Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity

Abstract

Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.

Fig. 1

Epigenomics and the spectrum of single-cell sequencing technologies. The diagram outlines the single-cell sequencing technologies currently available. A single cell is first isolated by means of droplet encapsulation, manual manipulation, fluorescence-activated cell sorting (FACS) or microfluidic processing. The first examples of single-cell multi-omic technologies have used parallel amplification or physical separation to measure gene expression (scRNA-seq) and DNA sequence (scDNA-seq) from the same cell. Note that single-cell bisulfite conversion followed by sequencing (scBS-seq) is not compatible with parallel amplification of RNA and DNA, as DNA methylation is not conserved during in vitro amplification. Single-cell epigenomics approaches utilize chemical treatment of DNA (bisulfite conversion), immunoprecipitation or enzymatic digest (e.g., by DNaseI) to study DNA modifications (scBS-seq and scRRBS), histone modifications (scChIP-seq), DNA accessibility (scATAC-seq, scDNase-seq), chromatin conformation (scDamID, scHiC)

Fig. 2

Future applications of single-cell epigenomics. The full potential of emerging single-cell epigenomic techniques will be realized through integration with transcriptome and genome sequencing. Single-cell multi-omics will be applied to biological questions involving the molecular mechanisms of epigenetic regulation (e.g., the functional consequences of rare DNA modifications), intercellular heterogeneity, and rare cell types (e.g., in early development). scATAC-seq single cell assay for transposase-accessible chromatin, scBS-seq single-cell bisulfite sequencing, scChIP-seq single-cell chromatin immunoprecipitation followed by sequencing, scDNase-seq single-cell DNase sequencing, scHiC single-cell HiC, scRRBS single-cell reduced representation bisulfite sequencing