Scientists at the Babraham Institute, in collaboration with the Wellcome Trust Sanger Institute Single Cell Genomics Center, report the development of a new single-cell technique to help investigate how the environment affects development and the traits inherited from one’s parents. The method, which can be used to map all of the epigenetic marks on the DNA within a single cell, is expected to boost the understanding of embryonic development and could enhance clinical applications like cancer therapy and fertility treatments, while also potentially reducing the number of mice currently needed for this research, according to the researchers.

“The ability to capture the full map of these epigenetic marks from individual cells will be critical for a full understanding of early embryonic development, cancer progression, and aid the development of stem cell therapies,” said Gavin Kelsey, Ph.D., from the Babraham Institute. “Epigenetics research has mostly been reliant on using the mouse as a model organism to study early development. Our new single-cell method gives us an unprecedented ability to study epigenetic processes in human early embryonic development, which has been restricted by the very limited amount of tissue available for analysis.”

The research (“Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity”), published in Nature Methods, specifically offers a new single-cell technique capable of analyzing DNA methylation across the whole genome. The method treats the cellular DNA with bisulphite and the treated DNA is then amplified and read on high-throughput sequencing machines to show up the location of methylation marks and the genes being affected.

“We report a single-cell bisulfite sequencing (scBS-seq) method that can be used to accurately measure DNA methylation at up to 48.4% of CpG sites,” wrote the investigators. “Embryonic stem cells grown in serum or in 2i medium displayed epigenetic heterogeneity, with '2i-like' cells present in serum culture. Integration of 12 individual mouse oocyte datasets largely recapitulated the whole DNA methylome, which makes scBS-seq a versatile tool to explore DNA methylation in rare cells and heterogeneous populations.”

These analyses will help to define how epigenetic changes in individual cells during early development drive cell fate, continued Dr. Kelsey, adding that current methods observe epigenetic marks in multiple, pooled cells. This can obscure modifications taking place in individual cells at a time in development when each cell has the potential to form in a unique way. The new method has already revealed that many of the methylation marks that differ between individual cells are precisely located in sites that control gene activity, pointed out Dr. Kelsey.

“Our work provides a proof-of-principle that large-scale, single-cell epigenetic analysis is achievable to help us understand how epigenetic changes control embryonic development,” he explained. “The application of single-cell approaches to epigenetic understanding goes far beyond basic biological research. Future clinical applications could include the analysis of individual cancer cells to provide clinicians with the information to tailor treatments, and improvements in fertility treatment by understanding the potential for epigenetic errors in assisted reproduction technologies.”

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