Clark, S.J. et al. Nat. Commun. 9, 781 (2018).

In sports, a 'hat trick' is a feat accomplished three times in a row by the same player. Clark et al. have achieved their own hat trick of a sort, with the first method for extracting three types of genome-wide data from the same cell. Their single-cell nucleosome, methylation and transcription sequencing (scNMT-seq) method combines features of their previous single-cell methylation and transcriptome sequencing (scM&T-seq) approach and of nucleosome occupancy and methylation sequencing (NOMe-seq). The researchers separate RNA and DNA, sequence the RNA fraction and apply a GpC methyltransferase to the DNA prior to bisulfite sequencing. The externally supplied GpC mark labels enzyme-accessible, nucleosome-poor regions of the genome, and provides higher-coverage information than other DNA accessibility assays, and bisulfite conversion of methylated cytosines also allows traditional CpG DNA methylation to be inferred. The authors explore links between transcription and these two epigenetic features in differentiating mouse embryonic stem cells.