%0 Journal Article %A Stephen J. Clark %A Ricard Argelaguet %A Chantriolnt-Andreas Kapourani %A Thomas M. Stubbs %A Heather J. Lee %A Felix Krueger %A Guido Sanguinetti %A Gavin Kelsey %A John C. Marioni %A Oliver Stegle %A Wolf Reik %T Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells %D 2017 %R 10.1101/138685 %J bioRxiv %P 138685 %X 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. %U https://www.biorxiv.org/content/biorxiv/early/2017/05/17/138685.full.pdf