scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.
Published version
Peer-reviewed
Repository URI
Repository DOI
Change log
Authors
Clark, Stephen J https://orcid.org/0000-0002-6183-491X
Argelaguet, Ricard
Kapourani, Chantriolnt-Andreas https://orcid.org/0000-0003-2303-1953
Stubbs, Thomas M
Lee, Heather J
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.
Description
Keywords
Animals, Cell Differentiation, Chromatin, DNA Methylation, Embryonic Stem Cells, Female, Histones, Male, Mice, Nucleosomes, Sequence Analysis, DNA, Single-Cell Analysis, Transcription, Genetic
Journal Title
Nat Commun
Conference Name
Journal ISSN
2041-1723
2041-1723
2041-1723
Volume Title
9
Publisher
Springer Science and Business Media LLC
Publisher DOI
Sponsorship
Biotechnology and Biological Sciences Research Council (1645504)
Cancer Research UK (22231)
Cancer Research UK (22231)