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Updated: Feb 14, 2026

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
Stephen J Clark1, Ricard Argelaguet2,3, Chantriolnt-Andreas Kapourani4
1Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK. stephen.clark@babraham.ac.uk.
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.
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