Chapter 8 - Single-cell technologies in stem cell epigenetics

Abstract

Single-cell sequencing is a powerful methodology for revealing traits of individual cells in heterogeneous populations such as embryonic stem cell cultures or whole tissues. As cellular behaviors typically depend on coordinated expression of many genes and translated proteins, unbiased sequencing methods that can extract genome-wide profiles from single cells without prior knowledge about the initial cellular sample are needed. In recent years, single-cell RNA sequencing was used to identify complex cell populations, reconstruct developmental trajectories, and model transcriptional dynamics. As the DNA representation in a cell is much lower than that of RNA, single-cell DNA-based methods such as genomic sequencing, ChIP-seq, ATAC-seq, and methods for studying the 3-D architecture of genomes are limited by the low number of molecules that can be detected making them less sensitive and more challenging for computational analysis. In this chapter, we review current single-cell sequencing techniques, discuss the power and limitations of these methods, and discuss their implementation in the context of pluripotency and differentiation studies.