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Fluctuating methylation clocks can trace cell fates

Researchers have shown that fluctuating DNA methylation sites can be used as ‘clocks’ to trace the lineage of a cell. Their new model could help us understand how cell dynamics change during disease.­

What are cell fates?

Each cell in our body has a so-called ‘fate’ – a final cell type that the cell will eventually develop into. In vivo, it is very difficult to reconstruct the fate of an individual human cell. This is because once a cell has reached its final form, it is very challenging to trace its lineage back. Traditional methods are extremely time-consuming and require a large amount of data. This presents many problems for research into cell development.

Therefore, the team behind a new study, published in Nature Biotechnology, investigated ways of tracing cell lineage. They found that DNA methylation sites could be used as a ‘molecular clock’ which revealed the ancestry and dynamics of a cell population.

Fluctuating DNA methylation

In some cells, regions of DNA ‘flip-flop’ between methylation states. These sites, known as fluctuating CpG (fCpG) sites, switch between being methylated and demethylated over time. There are three possible methylation states: 0% methylated, 50% methylated and 100% methylated. Some regions fluctuate over a period of hours. However, others have a longer oscillation time, changing state at a timescale on the order of decades. It is these regions that the researchers investigated for use as a molecular clock.

Methylation in intestinal crypts

The team isolated DNA from samples of intestinal crypts and measured DNA methylation levels using commercial microarrays. From their samples, the researchers selected fCpG sites that they deemed unlikely to rapidly oscillate between methylation states. The methylation profile of the fCpG sites was also found to be conserved between stem and differentiated cells within crypts. This allowed the team to use the sites to measure stem cell dynamics.

Interestingly, the team observed that the distribution of methylation states within individual crypts had a characteristic W-shape: there were peaks at 0%, 50% and 100% methylation for each fCpG site. They suggested that it was likely that this distribution would be similar to the methylation pattern of the most recent common ancestor of the crypt population.

Next, the team developed a mathematical model to describe the methylation status of cells within individual crypts. When the simulated methylation rate was correct, the model produced the characteristic W-shape. The model could then run simulations of dynamics over time. Upon validation with known dynamics, the model was found to be highly accurate.

Measuring stem cell dynamics

The researchers then tested to see if other tissues had suitable fCpG sites that could act as a molecular clock. To do this, they analysed DNA samples from both blood and endometrial glands and once again found fCpG sites with the characteristic W-shaped distribution. Once the team applied their mathematical model to these samples, they found that the stem cell dynamics were very similar to those in the intestinal crypts. In addition, the rate of stem cell replacement dropped over time in the endometrial glands, suggesting that cells are replaced less frequently as we age. 

Applications of fluctuating methylation clocks

The fluctuating clock methodology presented in this study has many valuable applications. Firstly, the model presents a much more efficient way of tracing the patterns of human somatic cell birth and death. This will allow for greater research into how cell populations develop. In addition, fluctuating methylation clocks work in multiple tissue types. Hopefully, this will lead to the inference of the dynamics of many cell populations, which could help disease prediction and prevention.

Picture credit: kjpargeter on