PT  - JOURNAL ARTICLE
AU  - Stephen J. Clark
AU  - Ricard Argelaguet
AU  - Chantriolnt-Andreas Kapourani
AU  - Thomas M. Stubbs
AU  - Heather J. Lee
AU  - Felix Krueger
AU  - Guido Sanguinetti
AU  - Gavin Kelsey
AU  - John C. Marioni
AU  - Oliver Stegle
AU  - Wolf Reik
TI  - Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells
AID  - 10.1101/138685
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 138685
4099  - http://biorxiv.org/content/early/2017/05/17/138685.short
4100  - http://biorxiv.org/content/early/2017/05/17/138685.full
AB  - Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report the first 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 mouse embryonic stem cells, finding links between all three molecular layers and revealing strong and widespread associations between chromatin accessibility and DNA methylation.