinting control regions.

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DOI

https://doi.org/10.1038/nature06008

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