The Dynamic Relationship Between DNA Methylation and Chromatin Accessibility During Cell Differentiation
DNA methylation is the most well-studied component of epigenetics and functions to balance patterns of gene expression throughout the life cycle of a cell. Along with DNA methylation, chromatin accessibility is necessary for gene regulation, especially in stem cells. Proper differentiation of stem cells requires that DNA methylation and chromatin accessibility be dynamic in nature. Recently, it was found that hypomethylated regions (HMRs) were the most specific to cell-type at particular intergenic sites called enhancers and that these sites tended to coincide with chromatin accessibility. However, the relationship between DNA methylation and accessibility to chromatin in differentiating cells remains elusive. To begin deciphering this relationship, we have previously developed a method for identifying genomic regions of dynamic DNA methylation and chromatin accessibility. Here, we propose a more targeted approach for modifying these epigenetic marks in previously identified areas of interest. We will fuse protein domains which are known to be important for DNA methylation, chromatin accessibility, or enhancer regulation to a catalytically-inactive form of the enzyme Cas9 nuclease. This enables DNA methylation or chromatin accessibility to be altered at specific intervals of differentiation in targeted areas, such as enhancer regions, thereby allowing us to analyze how the modifications dynamically impact each other and influence enhancer activity. The method presented here provides a tool to elucidate how the dynamics of DNA methylation and chromatin accessibility are interwoven in the regulation of gene expression. This, in turn, will provide an avenue for better understanding how diseases related to abnormal DNA methylation emerge.