Every cell in our body has a different function to fulfill. Scientists have been working to find evidence on how individual cells develop differently to become tissues, and what are the problems that come with disease onset. The next-generation sequencing technology is helping scientists learn about epigenetic modifications within every cell. 

It is important to profile epigenomes at single-cell resolution. This helps in understanding every cell’s function in the complex multicellular systems that are necessary for life. However, the main challenge is to uncover cellular heterogeneity if you’re using conventional bulk cell sample inputs. 

Here we have outlined some methods for single-cell measurements of the epigenome. 

Multicellular Development Starts With Single Cell

Human beings have more than 30 trillion cells in their body – all of them sourced from a single cells. All these cells are from different cell types, and they have distinct roles. These range from protecting against viral infections and carrying messages to the brain. Biological science has seen great developments. Over the last century, researchers have been able to thoroughly describe how every genetic molecule in a cell is attributed to the advent of Next-Gen Sequencing. (Biosite, 2020)

Single-Cell Methylome 

The ability to investigate the epigenome stands at the forefront of using Next-Gen sequencing technologies. DNA methylation happens to be one of the most researched and important epigenome marks. This has been shown as a crucial cellular process along with imprinting and cell-type-specific regulation of gene expression. 

In current times, we have whole-genome bisulfite sequencing (WGBS-seq) and array-based methods query DNA methylation that make use of DNA, with the help of high-quality DNA extraction kits from thousands of cells (bulk sequencing). After the initial DNA testing, it is isolated from the bulk of cells at a time, it makes it quite easy to miss the heterogeneity present there, and hides signals from all the rare cell populations like cancer cells and stems. Applications for bisulfite sequencing of single-cell have been developed in recent times, which has paved way for amazing exploration of methylation heterogeneity between the cells. Moreover, this also helps in the identification of new cell types and regulatory networks that differentiate the newly found cell types. 

Another new technique, sci-MET5 was made using Zymo EZ DNA methylation technology. By leveraging all these brilliant technologies, putting DNA methylation at single-cell levels helped in uncovering several heterogeneity in the methylomes of various cell types. These types include oocytes, fibroblasts, liver, and brain. With the help of basic single-cell methylomes of different cell types sequences, future scientists have the option to research single-nuclei methylomes for the disease states. This will aid in the investigation of cell-type specific changes and reveal new biomarkers. 

New Frontiers

There’s still no evidence of how the 3D architecture of chromosomes and methylation at specific locations regulate each other. However, with the coming of single-cell multi-omics methodologies, all transcription, chromatin accessibility, 3D chromosomal structures, and DNA methylation in several combinations can be measured from the each cell, at the same time. 

To evaluate 3D chromatic architecture and methylation in a cell, several methods have been devised. For instance, scMethyl-HiC11 and sc-m3C-seq12 have been used to study stem cells and investigate the brain cells, respectively. Researchers have shown the presence of cell-type-specific architectures linked with particular methylation patterns. Examining these events at the same time has helped discover important insights about how DNA methylation, chromatin accessibility, and gene expression can be regulated. With the consolidation of several layers of ‘omics’ information, it gets easy to explain the relationship between methylation, 3D architecture, and transcription. 

Single-cell DNA methylation sequencing technologies are growing, and these new techniques are assisting researchers to understand the cell type diversity in all the organisms. Moreover, this process has also allowed unprecedented resolution of developmental and disease onset events. 

References

Biosite, N. (2020). Diving Into Single-Cell Epigenomes.