Emerging techniques in single-cell epigenomics and their applications to cancer research

Abstract

Epigenomics encompasses studies of the chemical modifications of genomic DNA and associated histones, interactions between genomic DNA sequences and proteins, the dynamics of the chromosomal conformation, the functional relationships between these epigenetic events, and the regulatory impacts of these epigenetic events on gene expression in cells. In comparison to current techniques that are only capable of characterizing average epigenomic features across bulk cell ensembles, single-cell epigenomic methodologies are emerging as powerful new techniques to study cellular plasticity and heterogeneity, as seen in stem cells and cancer. Here we summarize available techniques for studies of single-cell epigenomics, review their current applications to cancer research, and discuss future possibilities. This review also highlights that the full potential of single-cell epigenetic studies will be comprehended through integrating the multi-omics information of genomics, epigenomics and transcriptomics.

Keywords: Chemotherapeutic treatments; Epigenomics; Genomic DNA; Oncogenesis; intratumor heterogeneity; single-cell techniques.

Figure 1:

The timeline diagram for illustrating the evolution of technologies on single-cell epigenomics and their derived multi-omics methods.

Figure 2:

The flow diagram for showing the technical procedures of scBS-seq, scRRBS and scCGI-seq methods that profile DNA methylation in a single cell.

Figure 3:

The schematic flow diagram of combinatorial cellular indexing in scATAC-seq for measuring single-cell chromatin accessibility. In the first indexing, nuclei are isolated and molecularly tagged in bulk with barcoded Tn5 transposases in wells. After the first indexing, nuclei are then pooled and a limited number of nuclei are redistributed into a second set of wells via cell sorting. In the second indexing, a second unique barcode is introduced during PCR in each well.

Figure 4:

The diagram of the scNOMe-seq technology in the scCOOL-seq method. The GpC methyltransferase adds the methyl group to cytosine residues of GpC dinucleotides in the open chromatin regions, but not in the closed chromatin regions. After the GpC methylation reaction, genomic DNA is subjected to post-bisulfite adaptor-tagging sequencing (PBAT-seq) analysis. DNA methylation and chromatin accessibility can be profiled simultaneously according to CpG and GpC methylation patterns, respectively.

Figure 5:

The diagram for illustrating the roles of genomic, epigenomic and transcriptomic alterations in tumorigenesis and metastasis. The current established single-cell genomics, epigenomics, transcriptomics and their derived multi-omics methods are also shown in the diagram to indicate their applications.