BASELINE: single cell lineage tracing with Cas12a-ABE

CRISPR-based recording technologies are a promising solution to map the importance of lineage, yet challenges remain regarding single-cell recovery, engineering complexity, and scale. Here, we introduce BASELINE, which uses base editing to generate high-resolution lineage trees in conjunction with single-cell profiling.

BASELINE uses the Cas12a adenine base editor to irreversibly edit nucleotides within 50 synthetic target sites, which are integrated multiple times into a cell’s genome. We show that BASELINE accumulates lineage-specific marks over a wide range of biologically relevant intervals, recording more than 4300 bits of information in a model of pancreatic cancer. Single-cell sequencing reveals high-fidelity capture of these lineage recorders, recovering lineage reconstructions up to 46 cell-divisions deep, within the estimated range of mammalian development.