Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance

The epigenome, including DNA methylation, is stably propagated during mitotic division. However, single-cell clonal expansion produces heterogeneous methylomes, raising the question of how the DNA methylome remains stable despite constant epigenetic drift. Here, we report that a clonal population of DNA (cytosine-5)-methyltransferase 1 (DNMT1)-only cells produces a heterogeneous methylome, which is robustly propagated on cell expansion and differentiation. Our data show that DNMT1 has imprecise maintenance activity and likely possesses weak de novo activity, leading to spontaneous 'epimutations'. However, these epimutations tend to be corrected through a neighbor-guided mechanism, ikely enabled by environment-sensitive de novo activity ('tuner') and maintenance activity ('stabilizer') of DNMT1. By generating base-resolution maps of de novo and maintenance activities, we find that H3K9me2/3-marked regions show enhanced de novo activity, and CpG islands have both poor maintenance and de novo activities. The imprecise epigenetic machinery coupled with neighbor-guided correction may be a fundamental mechanism underlying robust yet flexible epigenetic inheritance. Overall design: In this study, we showed that the epigenetic mosaicism is an intrinsic property of imprecise DNMT1 activity which leads to spontaneous DNA methylation “epimutations”. However, such “epimutations” tend to be corrected over time in a neighbor DNA methylation-guided manner. In silico modeling and base-resolution mapping of DNMT1 maintenance and de novo activity support a model that the de novo activity of DNMT1 is not simply a leaky activity, but rather a major factor in an environment-sensitive “Tuner-Stabilizer” system, to achieve robust-yet-flexible maintenance of the methylome.