Tracking Epigenetic Changes at the Single-Cell Level

Diagram of how DNA methylation effects gene expression.[Courtesy of the National Institutes of Health]

If every cell in the human body contains the same genetic information than what makes a cell from the eye different from a liver cell? This question is often posed to biology students before introducing the concepts of gene expression and regulation—an integral part of the broader discipline of epigenetics.

DNA methylation is the foundation of epigenetics and is critical for the proper control of gene expression and cell identity—what enables cells with the same genetic material to become, for example, an eye cell, a muscle cell, or a liver cell. Moreover, various diseases, such as cancer, involve changes in DNA methylation patterns, and researchers are always looking for improved methods to document these alterations, with the hope of aiding the development of novel therapeutic interventions.

Now researchers at the Whitehead Institute for Biomedical Research have developed new methodology to monitor changes in DNA methylation over time in individual cells. The investigators developed a DNA methylation reporter system that mirrors whether a nearby region is methylated. When the target region is unmethylated, the reporter is also unmethylated, which allows expression and visualization of a fluorescent protein encoded by the reporter.

“Methylation is really key in development, in disease, and in cancer,” explained senior author and Whitehead Founding Member Rudolf Jaenisch, who is also a professor of biology at MIT. “This reporter is a very important tool. We believe it will allow us to look in a very detailed way at issues like imprinting during development and screening for the activation of genes silenced in diseases like cancer. This method will allow us to see which drug will activate a given gene.”

The findings from this study were published recently in Cell through an article entitled “Tracing dynamic changes of DNA methylation at single-cell resolution.”

Before this study, scientists have only been able to study methylation within a population of cells by sampling a few cells, a process that destroys the very cells under study. Because most cell populations in vivo are heterogeneous, and methylation can change over time, existing approaches have offered limited insight into this fundamental biological control.

“To enable monitoring of methylation status as it changes over time, we establish a reporter of genomic methylation (RGM) that relies on a minimal imprinted gene promoter driving a fluorescent protein. We show that insertion of RGM proximal to promoter-associated CpG islands reports the gain or loss of DNA methylation,” the authors wrote.

The authors’ goal was to create a system that could dynamically visualize methylation at the level of a single cell, which should open up avenues for future research to better understand methylation and its greater role in epigenetic changes.

“This opens up a whole new field of research,” noted co-author Chikdu Shivalila, a graduate student in Dr. Jaenisch’s laboratory. “You can use it to answer all of these questions about methylation that are completely unknown, including how methylation regulates gene transcription and expression patterns in cells. It's very exciting.”

The Whitehead researchers were excited by their findings and hope that their method can be applied to help fight diseases that have been difficult to treat due to their elusiveness and dynamic nature, such as various forms of cancer.

“Pharmaceutical companies have been interested in manipulating methylation in disease,” stated lead author Yonatan Stelzer, Ph.D., postdoctoral researcher in Dr. Jaenisch’s laboratory. “Now that we have a reporter for methylation, they can screen for small molecules or genes that can change a cell's phenotype. For example, they could look for a drug that could change the hypermethylation that has been associated with a specific cancer.”