Thank you. Listen to this article using the player above. ✖
Want to listen to this article for FREE?
Complete the form below to unlock access to ALL audio articles.
Scientists at the Van Andel Institute have introduced a new method for analyzing DNA methylation in individual cells. The technique, called scDEEP-mC, enables high-resolution mapping of methylation patterns across the genome, enhancing the ability to detect subtle and cell-specific epigenetic features.
DNA methylation is a chemical modification that helps regulate gene expression and cell identity without altering the DNA sequence itself. It plays a critical role in development, cell differentiation and genomic stability. Aberrant methylation patterns have been linked to a range of diseases, including cancer.
Until now, techniques for assessing methylation in single cells have lacked the resolution and efficiency required for broad application. scDEEP-mC addresses these limitations by generating comprehensive methylation maps of of DNA methylation that allow researchers to identify distinct cell types and trace developmental changes at the individual cell level. The method also allows for comparisons between newly replicated and older cells, which could provide insights into aging and disease progression.
Detailed epigenetic profiles in individual cells
The study, published in Nature Communications, describes how scDEEP-mC supports several advanced analyses in single cells. These include the estimating of cellular age using epigenetic clocks, analysis of hemimethylation and creation of whole-chromosome X-inactivation epigenetic profiles.
The improved resolution allows researchers to study methylation dynamics during DNA replication, a process that was previously difficult to observe at the single-cell level.
“scDEEP-mC allows us to see DNA methylation at varying stages of DNA replication in individual cells — something that has not been possible until now,” said Nathan Spix, Ph.D., co-first author of the study and a postdoctoral fellow. “For example, scDEEP-mC can help us pinpoint early DNA methylation changes in single cells that go on to become cancerous. If we know what goes wrong in the early stages of this process, we can use that information to develop new ways to detect and treat disease.”
Previous single-cell methylation methods relied on pooled data from multiple cells, which obscured cell-specific differences. Such averaging techniques limited the ability to identify rare cell types or detect nuanced epigenetic variations. In contrast, scDEEP-mC generates detailed individual cell profiles, revealing differences that would otherwise remain hidden.
The method’s efficiency and depth of coverage position it as a valuable tool for studying complex tissues, where understanding individual cell behavior is essential for unraveling disease mechanisms.
Reference: Spix NJ, Habib WA, Zhang Z, et al. High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and replication dynamics. Nat Commun. 2025;16(1):6273. doi: 10.1038/s41467-025-61589-1
This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source. Our press release publishing policy can be accessed here.
This content includes text that has been generated with the assistance of AI. Technology Networks’ AI policy can be found here.