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

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 (), Oliver Stegle () and Wolf Reik ()
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Stephen J. Clark: Babraham Institute
Ricard Argelaguet: European Bioinformatics Institute
Chantriolnt-Andreas Kapourani: University of Edinburgh
Thomas M. Stubbs: Babraham Institute
Heather J. Lee: Babraham Institute
Celia Alda-Catalinas: Babraham Institute
Felix Krueger: Babraham Institute
Guido Sanguinetti: University of Edinburgh
Gavin Kelsey: Babraham Institute
John C. Marioni: European Bioinformatics Institute
Oliver Stegle: European Bioinformatics Institute
Wolf Reik: Babraham Institute

Nature Communications, 2018, vol. 9, issue 1, 1-9

Abstract: 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.

Date: 2018
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03149-4

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DOI: 10.1038/s41467-018-03149-4

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