Abstract
Epigenomes, characterized by patterns of different signatures such as chromatin accessibility, chromatin interactions, and DNA methylation, vary across cell types and play a pivotal role in regulating gene expression. By mapping these signatures, the underlying mechanisms of development and diseases can be uncovered. However, many canonical epigenetic methods focus on mapping only one signature. Simultaneous measurement of epigenetic signatures from the same cell or tissue provides significant benefits for research, especially when resources are limited, and precise analysis is essential. Here, we report a technique called Methyl-Micro-C (MMC), which simultaneously profiles chromatin accessibility, chromatin interactions, and DNA methylation in the same sample. MMC enhances the resolution of chromatin interactions and the coverage of CpGs by combining MNase-mediated fragmentation with enzymatic conversion. This technique allows for the profiling of three-dimensional epigenomes, capturing consistent chromatin accessibility, chromatin interactions, and DNA methylation signals in an efficient manner. It is also relatively straightforward, allowing researchers to implement and apply it easily.