MethylTree: High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylation epimutations

In vivo lineage tracing holds great potential to reveal fundamental principles of tissue development and homeostasis. However, current lineage tracing in humans relies on extremely rare somatic mutations, which has limited temporal resolution and lineage accuracy. Here, we developed a generic lineage tracing tool based on frequent epimutations on DNA methylation, enabled by our new computational method MethylTree. Using both in-house and public single-cell genome-wide DNA methylation datasets with known lineage labels, MethylTree reconstructed lineage histories at nearly 100% accuracy across different cell types, developmental stages, and species. We demonstrated the epimutation-based single-cell multi-omic lineage tracing in mouse and human blood, where MethylTree recapitulated the differentiation hierarchy in hematopoiesis. Applying MethylTree to human embryos, we resolved cell division histories at an unprecedented temporal resolution and revealed early fate commitment at the four-cell stage for the first time. In native mouse blood, we identified previously unknown ~250 clones of hematopoietic stem cells. MethylTree opens the door for high-resolution, noninvasive, and multi-omic lineage tracing in humans and beyond.