Innovative method reveals the dynamics of epigenomic maintenance

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Although all cells of an individual contain the same genetic material, they exhibit a wide variety of form and function. This diversity is enabled by various mechanisms: In DNA methylation, individual building blocks of the genetic substance are marked in order to control the activity of genes. This is a perfectly natural process, just like histone modification, which involves the chemical alteration of proteins around which the DNA is wrapped – which also influences the activity of genes. In addition, the three-dimensional arrangement of genetic material plays a role. These mechanisms, which do not change the genetic code itself, are collectively known as the “epigenome.” Inherited in the course of cell division, they interact in a wide variety of ways and are dysregulated in tumor diseases.

An international team of researchers from Utrecht (Netherlands), Oxford (UK), Wuhan (China), and Munich has developed a technique called scEpi2-seq, which detects two of these parameters – DNA methylation and histone modifications – simultaneously in individual cells. To do this, the researchers combined two methods: antibody-controlled MNase digestion, whereby the DNA is specifically cut with a type of molecular scissors, and a chemical-enzymatic technique for making DNA methylation measurable (TAPS). This made it possible for the first time to decode the interaction of epigenetic mechanisms in certain cell types.

Mechanisms are closely interlinked

The new method reveals how the investigated biological mechanisms are interlinked and underscores how closely the inheritance of methylation patterns is linked to the timing of DNA replication and the binding of proteins. Particularly in late-replicating regions of the genome, the copying process for DNA methylation is slower. Furthermore, the study revealed that nucleosomes impede remethylation – the methylation loss is stronger on nucleosomes than in the region of linker DNA. And so scEpi2-seq furnishes the first direct indication that the activity of methyl transferases subsequent to replication is influenced by the chromatin context.

By applying the technique to cells taken from the small intestine of a mouse, for example, the scientists showed that cell-type-specific methylation patterns can be found inside regions with the histone modification H3K27me3. These results demonstrate that cells use partially redundant repressive control mechanisms.

“Single-cell Epi2-seq allows us to measure the interaction of two key epigenetic levels in the same individual cells, both in vitro and in vivo,” says Christoph Geisenberger from the Institute of Pathology at LMU, one of the lead authors of the paper, which has just been published in the prestigious journal Nature Methods. “This affords us more precise insights into the interplay and inheritance of epigenetic information. In the long term, this will help us understand which control mechanisms are dysregulated in the context of carcinogenesis.”

Christoph Geisenberger, Jeroen van der Berg, Vincent van Batenburg et al. Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance. Nature Methods, 2025