Linking Gene Expression, DNA Methylation in Single Cells

    Single-cell sequencing technology has progressed rapidly in recent years, and is widely used to study how gene expression profiles (‘transcriptomes’) vary between cells. Recent single-cell protocols also allow researchers to explore chemical modification of DNA (‘epigenetics’), for example DNA methylation, which is a driving force behind changes to gene expression. Until now, it has only been possible to study single-cell transcriptomes and epigenomes separately.

    Now, a study by researchers in the UK and Belgium makes it possible to study the epigenome and transcriptome of a single cell at the same time. The investigators hope that their new method, which they have dubbed scM&T-seq, will help them pinpoint the relationship between changes in DNA methylation and gene expression.

    “This new experimental protocol lets you assay both DNA methylation and RNA of the same single cell in parallel,” explained co-senior author Oliver Stegle, Ph.D., group leader at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI). “Our approach provides the first direct view of the relationship between heterogeneity in DNA methylation and variation of expression in specific genes across single cells.”

    The findings from this study were published recently in Nature Methods through an article entitled “Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.”

    “This method combines our previously developed protocol for parallel DNA and RNA sequencing with new advances in single-cell epigenetics,” noted coauthor Thierry Voet, Ph.D., group leader at the Wellcome Trust Sanger Institute and Katholieke Universiteit Leuven, Belgium. “The result is an optimized approach that maximizes the amount of biological information that can be obtained from a single cell.”

    The European scientists profiled 61 mouse embryonic stem cells (ESCs) at a stage when they switch continuously between different gene-expression states. The researchers used two techniques in parallel: one that revealed detailed information about gene expression and another to study DNA methylation in the same cells. They obtained sufficient genetic coverage from each cell to study epigenetic and transcriptome diversity of several thousand genes.

    “The epigenetic state of ESCs is highly variable, and this variation is associated with changes in gene expression,” remarked co-senior author Wolf Reik, Ph.D., laboratory head at the Babraham Institute and Wellcome Trust Sanger Institute. “Much of the transcriptional variability we see is thought to be driven by modifications of DNA, but now we have a technique that allows us to look at a single cell and discover relationships between DNA methylation and gene expression that were previously unknown. To understand development, it is really important that we pin these relationships down, and get them right.”

    “Our statistical approach revealed hundreds of individual associations between variable epigenetic regions and gene expression,” added lead author Christof Angermueller, a doctoral candidate at EMBL-EBI. “These associations can provide important insights into how pluripotency is maintained and how cell differentiation is regulated.”

    The scientists were excited by the results of their new method and believe that the new protocol will offer new opportunities for studying multiple different molecular layers simultaneously. Moreover, the researchers feel that this method could have broad implications for improving our understanding of normal development and the changes that occur with aging and cancer.