In molecular heredity, scientists think of genes, but other factors impact the process as well. Epigenetics covers the molecular mechanisms that create inheritable changes that do not involve alterations in DNA sequences. So, epigenetic transformations include things like chemical modifications to DNA and histones. To look deeply into the impacts of these chromosomal adjustments, scientists explore these changes in single cells, and recent technological advances have made that easier than ever.
In a 2018 article in the Journal of Clinical Genomics, Pang-Kuo Lo and Qun Zhou, both of the University of Maryland School of Medicine, wrote: “Technological advances in single-cell epigenomics overall involve the development of indexing systems in genome-wide sequencing” and these can be used to improve “the recovery yields of epigenetic materials isolated from a single cell,” or the material from a limited number of cells. These tools can be used to study DNA methylation, histone modifications, chromatin conformation, and other epigenetic features.
As explained by Fergus Chan, senior product manager at 10x Genomics, “Chromatin structure varies from cell to cell—despite identical DNA sequences—and such epigenetic variability is a key mechanism to generate cell-specific patterning of DNA and expression of protein coding genes.” Moreover, Chan points out” “Unlike genetic mutations, epigenetic alterations are dynamic and potentially reversible.”
There are many reasons to explore the chromosome-related chemical changes in single cells. “Single-cell epigenomics provides a complementary description of transcriptional states,” bioinformatics expert Stein Aerts of Belgium’s University of Leuven and his colleagues recently wrote in Briefings in Functional Genomics. “Single-cell epigenomes are bound to increase the insight into the cellular (transcriptional) heterogeneity.”
The more techniques available to scientists to study epigenetics in single cells, the more likely we are to understand heredity at this high level of resolution.
A trio of applications
When asked about the most important applications of single-cell epigenetics, research associate Chongyuan Luo of The Salk Institute for Biological Studies talks about three.
“The first is to annotate the cell-type specific function elements in the genome, such as enhancers or insulators, which control gene expression,” Luo says. “The idea of using epigenomic signatures to annotate functional elements was pioneered by consortium efforts, such as ENCODE.” Most existing data, though, come from bulk tissue samples. “Single-cell epigenomics allows the identification of functional elements in virtually all cell types in the human body,” Luo explains. “Single-cell epigenomics has already been applied to map functional elements in healthy tissues, and should also contribute to identifying elements that play roles in human diseases.”
A second major application that Luo points out is finding the kinds of cells that respond to environmental stimuli. “Single-cell epigenomic profiling allows cell-type identification, and at the same time, measurements of environment-induced epigenetic alterations,” he says.
Third, Luo says, single-cell epigenetics can “extend the ability of molecular phenotyping for diseases to cell-type or single-cell levels to better understand the contribution of aberrant gene regulatory networks in pathology.”
Methylation and more
To collect more information, scientists want to analyze more cells in an experiment. Often that involves tracking methylation. In 2017 in a Science article, Luo and his colleagues, 
“published the first method to generate thousands of single-cell methylome profiles.” Also, at Oregon Health & Science University in Portland, genomics expert Andrew Adey and his colleagues developed a combinatorial indexing approach that generates thousands of single-cell methylome libraries.
Image: A map of methylated DNA in neurons can show how epigenetic differences impact neuronal development. Image courtesy of Jamie Simon, The Salk Institute for Biological Studies.
Some techniques also analyze changes in chromatin. “The Single-cell Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a very important application in single-cell epigenomic analysis,” says Mark Lynch, director of the global single-cell genomics business at Fluidigm. “The C1 system was the first commercial platform to implement ATAC-seq and to date provides researchers with the most sensitive method for studying the open chromatin in single-cells, which provides researchers with data on promoters, enhancers, or other regulatory elements that may actually control the transcription/expression profile of the cells being studied.” Fluidigm’s C1 is also automated for single-cell analysis. As Lynch says, “In short, ATAC-seq provides data on why expression occurs the way it does when analyzing single-cell mRNA sequencing data.”
ATAC-seq can also be used in healthcare. “Due to the more upstream and mechanistic nature of chromatin accessibility compared to gene expression, pharmaceutical and biotech companies can also use single-cell ATAC-seq in target identification and mechanism of action in drug discovery, as well as patient selection and prognostic-marker development in clinical studies,” says Chan. But these can be complicated methods or lower than desired throughput, in some cases. “With that in mind, 10x Genomics will be launching its Chromium Single Cell ATAC Solution by the end of 2018,” says Chan. “This easy-to-use and scalable solution will be scalable from 500–10,000 nuclei, with high nuclei capture efficiency, low mitochondrial reads, and turn-key analysis and visualization software.”
Pathology instructor Ansuman Satpathy of Stanford University and his colleagues used ATAC-seq on the C1 to study T-cell receptors (TCRs) in patients with cutaneous T-cell lymphoma (CTCL). Satpathy’s team reported in a 2018 Nature Medicine article: “We identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers, and primary leukemic T cells from patient samples.” With more research, this approach could lead to clinical applications. “Future studies on larger patient cohorts are needed to establish whether integration of epigenomic information with T-cell clonality can (i) improve diagnostic precision as compared to the standard clinical techniques currently in use and (ii) predict or monitor successful clinical responses to therapies that target the epigenome,” Satpathy and his colleagues concluded.
As these examples reveal, there’s more to understand about heredity than changes in gene sequence. Chemical modifications to genes also impact the future of a person and, in some cases, that person’s progeny. As scientists explore single-cell epigenetics from more cells and in more detail, the impact of these chemical changes could teach us even more about our futures.