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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

Author

Listed:
  • Stephen J. Clark

    (Babraham Institute)

  • Ricard Argelaguet

    (European Bioinformatics Institute
    University of Cambridge)

  • Chantriolnt-Andreas Kapourani

    (University of Edinburgh)

  • Thomas M. Stubbs

    (Babraham Institute)

  • Heather J. Lee

    (Babraham Institute
    Wellcome Trust Sanger Institute
    The University of Newcastle)

  • Celia Alda-Catalinas

    (Babraham Institute)

  • Felix Krueger

    (Babraham Institute)

  • Guido Sanguinetti

    (University of Edinburgh)

  • Gavin Kelsey

    (Babraham Institute
    University of Cambridge)

  • John C. Marioni

    (European Bioinformatics Institute
    University of Cambridge
    Wellcome Trust Sanger Institute)

  • Oliver Stegle

    (European Bioinformatics Institute)

  • Wolf Reik

    (Babraham Institute
    Wellcome Trust Sanger Institute
    University of Cambridge)

Abstract

Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.

Suggested Citation

  • Stephen J. Clark & Ricard Argelaguet & Chantriolnt-Andreas Kapourani & Thomas M. Stubbs & Heather J. Lee & Celia Alda-Catalinas & Felix Krueger & Guido Sanguinetti & Gavin Kelsey & John C. Marioni & O, 2018. "scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03149-4
    DOI: 10.1038/s41467-018-03149-4
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    Cited by:

    1. Caglar Berkel & Ercan Cacan, 2019. "Single-Cell Epigenomics In Cancer Research," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 21(3), pages 15966-15973, September.

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