Imaging cell lineage with a synthetic digital recording system.

Area of Science:

• Developmental Biology
• Genetics
• Bioengineering

Background:

• Cell fate decisions during development are influenced by spatial position and lineage history.
• Accurate lineage tracing is crucial for understanding multicellular development.

Purpose of the Study:

• To engineer a novel genetic system for in situ lineage recording.
• To enable the reconstruction of lineage relationships and clonal history in living cells and tissues.

Main Methods:

• Developed integrase-editable memory by engineered mutagenesis with optical in situ readout (intMEMOIR), a serine integrase-based system.
• Utilized an array of independent three-state genetic memory elements for stochastic and irreversible recombination.
• Applied intMEMOIR to cultured mouse cells and *Drosophila* brain sections for lineage reconstruction.

Main Results:

• intMEMOIR successfully reconstructed lineage trees in stem cells.
• The system allowed for up to 59,049 distinct digital states, recording lineage information in situ.
• Enabled simultaneous analysis of single-cell clonal history, spatial position, and gene expression in *Drosophila* brain sections.

Conclusions:

• intMEMOIR provides a powerful tool for microscopy-readable lineage recording.
• This technology establishes a foundation for analyzing lineage relationships in diverse biological systems.
• Facilitates a deeper understanding of cell fate decisions in multicellular development.