A person’s full genetic code has the instructions to create every protein needed for every cell in the body, but, somehow, these instructions are selectively applied to create unique cell types. Multicellular organisms such as humans use epigenetic modifications to ensure that each cell type only expresses genes that generate proteins relevant to its function.
Through DNA modifications such as methylation, stem cells, when differentiating into specialized cell types, make portions of the genome more or less permissive to RNA transcription, which limits the types of proteins that cell can make. Historically, DNA methylation was thought to repress transcription and that removing it was required for changes in gene expression.
The laboratory of Emily Hodges, associate professor of biochemistry, has robust experience in epigenetics and chromatin accessibility. A recent paper published in Cell Reports looks at the timing of chromatin accessibility and DNA methylation changes during the process of cell differentiation and how they affect gene expression. They found that DNA methylation doesn’t always limit gene transcription, especially early in differentiation. In fact, both modifications collaborate on different timescales to shape the short- and long-term regulation of enhancers during cell fate specification. Enhancers are short regions in the DNA to which certain proteins can bind to regulate how much a particular gene is expressed.
We sat down with the first author of the paper, Lindsey Guerin, a Ph.D. student in the Hodges, lab, who told us more about the paper.
What issue/problem does your research address?
Before this study, it was unclear how chromatin accessibility and DNA methylation impacted gene expression during cell differentiation, so our studies explored their effects, particularly those of DNA methylation. We also investigated the relationship between the temporal dynamics of these two modifications.
What were your top three findings?
- During cell differentiation, most regions lose DNA methylation, and this change happens at a different time than chromatin accessibility changes.
- Before losing methylation, enhancers start accumulating a chemical marker called 5-hmC, which is an intermediate in active demethylation.
- We can use machine learning to predict chromatin accessibility from DNA methylation data.
What was unique about your approach to the research?
We really wanted to focus on timing and on figuring out when epigenetic modifications change during dynamic processes to try and understand their influence on gene regulation. Our approach was to use a dense time course paired with a joint profiling sequencing technique to establish how DNA methylation and chromatin accessibility change relative to each other. Using that approach, we could ask how these dynamics affect gene expression.
The joint-profiling approach I used, ATAC-Me, was previously developed by our lab and was critical to understanding the relationship between DNA methylation and accessibility.
Who or what made the difference in your research?
Being able to discuss this project with lab mates and peers in the biochemistry department was very helpful. Rebecca Ihrie, a co-author on this paper, was also instrumental as our lab had limited experience with the neural progenitor cell system and flow cytometry we used in this project. Kelly Barnett initially developed the ATAC-Me protocol, and we could not have applied it to this project without his work to build on.
What do you hope will be achieved with the research results on the short term?
I hope that we can follow up on these observations in other models to determine how widespread our observations may be. We found a temporal separation between DNA methylation changes and changes in accessibility and gene expression, but they may be unique to this model of neural progenitor cell differentiation.
Where is this research taking you next? What will you personally be doing, or how will other researchers build on this work?
Since it was so prevalent, we’d like to investigate the demethylation process more. For example, we are interested in manipulating TET enzymes, which aid in active demethylation, to characterize what happens to differentiation when demethylation is accelerated or stalled.
What are your highest translational/clinical aspirations that might result from this research?
Mutations in the enzymes that place and remove DNA methylation have big impacts on cell differentiation and early human development. Understanding when and where DNA methylation is supposed to change in a healthy state will give us a benchmark to compare disease states to. In turn, this can help us create targeted therapies for diseases with dysregulated DNA methylation, such as acute myeloid leukemia or other cancers.
Go deeper
The paper “Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification” was published in Cell Reports in May 2025.
Funding
This research used funds from the National Institutes of Health, the American Cancer Society, the Michael David Greene Brain Cancer Fund at the Vanderbilt-Ingram Cancer Center, the Vanderbilt University Stanley Cohen Innovation Fund, a Vanderbilt University School of Medicine Dean’s Faculty Fellow Award, and funds from the Vanderbilt-Ingram Cancer Center.